Starting phenix.real_space_refine on Sat Mar 23 21:58:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6szs_10353/03_2024/6szs_10353.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6szs_10353/03_2024/6szs_10353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6szs_10353/03_2024/6szs_10353.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6szs_10353/03_2024/6szs_10353.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6szs_10353/03_2024/6szs_10353.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6szs_10353/03_2024/6szs_10353.pdb" } resolution = 3.06 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= 0.001 sd= 0.009 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 4646 5.49 5 S 160 5.16 5 C 74285 2.51 5 N 27468 2.21 5 O 40802 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 ARG 10": "NH1" <-> "NH2" Residue "0 ARG 16": "NH1" <-> "NH2" Residue "0 ARG 40": "NH1" <-> "NH2" Residue "0 ASP 46": "OD1" <-> "OD2" Residue "0 ARG 52": "NH1" <-> "NH2" Residue "1 PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 32": "OE1" <-> "OE2" 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 ASP 20": "OD1" <-> "OD2" Residue "4 ARG 24": "NH1" <-> "NH2" Residue "5 ASP 4": "OD1" <-> "OD2" Residue "5 PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 50": "OD1" <-> "OD2" Residue "5 ARG 56": "NH1" <-> "NH2" Residue "5 ASP 58": "OD1" <-> "OD2" 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 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 114": "OD1" <-> "OD2" Residue "C ARG 133": "NH1" <-> "NH2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C ASP 187": "OD1" <-> "OD2" Residue "C ASP 229": "OD1" <-> "OD2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D ASP 18": "OD1" <-> "OD2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D ARG 33": "NH1" <-> "NH2" 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 89": "OE1" <-> "OE2" Residue "D ASP 103": "OD1" <-> "OD2" Residue "D ASP 108": "OD1" <-> "OD2" Residue "D GLU 168": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ASP 7": "OD1" <-> "OD2" Residue "E PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 21": "NH1" <-> "NH2" 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 GLU 127": "OE1" <-> "OE2" Residue "E ASP 140": "OD1" <-> "OD2" Residue "E GLU 144": "OE1" <-> "OE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ASP 168": "OD1" <-> "OD2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E ASP 171": "OD1" <-> "OD2" Residue "F GLU 11": "OE1" <-> "OE2" Residue "F ASP 46": "OD1" <-> "OD2" Residue "F ASP 56": "OD1" <-> "OD2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F ARG 80": "NH1" <-> "NH2" Residue "F TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 113": "OD1" <-> "OD2" Residue "F PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 133": "NH1" <-> "NH2" Residue "F ASP 153": "OD1" <-> "OD2" Residue "F ASP 163": "OD1" <-> "OD2" Residue "F GLU 164": "OE1" <-> "OE2" Residue "F ASP 174": "OD1" <-> "OD2" Residue "G PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 124": "OE1" <-> "OE2" Residue "G GLU 130": "OE1" <-> "OE2" Residue "G ASP 137": "OD1" <-> "OD2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G ASP 166": "OD1" <-> "OD2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "H ASP 7": "OD1" <-> "OD2" Residue "H GLU 45": "OE1" <-> "OE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "H GLU 109": "OE1" <-> "OE2" Residue "H ARG 123": "NH1" <-> "NH2" Residue "H GLU 129": "OE1" <-> "OE2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ASP 71": "OD1" <-> "OD2" Residue "J TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 95": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "J TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 56": "OD1" <-> "OD2" Residue "K ASP 80": "OD1" <-> "OD2" 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 136": "OE1" <-> "OE2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ASP 25": "OD1" <-> "OD2" 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 GLU 75": "OE1" <-> "OE2" Residue "M TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 106": "OD1" <-> "OD2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "M GLU 115": "OE1" <-> "OE2" 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 ARG 46": "NH1" <-> "NH2" Residue "N GLU 49": "OE1" <-> "OE2" 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 GLU 74": "OE1" <-> "OE2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 33": "NH1" <-> "NH2" Residue "O ARG 81": "NH1" <-> "NH2" 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 ASP 16": "OD1" <-> "OD2" Residue "P PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 21": "NH1" <-> "NH2" Residue "P ARG 39": "NH1" <-> "NH2" 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 ARG 101": "NH1" <-> "NH2" Residue "P GLU 102": "OE1" <-> "OE2" 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 ASP 49": "OD1" <-> "OD2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "Q GLU 111": "OE1" <-> "OE2" 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 ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S GLU 2": "OE1" <-> "OE2" Residue "S ASP 22": "OD1" <-> "OD2" Residue "S GLU 52": "OE1" <-> "OE2" Residue "S ASP 62": "OD1" <-> "OD2" Residue "S GLU 78": "OE1" <-> "OE2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ASP 94": "OD1" <-> "OD2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T GLU 4": "OE1" <-> "OE2" Residue "T GLU 18": "OE1" <-> "OE2" Residue "T ASP 37": "OD1" <-> "OD2" Residue "T GLU 42": "OE1" <-> "OE2" Residue "T PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 82": "NH1" <-> "NH2" Residue "U PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 86": "NH1" <-> "NH2" Residue "U PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 94": "NH1" <-> "NH2" Residue "U PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 101": "OE1" <-> "OE2" Residue "V PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 17": "OE1" <-> "OE2" Residue "W PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 29": "OE1" <-> "OE2" Residue "W PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 8": "OE1" <-> "OE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 11": "NH1" <-> "NH2" Residue "Z ARG 30": "NH1" <-> "NH2" Residue "Z GLU 37": "OE1" <-> "OE2" Residue "Z ARG 45": "NH1" <-> "NH2" Residue "b PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 44": "OE1" <-> "OE2" Residue "b ARG 63": "NH1" <-> "NH2" Residue "b ARG 113": "NH1" <-> "NH2" Residue "b ASP 116": "OD1" <-> "OD2" Residue "b PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 142": "OE1" <-> "OE2" Residue "b GLU 145": "OE1" <-> "OE2" Residue "b ASP 165": "OD1" <-> "OD2" Residue "b PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 194": "OD1" <-> "OD2" Residue "b PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 205": "OD1" <-> "OD2" Residue "b ARG 208": "NH1" <-> "NH2" Residue "b ARG 222": "NH1" <-> "NH2" Residue "b GLU 223": "OE1" <-> "OE2" Residue "c PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 93": "OD1" <-> "OD2" Residue "c ARG 107": "NH1" <-> "NH2" Residue "c PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 131": "NH1" <-> "NH2" Residue "d ASP 29": "OD1" <-> "OD2" Residue "d ASP 50": "OD1" <-> "OD2" Residue "d GLU 57": "OE1" <-> "OE2" Residue "d TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 147": "OE1" <-> "OE2" Residue "d GLU 163": "OE1" <-> "OE2" Residue "d ASP 174": "OD1" <-> "OD2" Residue "d ARG 184": "NH1" <-> "NH2" Residue "e ARG 20": "NH1" <-> "NH2" Residue "e GLU 55": "OE1" <-> "OE2" Residue "e ARG 68": "NH1" <-> "NH2" Residue "e ARG 93": "NH1" <-> "NH2" Residue "e GLU 145": "OE1" <-> "OE2" Residue "e ARG 157": "NH1" <-> "NH2" Residue "f TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 40": "OE1" <-> "OE2" Residue "f ASP 41": "OD1" <-> "OD2" Residue "f ASP 72": "OD1" <-> "OD2" Residue "f ARG 91": "NH1" <-> "NH2" Residue "g GLU 67": "OE1" <-> "OE2" Residue "g ARG 78": "NH1" <-> "NH2" Residue "g TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 129": "OE1" <-> "OE2" Residue "h ASP 5": "OD1" <-> "OD2" Residue "h ASP 9": "OD1" <-> "OD2" Residue "h ASP 48": "OD1" <-> "OD2" Residue "h PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 73": "OE1" <-> "OE2" Residue "i PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 45": "NH1" <-> "NH2" Residue "i ARG 49": "NH1" <-> "NH2" Residue "i GLU 53": "OE1" <-> "OE2" Residue "i TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 99": "NH1" <-> "NH2" Residue "i PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 124": "NH1" <-> "NH2" Residue "j ASP 14": "OD1" <-> "OD2" Residue "j ASP 19": "OD1" <-> "OD2" Residue "j GLU 27": "OE1" <-> "OE2" Residue "j GLU 47": "OE1" <-> "OE2" Residue "j ASP 63": "OD1" <-> "OD2" Residue "j ARG 68": "NH1" <-> "NH2" Residue "k PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 72": "OD1" <-> "OD2" Residue "k ARG 93": "NH1" <-> "NH2" 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 62": "OE1" <-> "OE2" Residue "l ARG 83": "NH1" <-> "NH2" Residue "l ASP 109": "OD1" <-> "OD2" Residue "m GLU 41": "OE1" <-> "OE2" Residue "m GLU 47": "OE1" <-> "OE2" Residue "m GLU 50": "OE1" <-> "OE2" Residue "m ASP 58": "OD1" <-> "OD2" Residue "m PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 66": "OE1" <-> "OE2" Residue "n ASP 18": "OD1" <-> "OD2" Residue "n TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ASP 40": "OD1" <-> "OD2" 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 PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 23": "OD1" <-> "OD2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "p PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 48": "OE1" <-> "OE2" Residue "q ARG 11": "NH1" <-> "NH2" Residue "q ASP 15": "OD1" <-> "OD2" Residue "q ARG 27": "NH1" <-> "NH2" Residue "q GLU 80": "OE1" <-> "OE2" Residue "r ARG 12": "NH1" <-> "NH2" Residue "r TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 35": "OE1" <-> "OE2" Residue "r ARG 61": "NH1" <-> "NH2" Residue "s ARG 32": "NH1" <-> "NH2" Residue "t ARG 24": "NH1" <-> "NH2" 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 GLU 31": "OE1" <-> "OE2" Residue "u ARG 33": "NH1" <-> "NH2" Residue "u GLU 36": "OE1" <-> "OE2" Residue "u GLU 44": "OE1" <-> "OE2" Residue "u ARG 45": "NH1" <-> "NH2" Residue "u ARG 55": "NH1" <-> "NH2" Residue "u GLU 63": "OE1" <-> "OE2" Residue "u ARG 66": "NH1" <-> "NH2" Residue "u ARG 69": "NH1" <-> "NH2" Residue "y ARG 10": "NH1" <-> "NH2" Residue "y ASP 20": "OD1" <-> "OD2" Residue "y ARG 25": "NH1" <-> "NH2" Residue "y PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 16": "NH1" <-> "NH2" Residue "z ASP 37": "OD1" <-> "OD2" Residue "z PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z GLU 111": "OE1" <-> "OE2" Residue "z GLU 120": "OE1" <-> "OE2" Residue "z GLU 156": "OE1" <-> "OE2" Residue "z GLU 163": "OE1" <-> "OE2" Residue "z TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 211": "NH1" <-> "NH2" Residue "z PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 234": "NH1" <-> "NH2" Residue "z ASP 237": "OD1" <-> "OD2" Residue "z ASP 241": "OD1" <-> "OD2" Residue "z TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z GLU 276": "OE1" <-> "OE2" Residue "z ARG 277": "NH1" <-> "NH2" Residue "z ARG 283": "NH1" <-> "NH2" Residue "z ARG 297": "NH1" <-> "NH2" Residue "z GLU 300": "OE1" <-> "OE2" Residue "z GLU 301": "OE1" <-> "OE2" Residue "z GLU 305": "OE1" <-> "OE2" Residue "z ASP 307": "OD1" <-> "OD2" Residue "z GLU 315": "OE1" <-> "OE2" Residue "z TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 362": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 147361 Number of models: 1 Model: "" Number of chains: 56 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: "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': 254, 'rna2p_pyr': 131, 'rna3p_pur': 1420, 'rna3p_pyr': 1098} Link IDs: {'rna2p': 385, 'rna3p': 2517} 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: {'PCIS': 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: "a" Number of atoms: 33037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1540, 33037 Classifications: {'RNA': 1540} Modifications used: {'rna2p_pur': 113, 'rna2p_pyr': 66, 'rna3p_pur': 762, 'rna3p_pyr': 599} Link IDs: {'rna2p': 179, 'rna3p': 1360} 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: "v" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 1, 'rna3p_pyr': 4} Link IDs: {'rna3p': 5} Chain: "x" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1646 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 33, 'rna3p_pyr': 31} Link IDs: {'rna2p': 13, 'rna3p': 63} Chain: "y" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 434 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "z" Number of atoms: 2742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2742 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 10, 'TRANS': 351} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 9, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 112 Time building chain proxies: 58.48, per 1000 atoms: 0.40 Number of scatterers: 147361 At special positions: 0 Unit cell: (269.445, 274.77, 225.78, 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 160 16.00 P 4646 15.00 O 40802 8.00 N 27468 7.00 C 74285 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 62.65 Conformation dependent library (CDL) restraints added in 7.7 seconds 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11220 Finding SS restraints... Secondary structure from input PDB file: 187 helices and 74 sheets defined 37.7% alpha, 19.3% beta 1592 base pairs and 2628 stacking pairs defined. Time for finding SS restraints: 56.58 Creating SS restraints... Processing helix chain '0' and resid 9 through 17 Processing helix chain '2' and resid 8 through 17 Processing helix chain '2' and resid 17 through 23 Processing helix chain '2' and resid 25 through 38 removed outlier: 3.584A pdb=" N GLY 2 38 " --> pdb=" O ARG 2 34 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 14 Processing helix chain '3' and resid 37 through 45 Processing helix chain '3' and resid 51 through 62 removed outlier: 3.949A pdb=" N ALA 3 60 " --> pdb=" O GLY 3 56 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS 3 61 " --> pdb=" O LEU 3 57 " (cutoff:3.500A) Processing helix chain '4' and resid 30 through 33 Processing helix chain '5' and resid 41 through 46 Processing helix chain '5' and resid 55 through 64 Processing helix chain 'C' and resid 10 through 15 Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 197 through 203 removed outlier: 4.035A pdb=" N MET C 201 " --> pdb=" O ALA C 198 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG C 203 " --> pdb=" O HIS C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 214 removed outlier: 3.886A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'D' and resid 61 through 71 removed outlier: 3.718A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 104 Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'D' and resid 182 through 184 No H-bonds generated for 'chain 'D' and resid 182 through 184' Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 39 Processing helix chain 'E' and resid 97 through 115 Processing helix chain 'E' and resid 130 through 141 removed outlier: 3.843A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 162 removed outlier: 3.636A pdb=" N ALA E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'E' and resid 190 through 201 Processing helix chain 'F' and resid 3 through 20 removed outlier: 4.919A pdb=" N VAL F 13 " --> pdb=" O LYS F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 45 removed outlier: 3.836A pdb=" N ILE F 44 " --> pdb=" O GLY F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 61 removed outlier: 4.229A pdb=" N LEU F 50 " --> pdb=" O ASP F 46 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 106 Processing helix chain 'F' and resid 136 through 138 No H-bonds generated for 'chain 'F' and resid 136 through 138' Processing helix chain 'F' and resid 162 through 173 removed outlier: 4.118A pdb=" N PHE F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'G' and resid 60 through 82 Processing helix chain 'G' and resid 137 through 152 removed outlier: 3.750A pdb=" N ARG G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 30 Processing helix chain 'H' and resid 41 through 50 Processing helix chain 'H' and resid 53 through 73 Processing helix chain 'H' and resid 95 through 106 removed outlier: 3.601A pdb=" N ILE H 99 " --> pdb=" O GLY H 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 Processing helix chain 'J' and resid 58 through 62 removed outlier: 3.799A pdb=" N VAL J 62 " --> pdb=" O ALA J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 96 through 109 removed outlier: 4.014A pdb=" N VAL J 100 " --> pdb=" O ARG J 96 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 121 Processing helix chain 'J' and resid 132 through 136 removed outlier: 3.758A pdb=" N GLN J 136 " --> pdb=" O ALA J 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 108 removed outlier: 3.666A pdb=" N LEU K 107 " --> pdb=" O THR K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 118 removed outlier: 4.229A pdb=" N LEU K 118 " --> pdb=" O LYS K 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 41 Processing helix chain 'L' and resid 56 through 61 removed outlier: 3.794A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.875A pdb=" N ALA L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 98 Processing helix chain 'L' and resid 128 through 139 Processing helix chain 'M' and resid 43 through 58 Processing helix chain 'M' and resid 109 through 122 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: 4.311A 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 82 Processing helix chain 'O' and resid 3 through 22 removed outlier: 3.832A pdb=" N ARG O 9 " --> pdb=" O SER O 5 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG O 10 " --> pdb=" O ALA O 6 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 60 Processing helix chain 'O' and resid 67 through 86 Processing helix chain 'O' and resid 101 through 114 Processing helix chain 'P' and resid 3 through 13 Processing helix chain 'P' and resid 97 through 103 removed outlier: 3.883A pdb=" N ARG P 101 " --> pdb=" O LEU P 97 " (cutoff:3.500A) Processing helix chain 'P' and resid 104 through 109 removed outlier: 4.092A pdb=" N ARG P 109 " --> pdb=" O LYS P 106 " (cutoff:3.500A) Processing helix chain 'Q' and resid 6 through 21 removed outlier: 3.754A pdb=" N ILE Q 17 " --> pdb=" O ARG Q 13 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 3.735A pdb=" N SER Q 29 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 71 removed outlier: 3.800A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 86 Processing helix chain 'Q' and resid 91 through 101 Processing helix chain 'Q' and resid 102 through 118 Processing helix chain 'S' and resid 13 through 22 removed outlier: 4.012A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 38 Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.750A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 89 through 91 No H-bonds generated for 'chain 'S' and resid 89 through 91' Processing helix chain 'T' and resid 2 through 10 Processing helix chain 'T' and resid 17 through 26 Processing helix chain 'T' and resid 39 through 51 Processing helix chain 'V' and resid 13 through 23 Processing helix chain 'V' and resid 44 through 51 Processing helix chain 'V' and resid 53 through 59 removed outlier: 4.229A pdb=" N TYR V 57 " --> pdb=" O LYS V 53 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 62 Processing helix chain 'X' and resid 63 through 75 Processing helix chain 'Y' and resid 2 through 8 Processing helix chain 'Y' and resid 10 through 35 Processing helix chain 'Y' and resid 40 through 61 removed outlier: 4.216A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA Y 61 " --> pdb=" O LEU Y 57 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 28 Processing helix chain 'Z' and resid 41 through 51 Processing helix chain 'b' and resid 6 through 13 Processing helix chain 'b' and resid 21 through 23 No H-bonds generated for 'chain 'b' and resid 21 through 23' Processing helix chain 'b' and resid 24 through 29 Proline residue: b 29 - end of helix Processing helix chain 'b' and resid 42 through 62 Proline residue: b 48 - end of helix Processing helix chain 'b' and resid 76 through 87 Processing helix chain 'b' and resid 103 through 122 removed outlier: 3.717A pdb=" N VAL b 107 " --> pdb=" O ASN b 103 " (cutoff:3.500A) Processing helix chain 'b' and resid 131 through 149 removed outlier: 4.120A pdb=" N ARG b 139 " --> pdb=" O LEU b 135 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU b 140 " --> pdb=" O MET b 136 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER b 147 " --> pdb=" O LYS b 143 " (cutoff:3.500A) Processing helix chain 'b' and resid 150 through 152 No H-bonds generated for 'chain 'b' and resid 150 through 152' Processing helix chain 'b' and resid 169 through 180 Processing helix chain 'b' and resid 206 through 227 Processing helix chain 'c' and resid 6 through 15 removed outlier: 4.423A pdb=" N GLY c 13 " --> pdb=" O GLY c 9 " (cutoff:3.500A) Processing helix chain 'c' and resid 28 through 47 Processing helix chain 'c' and resid 72 through 78 removed outlier: 3.738A pdb=" N VAL c 76 " --> pdb=" O ARG c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 96 Processing helix chain 'c' and resid 112 through 126 Processing helix chain 'c' and resid 129 through 145 Processing helix chain 'd' and resid 7 through 16 removed outlier: 3.937A pdb=" N LEU d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 32 Processing helix chain 'd' and resid 49 through 66 removed outlier: 3.780A pdb=" N TYR d 65 " --> pdb=" O VAL d 61 " (cutoff:3.500A) Processing helix chain 'd' and resid 68 through 82 Processing helix chain 'd' and resid 85 through 96 Processing helix chain 'd' and resid 97 through 106 Processing helix chain 'd' and resid 110 through 120 Processing helix chain 'd' and resid 152 through 165 removed outlier: 3.604A pdb=" N LYS d 156 " --> pdb=" O GLN d 152 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 191 removed outlier: 3.583A pdb=" N LEU d 191 " --> pdb=" O ARG d 188 " (cutoff:3.500A) Processing helix chain 'd' and resid 196 through 206 removed outlier: 3.730A pdb=" N ILE d 200 " --> pdb=" O ASN d 196 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS d 206 " --> pdb=" O GLU d 202 " (cutoff:3.500A) Processing helix chain 'e' and resid 55 through 70 removed outlier: 3.912A pdb=" N ARG e 69 " --> pdb=" O GLU e 65 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN e 70 " --> pdb=" O LYS e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 109 through 118 Processing helix chain 'e' and resid 132 through 147 Processing helix chain 'e' and resid 149 through 158 Processing helix chain 'e' and resid 160 through 165 Processing helix chain 'f' and resid 12 through 15 Processing helix chain 'f' and resid 17 through 31 Processing helix chain 'f' and resid 50 through 54 Processing helix chain 'f' and resid 67 through 81 removed outlier: 3.573A pdb=" N ILE f 71 " --> pdb=" O PRO f 67 " (cutoff:3.500A) Processing helix chain 'g' and resid 21 through 31 Processing helix chain 'g' and resid 35 through 55 removed outlier: 3.839A pdb=" N THR g 49 " --> pdb=" O SER g 45 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN g 52 " --> pdb=" O GLU g 48 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 69 Processing helix chain 'g' and resid 92 through 110 removed outlier: 3.528A pdb=" N LYS g 110 " --> pdb=" O GLU g 106 " (cutoff:3.500A) Processing helix chain 'g' and resid 116 through 130 Processing helix chain 'g' and resid 133 through 148 Processing helix chain 'h' and resid 5 through 20 Processing helix chain 'h' and resid 30 through 43 Processing helix chain 'h' and resid 95 through 99 Processing helix chain 'h' and resid 113 through 120 Processing helix chain 'i' and resid 34 through 39 Processing helix chain 'i' and resid 45 through 55 Proline residue: i 51 - end of helix Processing helix chain 'i' and resid 71 through 91 Processing helix chain 'i' and resid 94 through 102 removed outlier: 3.587A pdb=" N ARG i 99 " --> pdb=" O ARG i 95 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS i 100 " --> pdb=" O SER i 96 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA i 101 " --> pdb=" O GLU i 97 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 32 removed outlier: 4.030A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 89 Processing helix chain 'k' and resid 59 through 74 removed outlier: 3.729A pdb=" N VAL k 74 " --> pdb=" O CYS k 70 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 103 removed outlier: 3.793A pdb=" N ASN k 101 " --> pdb=" O ILE k 97 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA k 102 " --> pdb=" O ARG k 98 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 Processing helix chain 'm' and resid 14 through 20 Processing helix chain 'm' and resid 26 through 38 Processing helix chain 'm' and resid 49 through 62 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 3 through 30 removed outlier: 3.836A pdb=" N LYS n 7 " --> pdb=" O LYS n 3 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ALA n 22 " --> pdb=" O ASP n 18 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N LYS n 23 " --> pdb=" O LYS n 19 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU n 26 " --> pdb=" O ALA n 22 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 50 Processing helix chain 'n' and resid 52 through 60 Proline residue: n 57 - end of helix removed outlier: 3.642A pdb=" N GLN n 60 " --> pdb=" O PRO n 57 " (cutoff:3.500A) Processing helix chain 'n' and resid 80 through 91 Processing helix chain 'o' and resid 4 through 16 Processing helix chain 'o' and resid 24 through 44 Processing helix chain 'o' and resid 49 through 74 Processing helix chain 'o' and resid 74 through 86 Processing helix chain 'p' and resid 53 through 64 Processing helix chain 'p' and resid 68 through 81 Processing helix chain 'q' and resid 48 through 52 removed outlier: 4.247A pdb=" N GLU q 52 " --> pdb=" O GLU q 49 " (cutoff:3.500A) Processing helix chain 'r' and resid 11 through 17 Processing helix chain 'r' and resid 26 through 33 Processing helix chain 'r' and resid 41 through 45 Processing helix chain 'r' and resid 48 through 65 Processing helix chain 's' and resid 12 through 26 Processing helix chain 's' and resid 41 through 45 removed outlier: 3.808A pdb=" N ILE s 45 " --> pdb=" O PRO s 42 " (cutoff:3.500A) Processing helix chain 's' and resid 63 through 67 removed outlier: 3.797A pdb=" N MET s 66 " --> pdb=" O THR s 63 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL s 67 " --> pdb=" O ASP s 64 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 63 through 67' Processing helix chain 't' and resid 4 through 42 removed outlier: 3.592A pdb=" N GLY t 42 " --> pdb=" O ALA t 38 " (cutoff:3.500A) 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: 3.874A pdb=" N ALA t 87 " --> pdb=" O ILE t 83 " (cutoff:3.500A) Processing helix chain 'u' and resid 11 through 27 Processing helix chain 'u' and resid 28 through 35 Processing helix chain 'u' and resid 40 through 65 removed outlier: 3.889A pdb=" N ALA u 61 " --> pdb=" O ALA u 57 " (cutoff:3.500A) Processing helix chain 'u' and resid 66 through 68 No H-bonds generated for 'chain 'u' and resid 66 through 68' Processing helix chain 'y' and resid 4 through 16 Processing helix chain 'y' and resid 40 through 46 Processing helix chain 'z' and resid 6 through 25 removed outlier: 3.801A pdb=" N SER z 15 " --> pdb=" O GLU z 11 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA z 18 " --> pdb=" O ALA z 14 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE z 20 " --> pdb=" O ARG z 16 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP z 25 " --> pdb=" O ARG z 21 " (cutoff:3.500A) Processing helix chain 'z' and resid 25 through 37 Processing helix chain 'z' and resid 48 through 87 removed outlier: 4.185A pdb=" N ALA z 52 " --> pdb=" O ASP z 48 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N THR z 54 " --> pdb=" O GLN z 50 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN z 57 " --> pdb=" O GLN z 53 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N TYR z 65 " --> pdb=" O GLY z 61 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LYS z 70 " --> pdb=" O VAL z 66 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU z 79 " --> pdb=" O SER z 75 " (cutoff:3.500A) Processing helix chain 'z' and resid 93 through 118 removed outlier: 3.653A pdb=" N GLU z 97 " --> pdb=" O ASP z 93 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU z 99 " --> pdb=" O GLN z 95 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS z 100 " --> pdb=" O LEU z 96 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU z 111 " --> pdb=" O LYS z 107 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU z 118 " --> pdb=" O LEU z 114 " (cutoff:3.500A) Processing helix chain 'z' and resid 120 through 124 removed outlier: 3.871A pdb=" N ASP z 123 " --> pdb=" O GLU z 120 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS z 124 " --> pdb=" O PRO z 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 120 through 124' Processing helix chain 'z' and resid 139 through 159 removed outlier: 3.526A pdb=" N ARG z 157 " --> pdb=" O ARG z 153 " (cutoff:3.500A) Processing helix chain 'z' and resid 186 through 192 Processing helix chain 'z' and resid 193 through 195 No H-bonds generated for 'chain 'z' and resid 193 through 195' Processing helix chain 'z' and resid 278 through 310 removed outlier: 3.542A pdb=" N ASN z 282 " --> pdb=" O SER z 278 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS z 293 " --> pdb=" O MET z 289 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLN z 296 " --> pdb=" O ALA z 292 " (cutoff:3.500A) Processing helix chain 'z' and resid 344 through 350 removed outlier: 3.544A pdb=" N VAL z 348 " --> pdb=" O ASN z 344 " (cutoff:3.500A) Processing helix chain 'z' and resid 353 through 365 Processing sheet with id=AA1, first strand: chain '0' and resid 29 through 30 Processing sheet with id=AA2, first strand: chain '0' and resid 48 through 49 Processing sheet with id=AA3, first strand: chain '1' and resid 20 through 26 Processing sheet with id=AA4, first strand: chain '1' and resid 37 through 40 Processing sheet with id=AA5, first strand: chain '3' and resid 15 through 16 Processing sheet with id=AA6, first strand: chain '4' and resid 2 through 3 removed outlier: 6.526A pdb=" N LYS 4 2 " --> pdb=" O ARG 4 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain '4' and resid 14 through 19 Processing sheet with id=AA8, first strand: chain '5' and resid 21 through 26 removed outlier: 8.832A pdb=" N LEU 5 32 " --> pdb=" O GLU 5 11 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N THR 5 13 " --> pdb=" O LEU 5 32 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AB1, first strand: chain 'C' and resid 34 through 35 Processing sheet with id=AB2, first strand: chain 'C' and resid 101 through 105 removed outlier: 3.630A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU C 95 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N VAL C 78 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 129 through 131 removed outlier: 3.603A pdb=" N LEU C 130 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE C 164 " --> pdb=" O ARG C 175 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ARG C 175 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR C 171 " --> pdb=" O ASP C 168 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LYS C 183 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE C 267 " --> pdb=" O LYS C 183 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 4 through 15 removed outlier: 4.219A pdb=" N VAL D 26 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N MET D 11 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL D 24 " --> pdb=" O MET D 11 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ARG D 13 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE D 22 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU D 186 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL D 180 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU D 188 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASP D 176 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N THR D 171 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLY D 111 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLN D 173 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL D 109 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 77 through 82 removed outlier: 5.376A pdb=" N GLY D 78 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N THR D 52 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ALA D 47 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL D 37 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 117 through 119 Processing sheet with id=AB7, first strand: chain 'E' and resid 2 through 4 Processing sheet with id=AB8, first strand: chain 'E' and resid 118 through 121 removed outlier: 6.490A pdb=" N VAL E 146 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ARG E 170 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ILE E 148 " --> pdb=" O ARG E 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 66 through 69 removed outlier: 6.870A pdb=" N ARG F 150 " --> pdb=" O GLU F 134 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N GLU F 134 " --> pdb=" O ARG F 150 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 9 through 10 Processing sheet with id=AC2, first strand: chain 'G' and resid 17 through 20 Processing sheet with id=AC3, first strand: chain 'G' and resid 121 through 124 Processing sheet with id=AC4, first strand: chain 'G' and resid 95 through 99 Processing sheet with id=AC5, first strand: chain 'H' and resid 18 through 19 removed outlier: 3.609A pdb=" N VAL H 3 " --> pdb=" O VAL H 19 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 77 through 80 Processing sheet with id=AC7, first strand: chain 'J' and resid 122 through 124 Processing sheet with id=AC8, first strand: chain 'J' and resid 74 through 77 Processing sheet with id=AC9, first strand: chain 'K' and resid 6 through 10 removed outlier: 3.788A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL K 10 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ARG K 17 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA K 46 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL K 19 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N LYS K 44 " --> pdb=" O VAL K 19 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N CYS K 21 " --> pdb=" O THR K 42 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N THR K 42 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LEU K 86 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 69 through 70 removed outlier: 3.548A pdb=" N VAL K 69 " --> pdb=" O ILE K 77 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 89 through 90 Processing sheet with id=AD3, first strand: chain 'M' and resid 62 through 65 removed outlier: 6.240A pdb=" N VAL M 101 " --> pdb=" O ALA M 35 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA M 35 " --> pdb=" O VAL M 101 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 39 through 42 removed outlier: 5.490A pdb=" N VAL M 89 " --> pdb=" O GLU M 75 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLU M 75 " --> pdb=" O VAL M 89 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.860A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 47 through 52 removed outlier: 3.554A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 69 through 75 removed outlier: 3.835A pdb=" N ALA P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ARG P 62 " --> pdb=" O VAL P 47 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N VAL P 47 " --> pdb=" O ARG P 62 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N ILE P 64 " --> pdb=" O GLY P 45 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N GLY P 45 " --> pdb=" O ILE P 64 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TRP P 31 " --> pdb=" O VAL P 81 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL P 81 " --> pdb=" O TRP P 31 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 11 through 15 Processing sheet with id=AD9, first strand: chain 'R' and resid 19 through 23 removed outlier: 7.407A pdb=" N VAL R 96 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL R 64 " --> pdb=" O VAL R 96 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ILE R 98 " --> pdb=" O GLU R 62 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLU R 62 " --> pdb=" O ILE R 98 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'R' and resid 72 through 78 removed outlier: 4.198A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'S' and resid 4 through 10 removed outlier: 5.796A pdb=" N ILE S 4 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL S 107 " --> pdb=" O ILE S 4 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LYS S 6 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL S 105 " --> pdb=" O LYS S 6 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG S 8 " --> pdb=" O ILE S 103 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE S 103 " --> pdb=" O ARG S 8 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS S 73 " --> pdb=" O VAL S 106 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'S' and resid 82 through 88 removed outlier: 3.749A pdb=" N ARG S 92 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'T' and resid 11 through 14 removed outlier: 4.008A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL T 57 " --> pdb=" O THR T 86 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'T' and resid 69 through 70 Processing sheet with id=AE6, first strand: chain 'U' and resid 65 through 66 removed outlier: 3.692A pdb=" N LYS U 33 " --> pdb=" O LEU U 29 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'U' and resid 41 through 45 Processing sheet with id=AE8, first strand: chain 'U' and resid 83 through 87 removed outlier: 3.769A pdb=" N GLU U 101 " --> pdb=" O PHE U 96 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'V' and resid 3 through 8 removed outlier: 7.646A pdb=" N ASN V 5 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ASP V 43 " --> pdb=" O ASN V 5 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N GLN V 87 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLN V 78 " --> pdb=" O GLN V 87 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE V 89 " --> pdb=" O ASP V 76 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ASP V 76 " --> pdb=" O ILE V 89 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N PHE V 91 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA V 74 " --> pdb=" O PHE V 91 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG V 93 " --> pdb=" O VAL V 72 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL V 72 " --> pdb=" O ARG V 93 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE V 4 " --> pdb=" O VAL V 64 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'W' and resid 22 through 23 removed outlier: 6.917A pdb=" N LEU W 59 " --> pdb=" O ILE W 37 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'W' and resid 30 through 31 Processing sheet with id=AF3, first strand: chain 'X' and resid 13 through 18 Processing sheet with id=AF4, first strand: chain 'X' and resid 34 through 40 Processing sheet with id=AF5, first strand: chain 'Z' and resid 35 through 39 Processing sheet with id=AF6, first strand: chain 'b' and resid 16 through 19 removed outlier: 5.261A pdb=" N HIS b 39 " --> pdb=" O GLY b 17 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'b' and resid 90 through 92 removed outlier: 3.874A pdb=" N PHE b 90 " --> pdb=" O ILE b 67 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU b 68 " --> pdb=" O PHE b 162 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU b 161 " --> pdb=" O PHE b 184 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N ILE b 186 " --> pdb=" O LEU b 161 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N VAL b 163 " --> pdb=" O ILE b 186 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'c' and resid 52 through 58 removed outlier: 6.593A pdb=" N HIS c 69 " --> pdb=" O SER c 53 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE c 55 " --> pdb=" O THR c 67 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N THR c 67 " --> pdb=" O ILE c 55 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ILE c 57 " --> pdb=" O ARG c 65 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ARG c 65 " --> pdb=" O ILE c 57 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE c 64 " --> pdb=" O GLN c 100 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ASN c 102 " --> pdb=" O ILE c 64 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL c 66 " --> pdb=" O ASN c 102 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'c' and resid 164 through 171 removed outlier: 5.744A pdb=" N ASP c 181 " --> pdb=" O LYS c 204 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'd' and resid 128 through 129 Processing sheet with id=AG2, first strand: chain 'e' and resid 12 through 21 removed outlier: 4.938A pdb=" N GLU e 13 " --> pdb=" O GLY e 40 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLY e 40 " --> pdb=" O GLU e 13 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU e 15 " --> pdb=" O VAL e 38 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL e 38 " --> pdb=" O LEU e 15 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA e 17 " --> pdb=" O LEU e 36 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'e' and resid 85 through 88 removed outlier: 3.650A pdb=" N TYR e 128 " --> pdb=" O ARG e 93 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'f' and resid 36 through 45 removed outlier: 6.148A pdb=" N ILE f 36 " --> pdb=" O GLU f 65 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLU f 65 " --> pdb=" O ILE f 36 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ARG f 44 " --> pdb=" O ALA f 57 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ALA f 57 " --> pdb=" O ARG f 44 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA f 66 " --> pdb=" O ARG f 2 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG f 86 " --> pdb=" O MET f 9 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'g' and resid 73 through 76 Processing sheet with id=AG6, first strand: chain 'h' and resid 24 through 28 removed outlier: 6.313A pdb=" N GLU h 58 " --> pdb=" O VAL h 51 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL h 51 " --> pdb=" O GLU h 58 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLU h 60 " --> pdb=" O PHE h 49 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE h 49 " --> pdb=" O GLU h 60 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR h 62 " --> pdb=" O GLU h 47 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'h' and resid 74 through 77 removed outlier: 3.874A pdb=" N SER h 74 " --> pdb=" O ALA h 130 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'h' and resid 74 through 77 removed outlier: 3.874A pdb=" N SER h 74 " --> pdb=" O ALA h 130 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ILE h 125 " --> pdb=" O SER h 105 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N SER h 105 " --> pdb=" O ILE h 125 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS h 127 " --> pdb=" O VAL h 103 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'i' and resid 6 through 11 removed outlier: 6.320A pdb=" N VAL i 29 " --> pdb=" O ILE i 65 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N VAL i 67 " --> pdb=" O VAL i 29 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'j' and resid 40 through 52 removed outlier: 4.401A pdb=" N LEU j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR j 44 " --> pdb=" O THR j 69 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N THR j 69 " --> pdb=" O THR j 44 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LYS j 46 " --> pdb=" O ILE j 67 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ILE j 67 " --> pdb=" O LYS j 46 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ARG j 48 " --> pdb=" O TYR j 65 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TYR j 65 " --> pdb=" O ARG j 48 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N THR j 50 " --> pdb=" O ASP j 63 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASP j 63 " --> pdb=" O THR j 50 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'j' and resid 40 through 52 removed outlier: 4.401A pdb=" N LEU j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR j 44 " --> pdb=" O THR j 69 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N THR j 69 " --> pdb=" O THR j 44 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LYS j 46 " --> pdb=" O ILE j 67 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ILE j 67 " --> pdb=" O LYS j 46 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ARG j 48 " --> pdb=" O TYR j 65 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TYR j 65 " --> pdb=" O ARG j 48 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N THR j 50 " --> pdb=" O ASP j 63 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASP j 63 " --> pdb=" O THR j 50 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'k' and resid 41 through 46 removed outlier: 6.585A pdb=" N LEU k 82 " --> pdb=" O ILE k 107 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ASN k 109 " --> pdb=" O LEU k 82 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'l' and resid 79 through 82 removed outlier: 5.872A pdb=" N CYS l 34 " --> pdb=" O ARG l 56 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARG l 56 " --> pdb=" O CYS l 34 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR l 95 " --> pdb=" O THR l 64 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'p' and resid 50 through 52 removed outlier: 6.962A pdb=" N VAL p 21 " --> pdb=" O ILE p 33 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ARG p 35 " --> pdb=" O VAL p 19 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL p 19 " --> pdb=" O ARG p 35 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLY p 37 " --> pdb=" O TYR p 17 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N TYR p 17 " --> pdb=" O GLY p 37 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N PHE p 39 " --> pdb=" O PRO p 15 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR p 66 " --> pdb=" O VAL p 2 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'q' and resid 8 through 14 removed outlier: 7.853A pdb=" N GLN q 9 " --> pdb=" O GLU q 26 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N GLU q 26 " --> pdb=" O GLN q 9 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL q 22 " --> pdb=" O VAL q 13 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TRP q 73 " --> pdb=" O HIS q 45 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LEU q 75 " --> pdb=" O ARG q 62 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ARG q 62 " --> pdb=" O LEU q 75 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL q 79 " --> pdb=" O VAL q 58 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL q 58 " --> pdb=" O VAL q 79 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 's' and resid 31 through 33 Processing sheet with id=AH8, first strand: chain 'y' and resid 36 through 37 removed outlier: 6.651A pdb=" N LEU z 168 " --> pdb=" O LYS z 176 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N VAL z 178 " --> pdb=" O ASP z 166 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ASP z 166 " --> pdb=" O VAL z 178 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'y' and resid 36 through 37 removed outlier: 7.722A pdb=" N VAL z 197 " --> pdb=" O ARG z 323 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N TYR z 325 " --> pdb=" O VAL z 197 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ARG z 199 " --> pdb=" O TYR z 325 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'z' and resid 161 through 162 Processing sheet with id=AI2, first strand: chain 'z' and resid 239 through 243 2131 hydrogen bonds defined for protein. 6048 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4005 hydrogen bonds 6258 hydrogen bond angles 0 basepair planarities 1592 basepair parallelities 2628 stacking parallelities Total time for adding SS restraints: 280.54 Time building geometry restraints manager: 67.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 16202 1.32 - 1.44: 69276 1.44 - 1.57: 64923 1.57 - 1.69: 9287 1.69 - 1.82: 286 Bond restraints: 159974 Sorted by residual: bond pdb=" C HIS z 213 " pdb=" O HIS z 213 " ideal model delta sigma weight residual 1.236 1.294 -0.059 1.22e-02 6.72e+03 2.30e+01 bond pdb=" N ILE 3 32 " pdb=" CA ILE 3 32 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.68e+00 bond pdb=" N GLY f 34 " pdb=" CA GLY f 34 " ideal model delta sigma weight residual 1.444 1.476 -0.032 1.02e-02 9.61e+03 9.63e+00 bond pdb=" N HIS 3 31 " pdb=" CA HIS 3 31 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.32e-02 5.74e+03 8.13e+00 bond pdb=" CA HIS j 56 " pdb=" CB HIS j 56 " ideal model delta sigma weight residual 1.542 1.519 0.023 8.90e-03 1.26e+04 6.90e+00 ... (remaining 159969 not shown) Histogram of bond angle deviations from ideal: 98.29 - 106.02: 26318 106.02 - 113.75: 98660 113.75 - 121.48: 74272 121.48 - 129.21: 36059 129.21 - 136.94: 3685 Bond angle restraints: 238994 Sorted by residual: angle pdb=" N PRO z 90 " pdb=" CA PRO z 90 " pdb=" CB PRO z 90 " ideal model delta sigma weight residual 103.25 111.45 -8.20 1.05e+00 9.07e-01 6.10e+01 angle pdb=" C ARG H 50 " pdb=" N ARG H 51 " pdb=" CA ARG H 51 " ideal model delta sigma weight residual 121.54 132.29 -10.75 1.91e+00 2.74e-01 3.17e+01 angle pdb=" C VAL j 57 " pdb=" N ASN j 58 " pdb=" CA ASN j 58 " ideal model delta sigma weight residual 121.54 131.93 -10.39 1.91e+00 2.74e-01 2.96e+01 angle pdb=" C3' G A1930 " pdb=" O3' G A1930 " pdb=" P U A1931 " ideal model delta sigma weight residual 120.20 127.94 -7.74 1.50e+00 4.44e-01 2.67e+01 angle pdb=" C3' U a 960 " pdb=" O3' U a 960 " pdb=" P U a 961 " ideal model delta sigma weight residual 120.20 127.93 -7.73 1.50e+00 4.44e-01 2.66e+01 ... (remaining 238989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 90085 35.85 - 71.69: 11066 71.69 - 107.54: 1238 107.54 - 143.38: 25 143.38 - 179.23: 39 Dihedral angle restraints: 102453 sinusoidal: 85061 harmonic: 17392 Sorted by residual: dihedral pdb=" O4' U A1917 " pdb=" C1' U A1917 " pdb=" N1 U A1917 " pdb=" C2 U A1917 " ideal model delta sinusoidal sigma weight residual 200.00 22.31 177.69 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U a 516 " pdb=" C1' U a 516 " pdb=" N1 U a 516 " pdb=" C2 U a 516 " ideal model delta sinusoidal sigma weight residual 200.00 23.17 176.83 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U A1911 " pdb=" C1' U A1911 " pdb=" N1 U A1911 " pdb=" C2 U A1911 " ideal model delta sinusoidal sigma weight residual 200.00 23.50 176.50 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 102450 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 27786 0.088 - 0.176: 2451 0.176 - 0.265: 195 0.265 - 0.353: 36 0.353 - 0.441: 10 Chirality restraints: 30478 Sorted by residual: chirality pdb=" C1' C a 511 " pdb=" O4' C a 511 " pdb=" C2' C a 511 " pdb=" N1 C a 511 " both_signs ideal model delta sigma weight residual False 2.47 2.03 0.44 2.00e-01 2.50e+01 4.86e+00 chirality pdb=" C3' A a1201 " pdb=" C4' A a1201 " pdb=" O3' A a1201 " pdb=" C2' A a1201 " both_signs ideal model delta sigma weight residual False -2.74 -2.33 -0.41 2.00e-01 2.50e+01 4.29e+00 chirality pdb=" C3' G A1022 " pdb=" C4' G A1022 " pdb=" O3' G A1022 " pdb=" C2' G A1022 " both_signs ideal model delta sigma weight residual False -2.74 -2.36 -0.38 2.00e-01 2.50e+01 3.67e+00 ... (remaining 30475 not shown) Planarity restraints: 13035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A A1328 " 0.061 2.00e-02 2.50e+03 2.68e-02 1.98e+01 pdb=" N9 A A1328 " -0.057 2.00e-02 2.50e+03 pdb=" C8 A A1328 " -0.005 2.00e-02 2.50e+03 pdb=" N7 A A1328 " 0.000 2.00e-02 2.50e+03 pdb=" C5 A A1328 " -0.004 2.00e-02 2.50e+03 pdb=" C6 A A1328 " 0.005 2.00e-02 2.50e+03 pdb=" N6 A A1328 " 0.022 2.00e-02 2.50e+03 pdb=" N1 A A1328 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A A1328 " 0.007 2.00e-02 2.50e+03 pdb=" N3 A A1328 " -0.014 2.00e-02 2.50e+03 pdb=" C4 A A1328 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS H 41 " 0.019 2.00e-02 2.50e+03 3.83e-02 1.46e+01 pdb=" C LYS H 41 " -0.066 2.00e-02 2.50e+03 pdb=" O LYS H 41 " 0.025 2.00e-02 2.50e+03 pdb=" N LYS H 42 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A2902 " -0.040 2.00e-02 2.50e+03 2.55e-02 1.46e+01 pdb=" N1 C A2902 " 0.039 2.00e-02 2.50e+03 pdb=" C2 C A2902 " -0.029 2.00e-02 2.50e+03 pdb=" O2 C A2902 " 0.025 2.00e-02 2.50e+03 pdb=" N3 C A2902 " 0.007 2.00e-02 2.50e+03 pdb=" C4 C A2902 " -0.025 2.00e-02 2.50e+03 pdb=" N4 C A2902 " -0.002 2.00e-02 2.50e+03 pdb=" C5 C A2902 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C A2902 " 0.024 2.00e-02 2.50e+03 ... (remaining 13032 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 23136 2.75 - 3.29: 121557 3.29 - 3.82: 323513 3.82 - 4.36: 392981 4.36 - 4.90: 522815 Nonbonded interactions: 1384002 Sorted by model distance: nonbonded pdb=" O2' G A1826 " pdb=" OP2 U A1971 " model vdw 2.211 2.440 nonbonded pdb=" O6 G A 881 " pdb=" O2 U A 895 " model vdw 2.222 2.432 nonbonded pdb=" O2 C A 69 " pdb=" O2' A A 73 " model vdw 2.225 2.440 nonbonded pdb=" O2 U A2139 " pdb=" O6 G A2152 " model vdw 2.228 2.432 nonbonded pdb=" O2' C A1437 " pdb=" O2' G A1516 " model vdw 2.228 2.440 ... (remaining 1383997 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.310 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: 0.150 Extract box with map and model: 15.510 Check model and map are aligned: 1.700 Set scattering table: 1.020 Process input model: 569.080 Find NCS groups from input model: 2.860 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 596.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 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 0.134 159974 Z= 0.490 Angle : 0.935 16.231 238994 Z= 0.471 Chirality : 0.053 0.441 30478 Planarity : 0.007 0.090 13035 Dihedral : 23.475 179.227 91233 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.45 % Favored : 92.46 % Rotamer: Outliers : 0.56 % Allowed : 8.42 % Favored : 91.01 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.09), residues: 5998 helix: -2.32 (0.08), residues: 2095 sheet: -1.81 (0.15), residues: 1079 loop : -2.67 (0.09), residues: 2824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP C 213 HIS 0.021 0.002 HIS r 74 PHE 0.028 0.003 PHE F 175 TYR 0.024 0.003 TYR i 90 ARG 0.017 0.001 ARG d 111 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1488 residues out of total 5014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 1460 time to evaluate : 6.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 15 MET cc_start: 0.8463 (mtt) cc_final: 0.8246 (mtt) REVERT: 2 10 LEU cc_start: 0.8851 (tp) cc_final: 0.8466 (tp) REVERT: 5 48 GLN cc_start: 0.4337 (pm20) cc_final: 0.3963 (mm-40) REVERT: C 225 MET cc_start: 0.8037 (mtt) cc_final: 0.7821 (mtt) REVERT: D 128 ARG cc_start: 0.8073 (mtm-85) cc_final: 0.7861 (mtt180) REVERT: E 195 GLN cc_start: 0.8216 (mt0) cc_final: 0.7637 (mt0) REVERT: G 77 ILE cc_start: 0.8485 (mm) cc_final: 0.8171 (mm) REVERT: O 20 GLU cc_start: 0.7299 (tt0) cc_final: 0.7097 (tt0) REVERT: X 56 MET cc_start: 0.7515 (mtp) cc_final: 0.7178 (mtp) REVERT: X 60 ASP cc_start: 0.7746 (m-30) cc_final: 0.7406 (m-30) REVERT: X 74 ARG cc_start: 0.7745 (mtm110) cc_final: 0.7373 (mtp180) REVERT: Y 36 GLN cc_start: 0.7248 (mp-120) cc_final: 0.6714 (mm-40) REVERT: e 31 PHE cc_start: 0.8256 (m-80) cc_final: 0.8011 (m-80) REVERT: f 5 GLU cc_start: 0.7227 (tt0) cc_final: 0.6904 (tt0) REVERT: f 79 ARG cc_start: 0.7603 (ttm-80) cc_final: 0.7213 (ttm-80) REVERT: g 101 MET cc_start: 0.7333 (mtt) cc_final: 0.7126 (mtt) REVERT: h 38 ASN cc_start: 0.7445 (t0) cc_final: 0.6472 (t0) REVERT: i 27 LYS cc_start: 0.7471 (ptmt) cc_final: 0.7191 (pttt) REVERT: l 54 ARG cc_start: 0.7808 (mmm-85) cc_final: 0.7507 (mmm160) REVERT: l 105 SER cc_start: 0.8741 (p) cc_final: 0.8502 (p) REVERT: m 50 GLU cc_start: 0.7873 (tp30) cc_final: 0.7591 (mm-30) REVERT: n 89 MET cc_start: 0.8356 (mmt) cc_final: 0.7948 (mmp) REVERT: o 26 GLU cc_start: 0.7059 (mp0) cc_final: 0.6787 (mp0) REVERT: o 64 ARG cc_start: 0.8285 (tpt90) cc_final: 0.6967 (mmm160) REVERT: p 42 ILE cc_start: 0.8253 (pt) cc_final: 0.8009 (mt) REVERT: s 29 LYS cc_start: 0.7883 (ptpp) cc_final: 0.7676 (mtmm) REVERT: u 33 ARG cc_start: 0.7424 (ttm170) cc_final: 0.7208 (ttm110) REVERT: y 41 LYS cc_start: 0.8650 (tttp) cc_final: 0.8435 (tttp) REVERT: z 40 MET cc_start: 0.5289 (mmm) cc_final: 0.4988 (mmt) REVERT: z 102 LEU cc_start: 0.7328 (mp) cc_final: 0.7093 (mt) REVERT: z 126 ASN cc_start: 0.7911 (m110) cc_final: 0.7667 (m-40) REVERT: z 185 HIS cc_start: 0.7897 (t70) cc_final: 0.7671 (t-170) REVERT: z 302 GLN cc_start: 0.7906 (mt0) cc_final: 0.7703 (mt0) outliers start: 28 outliers final: 16 residues processed: 1480 average time/residue: 1.3785 time to fit residues: 3469.2327 Evaluate side-chains 1209 residues out of total 5014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1193 time to evaluate : 6.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 32 ILE Chi-restraints excluded: chain 5 residue 37 CYS Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 35 LYS Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain z residue 221 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1049 random chunks: chunk 885 optimal weight: 2.9990 chunk 795 optimal weight: 1.9990 chunk 441 optimal weight: 1.9990 chunk 271 optimal weight: 8.9990 chunk 536 optimal weight: 0.9990 chunk 424 optimal weight: 10.0000 chunk 822 optimal weight: 4.9990 chunk 318 optimal weight: 10.0000 chunk 499 optimal weight: 3.9990 chunk 611 optimal weight: 0.9990 chunk 952 optimal weight: 9.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 20 ASN 5 30 HIS C 86 ASN C 260 ASN D 32 ASN D 49 GLN D 67 HIS D 130 GLN D 150 GLN E 41 GLN ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN F 63 GLN G 45 HIS G 73 ASN H 18 GLN J 40 HIS L 54 GLN ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 67 ASN O 100 HIS O 104 GLN P 10 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 HIS R 89 HIS S 9 HIS S 31 GLN T 59 ASN U 69 ASN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 12 ASN W 76 ASN X 17 ASN Y 15 ASN Y 20 ASN Y 31 GLN b 39 HIS b 42 ASN b 120 GLN c 100 GLN d 71 GLN e 146 ASN f 55 HIS f 63 ASN g 9 GLN g 52 GLN h 18 GLN i 32 GLN i 126 GLN k 38 GLN ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 45 HIS q 47 HIS q 51 ASN r 31 ASN r 54 GLN s 69 HIS u 56 HIS y 12 HIS z 67 ASN z 76 HIS ** z 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 126 ASN z 252 HIS Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 159974 Z= 0.146 Angle : 0.556 12.854 238994 Z= 0.293 Chirality : 0.035 0.276 30478 Planarity : 0.004 0.066 13035 Dihedral : 23.770 179.759 79314 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.72 % Favored : 94.23 % Rotamer: Outliers : 2.52 % Allowed : 15.36 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.10), residues: 5998 helix: -0.34 (0.10), residues: 2104 sheet: -1.27 (0.15), residues: 1085 loop : -2.24 (0.10), residues: 2809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 213 HIS 0.006 0.001 HIS r 74 PHE 0.021 0.001 PHE H 46 TYR 0.018 0.001 TYR g 85 ARG 0.008 0.000 ARG f 2 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1460 residues out of total 5014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 1335 time to evaluate : 6.626 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: 2 10 LEU cc_start: 0.8854 (tp) cc_final: 0.8504 (tp) REVERT: 5 48 GLN cc_start: 0.4328 (pm20) cc_final: 0.3879 (mm-40) REVERT: C 269 ARG cc_start: 0.7157 (tmm-80) cc_final: 0.6789 (ttt180) REVERT: E 41 GLN cc_start: 0.8157 (tt0) cc_final: 0.7883 (tt0) REVERT: H 76 GLU cc_start: 0.2957 (mt-10) cc_final: 0.2385 (pt0) REVERT: K 13 ASN cc_start: 0.8324 (p0) cc_final: 0.8019 (p0) REVERT: O 74 VAL cc_start: 0.9174 (p) cc_final: 0.8854 (m) REVERT: R 21 ARG cc_start: 0.8150 (ttm170) cc_final: 0.7883 (ttm170) REVERT: X 60 ASP cc_start: 0.7797 (m-30) cc_final: 0.7484 (m-30) REVERT: c 36 ASP cc_start: 0.7777 (m-30) cc_final: 0.7555 (m-30) REVERT: c 144 LEU cc_start: 0.7914 (mm) cc_final: 0.7680 (mp) REVERT: f 79 ARG cc_start: 0.7482 (ttm-80) cc_final: 0.7189 (ttm-80) REVERT: i 27 LYS cc_start: 0.7414 (ptmt) cc_final: 0.7072 (pttt) REVERT: l 105 SER cc_start: 0.8624 (p) cc_final: 0.8386 (p) REVERT: n 89 MET cc_start: 0.8355 (mmt) cc_final: 0.7881 (mmp) REVERT: p 1 MET cc_start: 0.7003 (ttp) cc_final: 0.6560 (ttm) REVERT: s 29 LYS cc_start: 0.7922 (ptpp) cc_final: 0.7680 (mtmm) REVERT: t 86 LEU cc_start: 0.7109 (tt) cc_final: 0.6906 (tt) REVERT: y 41 LYS cc_start: 0.8625 (tttp) cc_final: 0.8417 (tttp) REVERT: z 40 MET cc_start: 0.5326 (mmm) cc_final: 0.5098 (mmt) REVERT: z 102 LEU cc_start: 0.7320 (mp) cc_final: 0.7015 (mt) REVERT: z 188 TYR cc_start: 0.7761 (t80) cc_final: 0.7499 (t80) REVERT: z 284 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7471 (tm-30) REVERT: z 289 MET cc_start: 0.7623 (ptp) cc_final: 0.7405 (ptt) outliers start: 125 outliers final: 82 residues processed: 1385 average time/residue: 1.3121 time to fit residues: 3127.6111 Evaluate side-chains 1301 residues out of total 5014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 1219 time to evaluate : 6.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 ASN Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 3 residue 32 ILE Chi-restraints excluded: chain 5 residue 21 VAL Chi-restraints excluded: chain 5 residue 37 CYS Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 42 ASN Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain R residue 102 SER Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain V residue 58 SER Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain Y residue 54 LYS Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 5 ILE Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain c residue 31 ASP Chi-restraints excluded: chain c residue 43 LEU Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 100 GLN Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 28 ILE Chi-restraints excluded: chain d residue 71 GLN Chi-restraints excluded: chain d residue 195 ILE Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 90 ASP Chi-restraints excluded: chain i residue 43 THR Chi-restraints excluded: chain i residue 52 LEU Chi-restraints excluded: chain i residue 98 LEU Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 97 THR Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain o residue 25 THR Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain q residue 18 GLU Chi-restraints excluded: chain r residue 24 LYS Chi-restraints excluded: chain r residue 44 ILE Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain z residue 221 VAL Chi-restraints excluded: chain z residue 350 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1049 random chunks: chunk 529 optimal weight: 0.7980 chunk 295 optimal weight: 20.0000 chunk 792 optimal weight: 2.9990 chunk 648 optimal weight: 10.0000 chunk 262 optimal weight: 10.0000 chunk 954 optimal weight: 9.9990 chunk 1030 optimal weight: 10.0000 chunk 849 optimal weight: 5.9990 chunk 946 optimal weight: 8.9990 chunk 325 optimal weight: 20.0000 chunk 765 optimal weight: 10.0000 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 28 ASN C 239 ASN D 126 ASN E 165 HIS G 48 ASN H 18 GLN H 28 ASN H 43 ASN J 47 HIS J 58 ASN ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 10 GLN ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 81 ASN R 66 HIS S 31 GLN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN b 42 ASN b 120 GLN ** c 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 71 GLN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 52 GLN i 32 GLN j 15 HIS k 38 GLN ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 46 ASN p 26 ASN u 64 ASN ** z 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 185 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 159974 Z= 0.327 Angle : 0.629 14.054 238994 Z= 0.326 Chirality : 0.039 0.310 30478 Planarity : 0.005 0.061 13035 Dihedral : 23.684 179.717 79308 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.05 % Favored : 92.90 % Rotamer: Outliers : 3.93 % Allowed : 18.12 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.10), residues: 5998 helix: 0.25 (0.11), residues: 2117 sheet: -1.11 (0.16), residues: 1089 loop : -2.08 (0.11), residues: 2792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 213 HIS 0.009 0.001 HIS r 74 PHE 0.015 0.002 PHE R 93 TYR 0.021 0.002 TYR g 85 ARG 0.013 0.001 ARG i 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1427 residues out of total 5014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 1232 time to evaluate : 6.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 36 GLU cc_start: 0.6782 (pt0) cc_final: 0.6481 (pt0) REVERT: 2 10 LEU cc_start: 0.8892 (tp) cc_final: 0.8528 (tp) REVERT: 5 48 GLN cc_start: 0.4434 (pm20) cc_final: 0.4119 (mm-40) REVERT: E 195 GLN cc_start: 0.8270 (mt0) cc_final: 0.7611 (mt0) REVERT: F 81 GLN cc_start: 0.8470 (tm-30) cc_final: 0.7910 (tm-30) REVERT: H 51 ARG cc_start: 0.5376 (OUTLIER) cc_final: 0.4912 (ptt-90) REVERT: K 13 ASN cc_start: 0.8447 (p0) cc_final: 0.8082 (p0) REVERT: O 63 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7846 (pptt) REVERT: O 100 HIS cc_start: 0.8254 (OUTLIER) cc_final: 0.7461 (p90) REVERT: P 10 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7793 (mp-120) REVERT: R 21 ARG cc_start: 0.8217 (ttm170) cc_final: 0.7942 (ttm170) REVERT: U 103 ILE cc_start: 0.8006 (mp) cc_final: 0.7775 (mp) REVERT: X 60 ASP cc_start: 0.7842 (m-30) cc_final: 0.7518 (m-30) REVERT: Y 17 GLU cc_start: 0.6975 (tp30) cc_final: 0.6683 (tp30) REVERT: b 194 ASP cc_start: 0.7662 (m-30) cc_final: 0.7337 (m-30) REVERT: c 144 LEU cc_start: 0.8245 (mm) cc_final: 0.7979 (mp) REVERT: f 79 ARG cc_start: 0.7637 (ttm-80) cc_final: 0.7313 (ttm-80) REVERT: g 146 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7433 (mt-10) REVERT: i 27 LYS cc_start: 0.7646 (ptmt) cc_final: 0.7295 (pttt) REVERT: l 105 SER cc_start: 0.8603 (p) cc_final: 0.8334 (p) REVERT: n 89 MET cc_start: 0.8480 (mmt) cc_final: 0.8008 (mmp) REVERT: r 24 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.6787 (pttp) REVERT: s 29 LYS cc_start: 0.7905 (ptpp) cc_final: 0.7669 (mtmm) REVERT: y 41 LYS cc_start: 0.8607 (tttp) cc_final: 0.8394 (tttp) REVERT: z 40 MET cc_start: 0.5036 (mmm) cc_final: 0.4779 (mmt) REVERT: z 102 LEU cc_start: 0.7259 (mp) cc_final: 0.6953 (mt) REVERT: z 188 TYR cc_start: 0.7935 (t80) cc_final: 0.7602 (t80) REVERT: z 284 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7417 (tm-30) outliers start: 195 outliers final: 147 residues processed: 1321 average time/residue: 1.2500 time to fit residues: 2860.4437 Evaluate side-chains 1350 residues out of total 5014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1198 time to evaluate : 6.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 0 residue 6 ASN Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 28 LEU Chi-restraints excluded: chain 1 residue 43 VAL Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 3 residue 32 ILE Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 5 residue 21 VAL Chi-restraints excluded: chain 5 residue 22 MET Chi-restraints excluded: chain 5 residue 37 CYS Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 165 HIS Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 63 LYS Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain P residue 10 GLN Chi-restraints excluded: chain P residue 66 ASN Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 102 SER Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 62 GLU Chi-restraints excluded: chain V residue 7 GLU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain X residue 64 ILE Chi-restraints excluded: chain Z residue 5 ILE Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 118 GLU Chi-restraints excluded: chain b residue 170 HIS Chi-restraints excluded: chain c residue 31 ASP Chi-restraints excluded: chain c residue 43 LEU Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 71 GLN Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain f residue 5 GLU Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 17 GLN Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 93 LYS Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain h residue 90 ASP Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain i residue 43 THR Chi-restraints excluded: chain i residue 52 LEU Chi-restraints excluded: chain i residue 98 LEU Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 64 GLN Chi-restraints excluded: chain k residue 97 ILE Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain l residue 16 VAL 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 87 VAL Chi-restraints excluded: chain l residue 97 THR Chi-restraints excluded: chain m residue 54 ASP Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 113 ARG Chi-restraints excluded: chain o residue 25 THR Chi-restraints excluded: chain q residue 38 ILE Chi-restraints excluded: chain q residue 57 ASP Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 24 LYS Chi-restraints excluded: chain r residue 44 ILE Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain s residue 47 LEU Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain z residue 221 VAL Chi-restraints excluded: chain z residue 306 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1049 random chunks: chunk 942 optimal weight: 10.0000 chunk 717 optimal weight: 10.0000 chunk 495 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 455 optimal weight: 9.9990 chunk 640 optimal weight: 10.0000 chunk 957 optimal weight: 4.9990 chunk 1013 optimal weight: 9.9990 chunk 500 optimal weight: 7.9990 chunk 907 optimal weight: 9.9990 chunk 273 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 243 HIS C 260 ASN D 126 ASN E 165 HIS H 18 GLN H 73 ASN J 136 GLN M 60 GLN N 13 ASN P 10 GLN ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN d 71 GLN ** d 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 46 GLN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 52 GLN i 32 GLN i 37 GLN k 38 GLN ** z 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 185 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.114 159974 Z= 0.402 Angle : 0.678 14.471 238994 Z= 0.349 Chirality : 0.042 0.333 30478 Planarity : 0.005 0.079 13035 Dihedral : 23.695 179.708 79308 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.72 % Favored : 92.23 % Rotamer: Outliers : 4.70 % Allowed : 19.43 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.10), residues: 5998 helix: 0.36 (0.11), residues: 2116 sheet: -1.13 (0.16), residues: 1086 loop : -2.00 (0.11), residues: 2796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 213 HIS 0.019 0.001 HIS R 66 PHE 0.019 0.002 PHE H 46 TYR 0.022 0.002 TYR g 85 ARG 0.015 0.001 ARG j 89 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1442 residues out of total 5014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 1209 time to evaluate : 6.577 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: 2 10 LEU cc_start: 0.8882 (tp) cc_final: 0.8518 (tp) REVERT: 5 48 GLN cc_start: 0.4473 (pm20) cc_final: 0.4183 (mm-40) REVERT: E 195 GLN cc_start: 0.8252 (mt0) cc_final: 0.7604 (mt0) REVERT: F 81 GLN cc_start: 0.8532 (tm-30) cc_final: 0.7986 (tm-30) REVERT: H 73 ASN cc_start: 0.7562 (m-40) cc_final: 0.7345 (m110) REVERT: H 76 GLU cc_start: 0.3186 (mt-10) cc_final: 0.2515 (pt0) REVERT: J 128 ASN cc_start: 0.8401 (t0) cc_final: 0.8030 (t0) REVERT: K 13 ASN cc_start: 0.8544 (p0) cc_final: 0.8188 (p0) REVERT: O 63 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7749 (pptt) REVERT: O 100 HIS cc_start: 0.8321 (OUTLIER) cc_final: 0.7378 (p90) REVERT: R 21 ARG cc_start: 0.8258 (ttm170) cc_final: 0.7957 (ttm170) REVERT: U 103 ILE cc_start: 0.8052 (mp) cc_final: 0.7743 (mp) REVERT: X 33 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8591 (mt) REVERT: X 60 ASP cc_start: 0.7891 (m-30) cc_final: 0.7577 (m-30) REVERT: Y 17 GLU cc_start: 0.6947 (tp30) cc_final: 0.6695 (tp30) REVERT: Y 36 GLN cc_start: 0.7416 (mp-120) cc_final: 0.7127 (mp10) REVERT: b 194 ASP cc_start: 0.7847 (m-30) cc_final: 0.7451 (m-30) REVERT: c 144 LEU cc_start: 0.8327 (mm) cc_final: 0.8049 (mp) REVERT: f 79 ARG cc_start: 0.7709 (ttm-80) cc_final: 0.7368 (ttm-80) REVERT: g 146 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7355 (mt-10) REVERT: l 105 SER cc_start: 0.8693 (p) cc_final: 0.8489 (p) REVERT: n 89 MET cc_start: 0.8525 (mmt) cc_final: 0.8151 (mmp) REVERT: r 24 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.6738 (pttp) REVERT: s 29 LYS cc_start: 0.7863 (ptpp) cc_final: 0.7613 (mtmm) REVERT: y 41 LYS cc_start: 0.8635 (tttp) cc_final: 0.8416 (tttp) REVERT: z 40 MET cc_start: 0.4826 (mmm) cc_final: 0.4578 (mmt) REVERT: z 102 LEU cc_start: 0.7301 (mp) cc_final: 0.7000 (mt) REVERT: z 188 TYR cc_start: 0.8025 (t80) cc_final: 0.7732 (t80) REVERT: z 279 GLN cc_start: 0.7677 (tt0) cc_final: 0.7446 (tt0) outliers start: 233 outliers final: 187 residues processed: 1319 average time/residue: 1.2814 time to fit residues: 2931.0954 Evaluate side-chains 1361 residues out of total 5014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1170 time to evaluate : 6.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 0 residue 6 ASN Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 28 LEU Chi-restraints excluded: chain 0 residue 54 VAL Chi-restraints excluded: chain 1 residue 5 ILE Chi-restraints excluded: chain 1 residue 17 THR Chi-restraints excluded: chain 1 residue 43 VAL Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 3 residue 32 ILE Chi-restraints excluded: chain 3 residue 34 THR Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 5 residue 12 ILE Chi-restraints excluded: chain 5 residue 21 VAL Chi-restraints excluded: chain 5 residue 22 MET Chi-restraints excluded: chain 5 residue 37 CYS Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 63 LYS Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain P residue 10 GLN Chi-restraints excluded: chain P residue 66 ASN Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain Q residue 17 ILE Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 87 SER 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 72 VAL Chi-restraints excluded: chain R residue 102 SER Chi-restraints excluded: chain S residue 94 ASP Chi-restraints excluded: chain S residue 105 VAL Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain U residue 39 ILE Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 62 GLU Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 7 GLU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 64 ILE Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 5 ILE Chi-restraints excluded: chain Z residue 54 MET Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 118 GLU Chi-restraints excluded: chain b residue 170 HIS Chi-restraints excluded: chain b residue 181 ILE Chi-restraints excluded: chain c residue 10 ILE Chi-restraints excluded: chain c residue 31 ASP Chi-restraints excluded: chain c residue 43 LEU Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 30 THR Chi-restraints excluded: chain d residue 71 GLN Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain f residue 5 GLU Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 62 MET Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 93 LYS Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 12 ILE Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain g residue 135 VAL Chi-restraints excluded: chain h residue 90 ASP Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain i residue 43 THR Chi-restraints excluded: chain i residue 52 LEU Chi-restraints excluded: chain i residue 98 LEU Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 64 GLN Chi-restraints excluded: chain k residue 97 ILE Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain l residue 16 VAL 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 87 VAL Chi-restraints excluded: chain l residue 97 THR Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 113 ARG Chi-restraints excluded: chain o residue 25 THR Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain q residue 17 MET Chi-restraints excluded: chain q residue 38 ILE Chi-restraints excluded: chain q residue 57 ASP Chi-restraints excluded: chain q residue 61 ILE Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 24 LYS Chi-restraints excluded: chain r residue 44 ILE Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain s residue 11 ILE Chi-restraints excluded: chain s residue 20 GLU Chi-restraints excluded: chain s residue 47 LEU Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain u residue 14 VAL Chi-restraints excluded: chain z residue 10 LEU Chi-restraints excluded: chain z residue 128 ILE Chi-restraints excluded: chain z residue 138 THR Chi-restraints excluded: chain z residue 221 VAL Chi-restraints excluded: chain z residue 306 LEU Chi-restraints excluded: chain z residue 350 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1049 random chunks: chunk 844 optimal weight: 0.9990 chunk 575 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 754 optimal weight: 10.0000 chunk 418 optimal weight: 9.9990 chunk 865 optimal weight: 0.7980 chunk 700 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 517 optimal weight: 9.9990 chunk 910 optimal weight: 9.9990 chunk 255 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 126 ASN G 22 GLN H 18 GLN J 136 GLN Q 20 GLN ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 HIS S 31 GLN T 15 HIS ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 38 GLN ** z 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 185 HIS z 303 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 159974 Z= 0.215 Angle : 0.590 13.232 238994 Z= 0.308 Chirality : 0.037 0.294 30478 Planarity : 0.004 0.067 13035 Dihedral : 23.719 179.639 79307 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.75 % Favored : 93.20 % Rotamer: Outliers : 4.07 % Allowed : 20.60 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.11), residues: 5998 helix: 0.64 (0.11), residues: 2113 sheet: -1.00 (0.16), residues: 1083 loop : -1.87 (0.11), residues: 2802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 213 HIS 0.007 0.001 HIS r 74 PHE 0.017 0.001 PHE 5 64 TYR 0.024 0.002 TYR z 360 ARG 0.008 0.000 ARG p 56 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1435 residues out of total 5014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1233 time to evaluate : 6.618 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: 0 22 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8256 (mp) REVERT: 0 36 GLU cc_start: 0.6768 (pt0) cc_final: 0.6508 (pt0) REVERT: 2 10 LEU cc_start: 0.8867 (tp) cc_final: 0.8504 (tp) REVERT: E 191 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7408 (p0) REVERT: E 195 GLN cc_start: 0.8195 (mt0) cc_final: 0.7511 (mt0) REVERT: F 81 GLN cc_start: 0.8510 (tm-30) cc_final: 0.7959 (tm-30) REVERT: H 73 ASN cc_start: 0.7551 (m-40) cc_final: 0.7294 (m110) REVERT: H 76 GLU cc_start: 0.3132 (mt-10) cc_final: 0.2501 (pt0) REVERT: J 128 ASN cc_start: 0.8454 (t0) cc_final: 0.8171 (t0) REVERT: K 13 ASN cc_start: 0.8525 (p0) cc_final: 0.8140 (p0) REVERT: M 63 ILE cc_start: 0.9176 (mm) cc_final: 0.8972 (tp) REVERT: O 63 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7530 (pptt) REVERT: O 100 HIS cc_start: 0.8202 (OUTLIER) cc_final: 0.7332 (p90) REVERT: P 11 GLU cc_start: 0.6813 (mt-10) cc_final: 0.6593 (mt-10) REVERT: P 101 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7548 (ptm160) REVERT: Q 62 ILE cc_start: 0.8605 (mm) cc_final: 0.8339 (mt) REVERT: R 21 ARG cc_start: 0.8198 (ttm170) cc_final: 0.7889 (ttm170) REVERT: U 103 ILE cc_start: 0.8009 (mp) cc_final: 0.7707 (mp) REVERT: X 60 ASP cc_start: 0.7841 (m-30) cc_final: 0.7529 (m-30) REVERT: Y 36 GLN cc_start: 0.7354 (mp-120) cc_final: 0.7065 (mp10) REVERT: c 36 ASP cc_start: 0.7752 (m-30) cc_final: 0.7436 (m-30) REVERT: c 144 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7897 (mt) REVERT: f 79 ARG cc_start: 0.7634 (ttm-80) cc_final: 0.7318 (ttm-80) REVERT: i 130 ARG cc_start: 0.7789 (ptp-110) cc_final: 0.7541 (ptp-110) REVERT: l 105 SER cc_start: 0.8679 (p) cc_final: 0.8470 (p) REVERT: n 89 MET cc_start: 0.8484 (mmt) cc_final: 0.8054 (mmp) REVERT: r 24 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.6586 (pttp) REVERT: s 29 LYS cc_start: 0.7901 (ptpp) cc_final: 0.7697 (mtmm) REVERT: y 41 LYS cc_start: 0.8625 (tttp) cc_final: 0.8402 (tttp) REVERT: z 40 MET cc_start: 0.4790 (mmm) cc_final: 0.4541 (mmt) REVERT: z 102 LEU cc_start: 0.7275 (mp) cc_final: 0.6964 (mt) REVERT: z 284 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7462 (tm-30) REVERT: z 288 LYS cc_start: 0.8087 (mtpt) cc_final: 0.7661 (mtmt) outliers start: 202 outliers final: 164 residues processed: 1327 average time/residue: 1.2805 time to fit residues: 2955.4941 Evaluate side-chains 1364 residues out of total 5014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1193 time to evaluate : 6.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 0 residue 6 ASN Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 22 LEU Chi-restraints excluded: chain 0 residue 28 LEU Chi-restraints excluded: chain 0 residue 54 VAL Chi-restraints excluded: chain 1 residue 5 ILE Chi-restraints excluded: chain 1 residue 17 THR Chi-restraints excluded: chain 3 residue 32 ILE Chi-restraints excluded: chain 4 residue 7 VAL Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 5 residue 21 VAL Chi-restraints excluded: chain 5 residue 22 MET Chi-restraints excluded: chain 5 residue 37 CYS Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 63 LYS Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain P residue 66 ASN Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 101 ARG 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 66 HIS Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 102 SER Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain U residue 39 ILE Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 58 ILE Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 64 ILE Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 54 MET Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain c residue 10 ILE Chi-restraints excluded: chain c residue 31 ASP Chi-restraints excluded: chain c residue 43 LEU Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 144 LEU Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 25 VAL Chi-restraints excluded: chain d residue 34 ILE Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain d residue 195 ILE Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 74 LEU Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 93 LYS Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 12 ILE Chi-restraints excluded: chain g residue 18 PHE Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 90 ASP Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain i residue 43 THR Chi-restraints excluded: chain i residue 52 LEU Chi-restraints excluded: chain i residue 98 LEU Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 64 GLN Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain l residue 16 VAL 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 87 VAL Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 54 ASP Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 113 ARG Chi-restraints excluded: chain o residue 25 THR Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain q residue 17 MET Chi-restraints excluded: chain q residue 38 ILE Chi-restraints excluded: chain q residue 57 ASP Chi-restraints excluded: chain r residue 24 LYS Chi-restraints excluded: chain r residue 44 ILE Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain u residue 14 VAL Chi-restraints excluded: chain z residue 10 LEU Chi-restraints excluded: chain z residue 128 ILE Chi-restraints excluded: chain z residue 221 VAL Chi-restraints excluded: chain z residue 306 LEU Chi-restraints excluded: chain z residue 350 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1049 random chunks: chunk 341 optimal weight: 10.0000 chunk 913 optimal weight: 4.9990 chunk 200 optimal weight: 10.0000 chunk 595 optimal weight: 4.9990 chunk 250 optimal weight: 10.0000 chunk 1014 optimal weight: 20.0000 chunk 842 optimal weight: 0.7980 chunk 469 optimal weight: 0.6980 chunk 84 optimal weight: 10.0000 chunk 335 optimal weight: 10.0000 chunk 532 optimal weight: 9.9990 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 126 ASN G 22 GLN J 136 GLN ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 60 GLN ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 HIS ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN k 38 GLN ** z 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 185 HIS z 303 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 159974 Z= 0.253 Angle : 0.589 13.452 238994 Z= 0.307 Chirality : 0.037 0.291 30478 Planarity : 0.004 0.064 13035 Dihedral : 23.640 179.762 79307 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.12 % Favored : 92.83 % Rotamer: Outliers : 4.64 % Allowed : 21.04 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.11), residues: 5998 helix: 0.75 (0.11), residues: 2123 sheet: -0.99 (0.16), residues: 1066 loop : -1.82 (0.11), residues: 2809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 213 HIS 0.025 0.001 HIS R 66 PHE 0.015 0.001 PHE 5 64 TYR 0.018 0.002 TYR g 85 ARG 0.007 0.000 ARG j 89 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1442 residues out of total 5014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1212 time to evaluate : 6.671 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: 0 22 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8249 (mp) REVERT: 2 10 LEU cc_start: 0.8892 (tp) cc_final: 0.8518 (tp) REVERT: E 191 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7465 (p0) REVERT: E 195 GLN cc_start: 0.8199 (mt0) cc_final: 0.7555 (mt0) REVERT: F 81 GLN cc_start: 0.8510 (tm-30) cc_final: 0.7988 (tm-30) REVERT: G 85 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7673 (mmtt) REVERT: H 73 ASN cc_start: 0.7553 (m-40) cc_final: 0.7286 (m110) REVERT: H 76 GLU cc_start: 0.2920 (mt-10) cc_final: 0.2328 (pt0) REVERT: J 128 ASN cc_start: 0.8484 (t0) cc_final: 0.8197 (t0) REVERT: K 13 ASN cc_start: 0.8489 (p0) cc_final: 0.8092 (p0) REVERT: L 1 MET cc_start: 0.7177 (pmm) cc_final: 0.6928 (pmm) REVERT: O 63 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7433 (pptt) REVERT: O 100 HIS cc_start: 0.8191 (OUTLIER) cc_final: 0.7381 (p90) REVERT: P 101 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7539 (ptm160) REVERT: Q 6 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7195 (ptt180) REVERT: Q 62 ILE cc_start: 0.8633 (mm) cc_final: 0.8387 (mt) REVERT: R 21 ARG cc_start: 0.8205 (ttm170) cc_final: 0.7904 (ttm170) REVERT: U 103 ILE cc_start: 0.8057 (mp) cc_final: 0.7768 (mp) REVERT: X 60 ASP cc_start: 0.7847 (m-30) cc_final: 0.7540 (m-30) REVERT: Y 17 GLU cc_start: 0.6933 (tp30) cc_final: 0.6690 (tp30) REVERT: Y 36 GLN cc_start: 0.7288 (mp-120) cc_final: 0.7023 (mp10) REVERT: c 36 ASP cc_start: 0.7765 (m-30) cc_final: 0.7455 (m-30) REVERT: c 144 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7899 (mt) REVERT: f 79 ARG cc_start: 0.7616 (ttm-80) cc_final: 0.7328 (ttm-80) REVERT: i 130 ARG cc_start: 0.7765 (ptp-110) cc_final: 0.7520 (ptp-110) REVERT: k 69 ARG cc_start: 0.8105 (mtp180) cc_final: 0.7860 (mtt180) REVERT: l 105 SER cc_start: 0.8660 (p) cc_final: 0.8458 (p) REVERT: n 89 MET cc_start: 0.8512 (mmt) cc_final: 0.8054 (mmp) REVERT: q 26 GLU cc_start: 0.7176 (tt0) cc_final: 0.6923 (tt0) REVERT: r 24 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.6574 (pttp) REVERT: r 61 ARG cc_start: 0.8580 (mtt90) cc_final: 0.8371 (mtt180) REVERT: s 29 LYS cc_start: 0.7860 (ptpp) cc_final: 0.7641 (mtmm) REVERT: y 41 LYS cc_start: 0.8622 (tttp) cc_final: 0.8412 (tttp) REVERT: z 40 MET cc_start: 0.4792 (mmm) cc_final: 0.4541 (mmt) REVERT: z 102 LEU cc_start: 0.7294 (mp) cc_final: 0.6977 (mt) REVERT: z 257 ASP cc_start: 0.7839 (OUTLIER) cc_final: 0.7626 (p0) outliers start: 230 outliers final: 186 residues processed: 1332 average time/residue: 1.2837 time to fit residues: 2972.2796 Evaluate side-chains 1387 residues out of total 5014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1191 time to evaluate : 6.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 0 residue 6 ASN Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 22 LEU Chi-restraints excluded: chain 0 residue 28 LEU Chi-restraints excluded: chain 0 residue 54 VAL Chi-restraints excluded: chain 1 residue 5 ILE Chi-restraints excluded: chain 1 residue 43 VAL Chi-restraints excluded: chain 3 residue 34 THR Chi-restraints excluded: chain 4 residue 7 VAL Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 5 residue 21 VAL Chi-restraints excluded: chain 5 residue 22 MET Chi-restraints excluded: chain 5 residue 37 CYS Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 165 HIS Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain G residue 85 LYS Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 63 LYS Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain P residue 66 ASN Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 101 ARG Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 87 SER 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 R residue 72 VAL Chi-restraints excluded: chain R residue 102 SER Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain U residue 39 ILE Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 64 ILE Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 54 MET Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 118 GLU Chi-restraints excluded: chain b residue 170 HIS Chi-restraints excluded: chain c residue 10 ILE Chi-restraints excluded: chain c residue 31 ASP Chi-restraints excluded: chain c residue 43 LEU Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 144 LEU Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 25 VAL Chi-restraints excluded: chain d residue 34 ILE Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain d residue 101 VAL Chi-restraints excluded: chain d residue 145 ILE Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain d residue 195 ILE Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 90 THR Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 61 LEU Chi-restraints excluded: chain f residue 74 LEU Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 93 LYS Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 12 ILE Chi-restraints excluded: chain g residue 18 PHE Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain g residue 135 VAL Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 90 ASP Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain i residue 43 THR Chi-restraints excluded: chain i residue 52 LEU Chi-restraints excluded: chain i residue 98 LEU Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 23 ILE Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 64 GLN Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain l residue 16 VAL 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 87 VAL Chi-restraints excluded: chain l residue 97 THR Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 54 ASP Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 113 ARG Chi-restraints excluded: chain o residue 25 THR Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain q residue 17 MET Chi-restraints excluded: chain q residue 38 ILE Chi-restraints excluded: chain q residue 57 ASP Chi-restraints excluded: chain q residue 61 ILE Chi-restraints excluded: chain r residue 24 LYS Chi-restraints excluded: chain r residue 44 ILE Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain s residue 20 GLU Chi-restraints excluded: chain s residue 47 LEU Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain u residue 14 VAL Chi-restraints excluded: chain z residue 10 LEU Chi-restraints excluded: chain z residue 35 GLU Chi-restraints excluded: chain z residue 128 ILE Chi-restraints excluded: chain z residue 197 VAL Chi-restraints excluded: chain z residue 221 VAL Chi-restraints excluded: chain z residue 257 ASP Chi-restraints excluded: chain z residue 267 THR Chi-restraints excluded: chain z residue 306 LEU Chi-restraints excluded: chain z residue 350 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1049 random chunks: chunk 978 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 578 optimal weight: 7.9990 chunk 741 optimal weight: 10.0000 chunk 574 optimal weight: 0.9990 chunk 854 optimal weight: 5.9990 chunk 566 optimal weight: 20.0000 chunk 1011 optimal weight: 9.9990 chunk 632 optimal weight: 10.0000 chunk 616 optimal weight: 20.0000 chunk 466 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 126 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 GLN G 128 GLN J 136 GLN ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 60 GLN ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 HIS ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN Y 25 GLN ** b 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 38 GLN k 119 ASN ** q 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 ASN ** z 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 185 HIS z 303 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 159974 Z= 0.374 Angle : 0.661 13.924 238994 Z= 0.341 Chirality : 0.041 0.325 30478 Planarity : 0.005 0.064 13035 Dihedral : 23.646 179.997 79305 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.69 % Favored : 92.26 % Rotamer: Outliers : 5.18 % Allowed : 21.46 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.11), residues: 5998 helix: 0.66 (0.11), residues: 2126 sheet: -1.03 (0.16), residues: 1085 loop : -1.85 (0.11), residues: 2787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 213 HIS 0.017 0.001 HIS R 66 PHE 0.016 0.002 PHE R 93 TYR 0.021 0.002 TYR z 325 ARG 0.007 0.001 ARG f 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1448 residues out of total 5014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 1191 time to evaluate : 8.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 22 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8303 (mp) REVERT: 2 10 LEU cc_start: 0.8882 (tp) cc_final: 0.8523 (tp) REVERT: 5 48 GLN cc_start: 0.4437 (pm20) cc_final: 0.4211 (mm-40) REVERT: E 191 ASP cc_start: 0.8026 (OUTLIER) cc_final: 0.7489 (p0) REVERT: E 195 GLN cc_start: 0.8232 (mt0) cc_final: 0.7544 (mt0) REVERT: F 81 GLN cc_start: 0.8531 (tm-30) cc_final: 0.7993 (tm-30) REVERT: G 85 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7690 (mmtt) REVERT: H 5 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8725 (mp) REVERT: H 51 ARG cc_start: 0.5287 (OUTLIER) cc_final: 0.4832 (ptt-90) REVERT: H 73 ASN cc_start: 0.7873 (m-40) cc_final: 0.7575 (m110) REVERT: H 76 GLU cc_start: 0.3207 (mt-10) cc_final: 0.2566 (pt0) REVERT: J 128 ASN cc_start: 0.8501 (t0) cc_final: 0.8212 (t0) REVERT: K 13 ASN cc_start: 0.8538 (p0) cc_final: 0.8119 (p0) REVERT: O 63 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7633 (pptt) REVERT: O 100 HIS cc_start: 0.8323 (OUTLIER) cc_final: 0.7397 (p90) REVERT: P 101 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7579 (ptm160) REVERT: Q 6 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7287 (ptt180) REVERT: Q 62 ILE cc_start: 0.8708 (mm) cc_final: 0.8469 (mt) REVERT: S 18 ARG cc_start: 0.8847 (mtt180) cc_final: 0.8633 (mtt180) REVERT: V 38 LEU cc_start: 0.8207 (tp) cc_final: 0.7941 (tp) REVERT: X 60 ASP cc_start: 0.7865 (m-30) cc_final: 0.7556 (m-30) REVERT: Y 17 GLU cc_start: 0.6944 (tp30) cc_final: 0.6719 (tp30) REVERT: Y 36 GLN cc_start: 0.7072 (mp-120) cc_final: 0.6812 (mp10) REVERT: b 194 ASP cc_start: 0.7640 (m-30) cc_final: 0.7273 (m-30) REVERT: c 144 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7908 (mt) REVERT: e 66 LYS cc_start: 0.8435 (mtpp) cc_final: 0.8222 (mtpp) REVERT: f 79 ARG cc_start: 0.7662 (ttm-80) cc_final: 0.7348 (ttm-80) REVERT: k 69 ARG cc_start: 0.8147 (mtp180) cc_final: 0.7854 (mtt180) REVERT: k 79 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8569 (mm) REVERT: l 105 SER cc_start: 0.8661 (p) cc_final: 0.8455 (p) REVERT: n 89 MET cc_start: 0.8547 (mmt) cc_final: 0.8166 (mmp) REVERT: s 29 LYS cc_start: 0.7861 (ptpp) cc_final: 0.7645 (mtmm) REVERT: y 41 LYS cc_start: 0.8641 (tttp) cc_final: 0.8439 (tttp) REVERT: z 40 MET cc_start: 0.4794 (mmm) cc_final: 0.4545 (mmt) REVERT: z 102 LEU cc_start: 0.7288 (mp) cc_final: 0.6967 (mt) REVERT: z 188 TYR cc_start: 0.8085 (t80) cc_final: 0.7697 (t80) REVERT: z 257 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7634 (p0) REVERT: z 279 GLN cc_start: 0.7678 (tt0) cc_final: 0.7436 (tt0) REVERT: z 339 ASN cc_start: 0.7667 (t0) cc_final: 0.7451 (t0) outliers start: 257 outliers final: 211 residues processed: 1329 average time/residue: 1.3371 time to fit residues: 3101.6636 Evaluate side-chains 1398 residues out of total 5014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 1175 time to evaluate : 6.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 0 residue 6 ASN Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 22 LEU Chi-restraints excluded: chain 0 residue 28 LEU Chi-restraints excluded: chain 0 residue 54 VAL Chi-restraints excluded: chain 1 residue 5 ILE Chi-restraints excluded: chain 1 residue 17 THR Chi-restraints excluded: chain 1 residue 43 VAL Chi-restraints excluded: chain 1 residue 51 GLU Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 3 residue 34 THR Chi-restraints excluded: chain 4 residue 7 VAL Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 5 residue 12 ILE Chi-restraints excluded: chain 5 residue 21 VAL Chi-restraints excluded: chain 5 residue 22 MET Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 165 HIS Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 85 LYS Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 63 LYS Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain P residue 66 ASN Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 101 ARG Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 87 SER 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 R residue 72 VAL Chi-restraints excluded: chain R residue 102 SER Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain S residue 94 ASP Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 37 GLU Chi-restraints excluded: chain U residue 39 ILE Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 58 ILE Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 7 GLU Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 80 ILE Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 64 ILE Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 5 ILE Chi-restraints excluded: chain Z residue 54 MET Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 118 GLU Chi-restraints excluded: chain b residue 170 HIS Chi-restraints excluded: chain b residue 181 ILE Chi-restraints excluded: chain c residue 10 ILE Chi-restraints excluded: chain c residue 43 LEU Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 144 LEU Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 25 VAL Chi-restraints excluded: chain d residue 30 THR Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain d residue 100 ASN Chi-restraints excluded: chain d residue 145 ILE Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain d residue 195 ILE Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 90 THR Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 61 LEU Chi-restraints excluded: chain f residue 74 LEU Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 93 LYS Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 12 ILE Chi-restraints excluded: chain g residue 18 PHE Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain g residue 135 VAL Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain i residue 43 THR Chi-restraints excluded: chain i residue 52 LEU Chi-restraints excluded: chain i residue 98 LEU Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 16 VAL 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 64 GLN Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain l residue 16 VAL 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 87 VAL Chi-restraints excluded: chain l residue 97 THR Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 43 VAL Chi-restraints excluded: chain m residue 54 ASP Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 113 ARG Chi-restraints excluded: chain o residue 25 THR Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain q residue 17 MET Chi-restraints excluded: chain q residue 38 ILE Chi-restraints excluded: chain q residue 57 ASP Chi-restraints excluded: chain q residue 61 ILE Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 18 VAL Chi-restraints excluded: chain r residue 44 ILE Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain r residue 74 HIS Chi-restraints excluded: chain s residue 11 ILE Chi-restraints excluded: chain s residue 20 GLU Chi-restraints excluded: chain s residue 47 LEU Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain u residue 14 VAL Chi-restraints excluded: chain z residue 10 LEU Chi-restraints excluded: chain z residue 35 GLU Chi-restraints excluded: chain z residue 128 ILE Chi-restraints excluded: chain z residue 138 THR Chi-restraints excluded: chain z residue 197 VAL Chi-restraints excluded: chain z residue 221 VAL Chi-restraints excluded: chain z residue 257 ASP Chi-restraints excluded: chain z residue 267 THR Chi-restraints excluded: chain z residue 289 MET Chi-restraints excluded: chain z residue 306 LEU Chi-restraints excluded: chain z residue 350 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1049 random chunks: chunk 625 optimal weight: 20.0000 chunk 403 optimal weight: 10.0000 chunk 603 optimal weight: 5.9990 chunk 304 optimal weight: 10.0000 chunk 198 optimal weight: 10.0000 chunk 195 optimal weight: 10.0000 chunk 642 optimal weight: 10.0000 chunk 688 optimal weight: 10.0000 chunk 499 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 794 optimal weight: 6.9990 overall best weight: 8.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 28 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 GLN J 136 GLN M 60 GLN ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 41 GLN Q 52 GLN R 66 HIS ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN ** b 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 196 ASN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 38 GLN o 80 GLN ** q 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 185 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.131 159974 Z= 0.464 Angle : 0.728 14.428 238994 Z= 0.373 Chirality : 0.044 0.350 30478 Planarity : 0.005 0.067 13035 Dihedral : 23.699 179.948 79304 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.32 % Favored : 91.63 % Rotamer: Outliers : 5.46 % Allowed : 21.85 % Favored : 72.69 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.10), residues: 5998 helix: 0.50 (0.11), residues: 2119 sheet: -1.09 (0.16), residues: 1058 loop : -1.90 (0.11), residues: 2821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 213 HIS 0.033 0.002 HIS R 66 PHE 0.019 0.002 PHE R 93 TYR 0.030 0.002 TYR z 360 ARG 0.013 0.001 ARG i 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1458 residues out of total 5014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 1187 time to evaluate : 6.659 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: 2 10 LEU cc_start: 0.8885 (tp) cc_final: 0.8522 (tp) REVERT: 5 48 GLN cc_start: 0.4569 (pm20) cc_final: 0.4152 (mm-40) REVERT: E 191 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7625 (p0) REVERT: E 195 GLN cc_start: 0.8262 (mt0) cc_final: 0.7622 (mt0) REVERT: F 81 GLN cc_start: 0.8545 (tm-30) cc_final: 0.7986 (tm-30) REVERT: G 85 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7643 (mmtt) REVERT: H 5 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8739 (mp) REVERT: H 51 ARG cc_start: 0.5428 (OUTLIER) cc_final: 0.5068 (ptt-90) REVERT: H 73 ASN cc_start: 0.7757 (m-40) cc_final: 0.7510 (m-40) REVERT: H 76 GLU cc_start: 0.3313 (mt-10) cc_final: 0.2620 (pt0) REVERT: K 13 ASN cc_start: 0.8552 (p0) cc_final: 0.8283 (p0) REVERT: O 100 HIS cc_start: 0.8411 (OUTLIER) cc_final: 0.7464 (p90) REVERT: P 101 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7730 (ptm160) REVERT: Q 6 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7345 (ptt180) REVERT: Q 62 ILE cc_start: 0.8754 (mm) cc_final: 0.8525 (mt) REVERT: R 43 ASN cc_start: 0.8340 (OUTLIER) cc_final: 0.8057 (p0) REVERT: T 1 MET cc_start: 0.5363 (ptp) cc_final: 0.5156 (ttm) REVERT: V 38 LEU cc_start: 0.8233 (tp) cc_final: 0.7963 (tp) REVERT: X 60 ASP cc_start: 0.7896 (m-30) cc_final: 0.7594 (m-30) REVERT: Y 17 GLU cc_start: 0.7010 (tp30) cc_final: 0.6794 (tp30) REVERT: Y 36 GLN cc_start: 0.7063 (mp-120) cc_final: 0.6775 (mp10) REVERT: b 194 ASP cc_start: 0.7787 (m-30) cc_final: 0.7482 (m-30) REVERT: c 144 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8062 (mp) REVERT: e 66 LYS cc_start: 0.8450 (mtpp) cc_final: 0.8213 (mtpp) REVERT: f 79 ARG cc_start: 0.7732 (ttm-80) cc_final: 0.7357 (ttm-80) REVERT: g 86 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7888 (mt0) REVERT: k 69 ARG cc_start: 0.8186 (mtp180) cc_final: 0.7897 (mtt180) REVERT: k 79 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8604 (mm) REVERT: l 105 SER cc_start: 0.8685 (p) cc_final: 0.8473 (p) REVERT: n 89 MET cc_start: 0.8557 (mmt) cc_final: 0.8188 (mmp) REVERT: s 29 LYS cc_start: 0.7887 (ptpp) cc_final: 0.7654 (mtmm) REVERT: t 54 MET cc_start: 0.8476 (tmm) cc_final: 0.7897 (ttp) REVERT: y 41 LYS cc_start: 0.8666 (tttp) cc_final: 0.8445 (tttp) REVERT: z 40 MET cc_start: 0.4980 (mmm) cc_final: 0.4745 (mmt) REVERT: z 102 LEU cc_start: 0.7381 (mp) cc_final: 0.7083 (mt) REVERT: z 188 TYR cc_start: 0.8115 (t80) cc_final: 0.7750 (t80) REVERT: z 257 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7641 (p0) REVERT: z 279 GLN cc_start: 0.7703 (tt0) cc_final: 0.7488 (tt0) REVERT: z 339 ASN cc_start: 0.7907 (t0) cc_final: 0.7684 (t0) outliers start: 271 outliers final: 227 residues processed: 1336 average time/residue: 1.2876 time to fit residues: 2982.1698 Evaluate side-chains 1406 residues out of total 5014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 1168 time to evaluate : 6.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 0 residue 6 ASN Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 28 LEU Chi-restraints excluded: chain 0 residue 54 VAL Chi-restraints excluded: chain 1 residue 5 ILE Chi-restraints excluded: chain 1 residue 17 THR Chi-restraints excluded: chain 1 residue 43 VAL Chi-restraints excluded: chain 1 residue 51 GLU Chi-restraints excluded: chain 1 residue 53 LYS Chi-restraints excluded: chain 2 residue 15 SER Chi-restraints excluded: chain 3 residue 34 THR Chi-restraints excluded: chain 4 residue 7 VAL Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 5 residue 12 ILE Chi-restraints excluded: chain 5 residue 21 VAL Chi-restraints excluded: chain 5 residue 22 MET Chi-restraints excluded: chain 5 residue 37 CYS Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 165 HIS Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 85 LYS Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain P residue 66 ASN Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 101 ARG Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 87 SER 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 43 ASN Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 102 SER Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain S residue 94 ASP Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 37 GLU Chi-restraints excluded: chain U residue 39 ILE Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 58 ILE Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 80 ILE Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 35 SER Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 64 ILE Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 5 ILE Chi-restraints excluded: chain Z residue 54 MET Chi-restraints excluded: chain b residue 30 PHE Chi-restraints excluded: chain b residue 47 VAL Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 118 GLU Chi-restraints excluded: chain b residue 153 ASP Chi-restraints excluded: chain b residue 170 HIS Chi-restraints excluded: chain b residue 181 ILE Chi-restraints excluded: chain c residue 10 ILE Chi-restraints excluded: chain c residue 31 ASP Chi-restraints excluded: chain c residue 43 LEU Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 144 LEU Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 25 VAL Chi-restraints excluded: chain d residue 30 THR Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain d residue 145 ILE Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain d residue 195 ILE Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 90 THR Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain e residue 165 LEU Chi-restraints excluded: chain f residue 5 GLU Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 61 LEU Chi-restraints excluded: chain f residue 74 LEU Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 93 LYS Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 12 ILE Chi-restraints excluded: chain g residue 18 PHE Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain g residue 135 VAL Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain i residue 43 THR Chi-restraints excluded: chain i residue 52 LEU Chi-restraints excluded: chain i residue 98 LEU Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 16 VAL 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 64 GLN Chi-restraints excluded: chain k residue 74 VAL Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain l residue 16 VAL 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 87 VAL Chi-restraints excluded: chain l residue 97 THR Chi-restraints excluded: chain l residue 119 VAL Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 43 VAL Chi-restraints excluded: chain m residue 54 ASP Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 113 ARG Chi-restraints excluded: chain o residue 25 THR Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain q residue 17 MET Chi-restraints excluded: chain q residue 38 ILE Chi-restraints excluded: chain q residue 57 ASP Chi-restraints excluded: chain q residue 61 ILE Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 18 VAL Chi-restraints excluded: chain r residue 44 ILE Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain r residue 74 HIS Chi-restraints excluded: chain s residue 11 ILE Chi-restraints excluded: chain s residue 20 GLU Chi-restraints excluded: chain s residue 47 LEU Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain u residue 14 VAL Chi-restraints excluded: chain z residue 10 LEU Chi-restraints excluded: chain z residue 35 GLU Chi-restraints excluded: chain z residue 128 ILE Chi-restraints excluded: chain z residue 138 THR Chi-restraints excluded: chain z residue 197 VAL Chi-restraints excluded: chain z residue 221 VAL Chi-restraints excluded: chain z residue 257 ASP Chi-restraints excluded: chain z residue 267 THR Chi-restraints excluded: chain z residue 289 MET Chi-restraints excluded: chain z residue 306 LEU Chi-restraints excluded: chain z residue 350 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1049 random chunks: chunk 919 optimal weight: 8.9990 chunk 968 optimal weight: 6.9990 chunk 883 optimal weight: 8.9990 chunk 942 optimal weight: 5.9990 chunk 567 optimal weight: 7.9990 chunk 410 optimal weight: 8.9990 chunk 739 optimal weight: 10.0000 chunk 289 optimal weight: 10.0000 chunk 851 optimal weight: 9.9990 chunk 891 optimal weight: 4.9990 chunk 938 optimal weight: 1.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 28 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 GLN J 136 GLN M 60 GLN ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 HIS ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN ** b 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 52 GLN k 38 GLN k 119 ASN ** q 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 185 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 159974 Z= 0.319 Angle : 0.641 13.924 238994 Z= 0.332 Chirality : 0.039 0.317 30478 Planarity : 0.005 0.070 13035 Dihedral : 23.687 179.678 79304 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.54 % Favored : 92.41 % Rotamer: Outliers : 4.94 % Allowed : 22.53 % Favored : 72.53 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.11), residues: 5998 helix: 0.69 (0.11), residues: 2114 sheet: -1.07 (0.16), residues: 1077 loop : -1.80 (0.11), residues: 2807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 213 HIS 0.022 0.001 HIS R 66 PHE 0.018 0.002 PHE 5 64 TYR 0.028 0.002 TYR z 360 ARG 0.011 0.000 ARG i 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1434 residues out of total 5014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 1189 time to evaluate : 6.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 10 LEU cc_start: 0.8863 (tp) cc_final: 0.8497 (tp) REVERT: 5 48 GLN cc_start: 0.4546 (pm20) cc_final: 0.3964 (mm-40) REVERT: E 191 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7534 (p0) REVERT: E 195 GLN cc_start: 0.8227 (mt0) cc_final: 0.7545 (mt0) REVERT: G 85 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7680 (mmtt) REVERT: H 73 ASN cc_start: 0.7774 (m-40) cc_final: 0.7548 (m-40) REVERT: H 76 GLU cc_start: 0.3220 (mt-10) cc_final: 0.2583 (pt0) REVERT: J 128 ASN cc_start: 0.8240 (t0) cc_final: 0.8034 (t0) REVERT: K 13 ASN cc_start: 0.8516 (p0) cc_final: 0.8262 (p0) REVERT: M 60 GLN cc_start: 0.8137 (mm-40) cc_final: 0.7790 (mp10) REVERT: O 100 HIS cc_start: 0.8311 (OUTLIER) cc_final: 0.7399 (p90) REVERT: P 101 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7633 (ptm160) REVERT: Q 6 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7276 (ptt180) REVERT: Q 62 ILE cc_start: 0.8692 (mm) cc_final: 0.8455 (mt) REVERT: T 1 MET cc_start: 0.5356 (ptp) cc_final: 0.5156 (ttm) REVERT: X 60 ASP cc_start: 0.7871 (m-30) cc_final: 0.7568 (m-30) REVERT: Y 36 GLN cc_start: 0.7291 (mp-120) cc_final: 0.6999 (mp10) REVERT: b 194 ASP cc_start: 0.7756 (m-30) cc_final: 0.7452 (m-30) REVERT: c 36 ASP cc_start: 0.7788 (m-30) cc_final: 0.7481 (m-30) REVERT: c 144 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7888 (mt) REVERT: e 66 LYS cc_start: 0.8444 (mtpp) cc_final: 0.8213 (mtpp) REVERT: f 79 ARG cc_start: 0.7684 (ttm-80) cc_final: 0.7366 (ttm-80) REVERT: g 31 MET cc_start: 0.7824 (ttm) cc_final: 0.7533 (ttp) REVERT: k 69 ARG cc_start: 0.8183 (mtp180) cc_final: 0.7852 (mtt180) REVERT: k 79 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8567 (mm) REVERT: l 105 SER cc_start: 0.8622 (p) cc_final: 0.8411 (p) REVERT: n 89 MET cc_start: 0.8535 (mmt) cc_final: 0.8158 (mmp) REVERT: r 24 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.6763 (pttp) REVERT: s 29 LYS cc_start: 0.7878 (ptpp) cc_final: 0.7653 (mtmm) REVERT: t 54 MET cc_start: 0.8439 (tmm) cc_final: 0.7851 (ttp) REVERT: y 41 LYS cc_start: 0.8650 (tttp) cc_final: 0.8443 (tttp) REVERT: z 40 MET cc_start: 0.4948 (mmm) cc_final: 0.4709 (mmt) REVERT: z 102 LEU cc_start: 0.7326 (mp) cc_final: 0.7003 (mt) REVERT: z 279 GLN cc_start: 0.7662 (tt0) cc_final: 0.7424 (tt0) REVERT: z 339 ASN cc_start: 0.7821 (t0) cc_final: 0.7590 (t0) outliers start: 245 outliers final: 212 residues processed: 1320 average time/residue: 1.3551 time to fit residues: 3119.8370 Evaluate side-chains 1395 residues out of total 5014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 1175 time to evaluate : 6.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 0 residue 6 ASN Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 54 VAL Chi-restraints excluded: chain 1 residue 5 ILE Chi-restraints excluded: chain 1 residue 17 THR Chi-restraints excluded: chain 1 residue 43 VAL Chi-restraints excluded: chain 1 residue 51 GLU Chi-restraints excluded: chain 1 residue 53 LYS Chi-restraints excluded: chain 3 residue 34 THR Chi-restraints excluded: chain 4 residue 7 VAL Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 5 residue 12 ILE Chi-restraints excluded: chain 5 residue 21 VAL Chi-restraints excluded: chain 5 residue 22 MET Chi-restraints excluded: chain 5 residue 37 CYS Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 85 LYS Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain P residue 66 ASN Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 101 ARG Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 100 VAL 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 72 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 102 SER Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 37 GLU Chi-restraints excluded: chain U residue 39 ILE Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 58 ILE Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain V residue 7 GLU Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 80 ILE Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 42 SER Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 64 ILE Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Z residue 54 MET Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 153 ASP Chi-restraints excluded: chain b residue 170 HIS Chi-restraints excluded: chain c residue 10 ILE Chi-restraints excluded: chain c residue 31 ASP Chi-restraints excluded: chain c residue 43 LEU Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 144 LEU Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 25 VAL Chi-restraints excluded: chain d residue 30 THR Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain d residue 145 ILE Chi-restraints excluded: chain d residue 171 LEU Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 90 THR Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain f residue 5 GLU Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 61 LEU Chi-restraints excluded: chain f residue 74 LEU Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 93 LYS Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 7 ILE Chi-restraints excluded: chain g residue 12 ILE Chi-restraints excluded: chain g residue 18 PHE Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain g residue 135 VAL Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain i residue 43 THR Chi-restraints excluded: chain i residue 52 LEU Chi-restraints excluded: chain i residue 98 LEU Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 16 VAL 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 64 GLN Chi-restraints excluded: chain k residue 74 VAL Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain l residue 16 VAL 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 87 VAL Chi-restraints excluded: chain l residue 97 THR Chi-restraints excluded: chain l residue 119 VAL Chi-restraints excluded: chain m residue 7 ILE Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 43 VAL Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 113 ARG Chi-restraints excluded: chain o residue 25 THR Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain o residue 89 ARG Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain q residue 17 MET Chi-restraints excluded: chain q residue 38 ILE Chi-restraints excluded: chain q residue 57 ASP Chi-restraints excluded: chain q residue 61 ILE Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 18 VAL Chi-restraints excluded: chain r residue 24 LYS Chi-restraints excluded: chain r residue 44 ILE Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain r residue 74 HIS Chi-restraints excluded: chain s residue 11 ILE Chi-restraints excluded: chain s residue 20 GLU Chi-restraints excluded: chain s residue 47 LEU Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain u residue 14 VAL Chi-restraints excluded: chain z residue 10 LEU Chi-restraints excluded: chain z residue 35 GLU Chi-restraints excluded: chain z residue 128 ILE Chi-restraints excluded: chain z residue 197 VAL Chi-restraints excluded: chain z residue 221 VAL Chi-restraints excluded: chain z residue 267 THR Chi-restraints excluded: chain z residue 306 LEU Chi-restraints excluded: chain z residue 350 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1049 random chunks: chunk 618 optimal weight: 10.0000 chunk 996 optimal weight: 5.9990 chunk 608 optimal weight: 7.9990 chunk 472 optimal weight: 10.0000 chunk 692 optimal weight: 10.0000 chunk 1045 optimal weight: 5.9990 chunk 961 optimal weight: 5.9990 chunk 832 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 642 optimal weight: 10.0000 chunk 510 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 HIS S 31 GLN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 17 ASN d 196 ASN f 46 GLN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 38 GLN ** q 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 185 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 159974 Z= 0.261 Angle : 0.620 13.603 238994 Z= 0.324 Chirality : 0.038 0.306 30478 Planarity : 0.005 0.069 13035 Dihedral : 23.697 179.899 79304 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.55 % Favored : 92.40 % Rotamer: Outliers : 4.51 % Allowed : 22.93 % Favored : 72.55 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.11), residues: 5998 helix: 0.74 (0.11), residues: 2121 sheet: -1.06 (0.16), residues: 1082 loop : -1.78 (0.11), residues: 2795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 213 HIS 0.007 0.001 HIS d 198 PHE 0.022 0.001 PHE Y 26 TYR 0.045 0.002 TYR f 59 ARG 0.016 0.000 ARG i 95 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11996 Ramachandran restraints generated. 5998 Oldfield, 0 Emsley, 5998 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1409 residues out of total 5014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 1185 time to evaluate : 6.100 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: 2 10 LEU cc_start: 0.8873 (tp) cc_final: 0.8503 (tp) REVERT: 5 48 GLN cc_start: 0.4533 (pm20) cc_final: 0.4214 (mm-40) REVERT: E 191 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7407 (p0) REVERT: E 195 GLN cc_start: 0.8210 (mt0) cc_final: 0.7525 (mt0) REVERT: G 85 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7682 (mmtt) REVERT: H 51 ARG cc_start: 0.5192 (OUTLIER) cc_final: 0.4932 (ptt-90) REVERT: H 73 ASN cc_start: 0.7760 (m-40) cc_final: 0.7536 (m-40) REVERT: H 76 GLU cc_start: 0.3202 (mt-10) cc_final: 0.2562 (pt0) REVERT: K 13 ASN cc_start: 0.8507 (p0) cc_final: 0.8257 (p0) REVERT: O 100 HIS cc_start: 0.8285 (OUTLIER) cc_final: 0.7375 (p90) REVERT: P 101 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7655 (ptm160) REVERT: Q 6 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7252 (ptt180) REVERT: Q 62 ILE cc_start: 0.8662 (mm) cc_final: 0.8427 (mt) REVERT: X 60 ASP cc_start: 0.7849 (m-30) cc_final: 0.7542 (m-30) REVERT: Y 36 GLN cc_start: 0.7283 (mp-120) cc_final: 0.6987 (mp10) REVERT: b 194 ASP cc_start: 0.7741 (m-30) cc_final: 0.7430 (m-30) REVERT: c 36 ASP cc_start: 0.7761 (m-30) cc_final: 0.7463 (m-30) REVERT: c 144 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7852 (mt) REVERT: e 66 LYS cc_start: 0.8438 (mtpp) cc_final: 0.8203 (mtpp) REVERT: f 79 ARG cc_start: 0.7668 (ttm-80) cc_final: 0.7352 (ttm-80) REVERT: g 31 MET cc_start: 0.7825 (ttm) cc_final: 0.7545 (ttp) REVERT: k 69 ARG cc_start: 0.8164 (mtp180) cc_final: 0.7874 (mtt180) REVERT: k 79 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8542 (mm) REVERT: l 105 SER cc_start: 0.8605 (p) cc_final: 0.8396 (p) REVERT: n 89 MET cc_start: 0.8520 (mmt) cc_final: 0.8121 (mmp) REVERT: r 24 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.6738 (pttp) REVERT: s 29 LYS cc_start: 0.7873 (ptpp) cc_final: 0.7648 (mtmm) REVERT: t 54 MET cc_start: 0.8424 (tmm) cc_final: 0.7821 (ttp) REVERT: y 41 LYS cc_start: 0.8663 (tttp) cc_final: 0.8445 (tttp) REVERT: z 40 MET cc_start: 0.4924 (mmm) cc_final: 0.4690 (mmt) REVERT: z 102 LEU cc_start: 0.7325 (mp) cc_final: 0.6998 (mt) REVERT: z 151 TYR cc_start: 0.7833 (m-80) cc_final: 0.7554 (m-10) REVERT: z 279 GLN cc_start: 0.7660 (tt0) cc_final: 0.7443 (tt0) REVERT: z 339 ASN cc_start: 0.7800 (t0) cc_final: 0.7565 (t0) outliers start: 224 outliers final: 203 residues processed: 1307 average time/residue: 1.2776 time to fit residues: 2898.9288 Evaluate side-chains 1386 residues out of total 5014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1174 time to evaluate : 6.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 VAL Chi-restraints excluded: chain 0 residue 6 ASN Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 54 VAL Chi-restraints excluded: chain 1 residue 5 ILE Chi-restraints excluded: chain 1 residue 17 THR Chi-restraints excluded: chain 1 residue 43 VAL Chi-restraints excluded: chain 1 residue 51 GLU Chi-restraints excluded: chain 1 residue 53 LYS Chi-restraints excluded: chain 4 residue 7 VAL Chi-restraints excluded: chain 5 residue 12 ILE Chi-restraints excluded: chain 5 residue 21 VAL Chi-restraints excluded: chain 5 residue 22 MET Chi-restraints excluded: chain 5 residue 37 CYS Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 85 LYS Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 70 ASP Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 133 LYS Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain P residue 66 ASN Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain P residue 101 ARG Chi-restraints excluded: chain Q residue 6 ARG Chi-restraints excluded: chain Q residue 83 LEU Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 100 VAL 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 72 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 102 SER Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 37 GLU Chi-restraints excluded: chain U residue 39 ILE Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 58 ILE Chi-restraints excluded: chain U residue 93 VAL Chi-restraints excluded: chain V residue 7 GLU Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 80 ILE Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 64 ILE Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Z residue 54 MET Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 153 ASP Chi-restraints excluded: chain b residue 170 HIS Chi-restraints excluded: chain c residue 10 ILE Chi-restraints excluded: chain c residue 31 ASP Chi-restraints excluded: chain c residue 43 LEU Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain c residue 56 VAL Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 144 LEU Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 25 VAL Chi-restraints excluded: chain d residue 34 ILE Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain d residue 145 ILE Chi-restraints excluded: chain d residue 171 LEU Chi-restraints excluded: chain d residue 173 VAL Chi-restraints excluded: chain d residue 196 ASN Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 90 THR Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain f residue 5 GLU Chi-restraints excluded: chain f residue 7 VAL Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 61 LEU Chi-restraints excluded: chain f residue 74 LEU Chi-restraints excluded: chain f residue 82 ASP Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 93 LYS Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 7 ILE Chi-restraints excluded: chain g residue 12 ILE Chi-restraints excluded: chain g residue 18 PHE Chi-restraints excluded: chain g residue 85 TYR Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain g residue 135 VAL Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain i residue 43 THR Chi-restraints excluded: chain i residue 52 LEU Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 16 VAL 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 64 GLN Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain l residue 16 VAL 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 87 VAL Chi-restraints excluded: chain l residue 97 THR Chi-restraints excluded: chain l residue 119 VAL Chi-restraints excluded: chain m residue 7 ILE Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 54 ASP Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 113 ARG Chi-restraints excluded: chain o residue 25 THR Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain q residue 17 MET Chi-restraints excluded: chain q residue 38 ILE Chi-restraints excluded: chain q residue 57 ASP Chi-restraints excluded: chain q residue 61 ILE Chi-restraints excluded: chain r residue 24 LYS Chi-restraints excluded: chain r residue 44 ILE Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain r residue 74 HIS Chi-restraints excluded: chain s residue 11 ILE Chi-restraints excluded: chain s residue 20 GLU Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain u residue 14 VAL Chi-restraints excluded: chain z residue 10 LEU Chi-restraints excluded: chain z residue 35 GLU Chi-restraints excluded: chain z residue 128 ILE Chi-restraints excluded: chain z residue 197 VAL Chi-restraints excluded: chain z residue 221 VAL Chi-restraints excluded: chain z residue 306 LEU Chi-restraints excluded: chain z residue 350 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1049 random chunks: chunk 661 optimal weight: 10.0000 chunk 886 optimal weight: 9.9990 chunk 254 optimal weight: 10.0000 chunk 767 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 231 optimal weight: 10.0000 chunk 833 optimal weight: 10.0000 chunk 348 optimal weight: 0.3980 chunk 855 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 overall best weight: 8.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 60 GLN ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 HIS S 31 GLN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN X 17 ASN d 196 ASN f 46 GLN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 38 GLN k 119 ASN ** q 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 185 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.083185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.069539 restraints weight = 436766.749| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.00 r_work: 0.3041 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.149 159974 Z= 0.344 Angle : 0.646 59.172 238994 Z= 0.341 Chirality : 0.041 0.520 30478 Planarity : 0.005 0.069 13035 Dihedral : 23.694 179.828 79304 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.55 % Favored : 92.38 % Rotamer: Outliers : 4.72 % Allowed : 22.75 % Favored : 72.53 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.11), residues: 5998 helix: 0.72 (0.11), residues: 2121 sheet: -1.07 (0.16), residues: 1083 loop : -1.78 (0.11), residues: 2794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 213 HIS 0.006 0.001 HIS d 198 PHE 0.023 0.002 PHE Y 26 TYR 0.032 0.002 TYR f 59 ARG 0.044 0.001 ARG i 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 42839.96 seconds wall clock time: 747 minutes 8.28 seconds (44828.28 seconds total)