Starting phenix.real_space_refine on Fri Mar 22 22:58:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsq_12575/03_2024/7nsq_12575_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsq_12575/03_2024/7nsq_12575.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsq_12575/03_2024/7nsq_12575_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsq_12575/03_2024/7nsq_12575_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsq_12575/03_2024/7nsq_12575_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsq_12575/03_2024/7nsq_12575.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsq_12575/03_2024/7nsq_12575.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsq_12575/03_2024/7nsq_12575_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nsq_12575/03_2024/7nsq_12575_updated.pdb" } resolution = 3.1 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= 0.014 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 4733 5.49 5 S 148 5.16 5 C 73227 2.51 5 N 27228 2.21 5 O 40822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 23": "OE1" <-> "OE2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "C PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 121": "OD1" <-> "OD2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "C PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D GLU 74": "OE1" <-> "OE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ASP 181": "OD1" <-> "OD2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "D ASP 200": "OD1" <-> "OD2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E GLU 25": "OE1" <-> "OE2" 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 111": "OE1" <-> "OE2" Residue "E PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 127": "OE1" <-> "OE2" Residue "E ASP 145": "OD1" <-> "OD2" Residue "E GLU 152": "OE1" <-> "OE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "F GLU 32": "OE1" <-> "OE2" Residue "F ASP 46": "OD1" <-> "OD2" Residue "F ASP 51": "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 GLU 98": "OE1" <-> "OE2" 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 ASP 123": "OD1" <-> "OD2" Residue "F ARG 133": "NH1" <-> "NH2" Residue "F PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "F ASP 144": "OD1" <-> "OD2" Residue "F ASP 147": "OD1" <-> "OD2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G ASP 47": "OD1" <-> "OD2" Residue "G ASP 60": "OD1" <-> "OD2" Residue "G GLU 81": "OE1" <-> "OE2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G ARG 163": "NH1" <-> "NH2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "G GLU 173": "OE1" <-> "OE2" Residue "H ASP 7": "OD1" <-> "OD2" Residue "H ASP 17": "OD1" <-> "OD2" Residue "H GLU 48": "OE1" <-> "OE2" Residue "H ASP 101": "OD1" <-> "OD2" Residue "H GLU 114": "OE1" <-> "OE2" Residue "H GLU 137": "OE1" <-> "OE2" Residue "J GLU 9": "OE1" <-> "OE2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ASP 19": "OD1" <-> "OD2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J GLU 43": "OE1" <-> "OE2" Residue "J TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 60": "OD1" <-> "OD2" Residue "J ARG 95": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J GLU 98": "OE1" <-> "OE2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "J GLU 129": "OE1" <-> "OE2" Residue "K ASP 37": "OD1" <-> "OD2" Residue "K GLU 45": "OE1" <-> "OE2" Residue "K ASP 56": "OD1" <-> "OD2" Residue "K ASP 73": "OD1" <-> "OD2" Residue "K ASP 80": "OD1" <-> "OD2" Residue "K GLU 106": "OE1" <-> "OE2" Residue "L GLU 10": "OE1" <-> "OE2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ASP 81": "OD1" <-> "OD2" Residue "L GLU 86": "OE1" <-> "OE2" Residue "L GLU 115": "OE1" <-> "OE2" 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 ARG 40": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M GLU 47": "OE1" <-> "OE2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 58": "OD1" <-> "OD2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 117": "OD1" <-> "OD2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ASP 2": "OD1" <-> "OD2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O GLU 20": "OE1" <-> "OE2" Residue "O TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 69": "OD1" <-> "OD2" Residue "O GLU 80": "OE1" <-> "OE2" 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 ASP 24": "OD1" <-> "OD2" Residue "P ARG 39": "NH1" <-> "NH2" Residue "P PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P GLU 71": "OE1" <-> "OE2" 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 "P GLU 112": "OE1" <-> "OE2" 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 TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "Q GLU 89": "OE1" <-> "OE2" Residue "Q PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 102": "OD1" <-> "OD2" Residue "R TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 16": "OE1" <-> "OE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R ASP 26": "OD1" <-> "OD2" Residue "R ASP 55": "OD1" <-> "OD2" 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 62": "OD1" <-> "OD2" 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 5": "OE1" <-> "OE2" Residue "T GLU 18": "OE1" <-> "OE2" Residue "T GLU 52": "OE1" <-> "OE2" Residue "T GLU 54": "OE1" <-> "OE2" Residue "T ARG 69": "NH1" <-> "NH2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "T ASP 79": "OD1" <-> "OD2" Residue "T TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 7": "NH1" <-> "NH2" Residue "U ASP 8": "OD1" <-> "OD2" Residue "U GLU 37": "OE1" <-> "OE2" Residue "U GLU 60": "OE1" <-> "OE2" Residue "U ARG 82": "NH1" <-> "NH2" Residue "U ARG 86": "NH1" <-> "NH2" Residue "U PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 89": "OD1" <-> "OD2" Residue "U ARG 94": "NH1" <-> "NH2" Residue "U PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 7": "OE1" <-> "OE2" Residue "V GLU 11": "OE1" <-> "OE2" Residue "V TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 69": "OE1" <-> "OE2" Residue "W GLU 29": "OE1" <-> "OE2" Residue "W ASP 56": "OD1" <-> "OD2" Residue "W PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 83": "OE1" <-> "OE2" Residue "X PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 60": "OD1" <-> "OD2" Residue "X ASP 65": "OD1" <-> "OD2" Residue "X GLU 76": "OE1" <-> "OE2" Residue "X TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 17": "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 ASP 40": "OD1" <-> "OD2" Residue "Z ARG 45": "NH1" <-> "NH2" Residue "Z PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 10": "NH1" <-> "NH2" Residue "0 ARG 16": "NH1" <-> "NH2" Residue "0 ARG 40": "NH1" <-> "NH2" Residue "0 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 52": "NH1" <-> "NH2" Residue "1 PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 35": "OE1" <-> "OE2" Residue "1 ASP 40": "OD1" <-> "OD2" Residue "1 ARG 44": "NH1" <-> "NH2" Residue "1 TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 51": "OE1" <-> "OE2" 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 ARG 30": "NH1" <-> "NH2" Residue "3 ARG 40": "NH1" <-> "NH2" Residue "3 ARG 42": "NH1" <-> "NH2" Residue "4 ARG 24": "NH1" <-> "NH2" Residue "5 GLU 10": "OE1" <-> "OE2" Residue "5 ASP 31": "OD1" <-> "OD2" Residue "5 PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 56": "NH1" <-> "NH2" Residue "5 PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 8": "OD1" <-> "OD2" Residue "b TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 44": "OE1" <-> "OE2" Residue "b ARG 63": "NH1" <-> "NH2" Residue "b PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 78": "OE1" <-> "OE2" Residue "b ARG 113": "NH1" <-> "NH2" Residue "b GLU 142": "OE1" <-> "OE2" Residue "b ASP 188": "OD1" <-> "OD2" Residue "b ASP 194": "OD1" <-> "OD2" Residue "b ASP 197": "OD1" <-> "OD2" Residue "b PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 208": "NH1" <-> "NH2" Residue "b ARG 222": "NH1" <-> "NH2" Residue "b GLU 223": "OE1" <-> "OE2" Residue "c PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 28": "OE1" <-> "OE2" Residue "c PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 107": "NH1" <-> "NH2" Residue "c GLU 110": "OE1" <-> "OE2" Residue "c ASP 112": "OD1" <-> "OD2" Residue "c GLU 125": "OE1" <-> "OE2" Residue "c PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 131": "NH1" <-> "NH2" Residue "c GLU 161": "OE1" <-> "OE2" Residue "c GLU 166": "OE1" <-> "OE2" Residue "c GLU 170": "OE1" <-> "OE2" Residue "d ASP 99": "OD1" <-> "OD2" Residue "d GLU 147": "OE1" <-> "OE2" Residue "d GLU 163": "OE1" <-> "OE2" Residue "d PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 184": "NH1" <-> "NH2" Residue "d GLU 187": "OE1" <-> "OE2" Residue "d GLU 202": "OE1" <-> "OE2" Residue "e GLU 13": "OE1" <-> "OE2" Residue "e ARG 20": "NH1" <-> "NH2" Residue "e PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 55": "OE1" <-> "OE2" Residue "e ARG 68": "NH1" <-> "NH2" Residue "e ARG 93": "NH1" <-> "NH2" Residue "e GLU 116": "OE1" <-> "OE2" Residue "e ASP 142": "OD1" <-> "OD2" Residue "e ARG 157": "NH1" <-> "NH2" Residue "e GLU 163": "OE1" <-> "OE2" Residue "f TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 13": "OD1" <-> "OD2" Residue "f GLU 23": "OE1" <-> "OE2" Residue "f GLU 33": "OE1" <-> "OE2" Residue "f GLU 40": "OE1" <-> "OE2" Residue "f TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 65": "OE1" <-> "OE2" Residue "f GLU 69": "OE1" <-> "OE2" Residue "f PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 82": "OD1" <-> "OD2" Residue "f ARG 91": "NH1" <-> "NH2" Residue "f GLU 98": "OE1" <-> "OE2" Residue "g GLU 21": "OE1" <-> "OE2" Residue "g GLU 40": "OE1" <-> "OE2" Residue "g GLU 48": "OE1" <-> "OE2" Residue "g GLU 58": "OE1" <-> "OE2" Residue "g GLU 60": "OE1" <-> "OE2" Residue "g GLU 63": "OE1" <-> "OE2" Residue "g ARG 78": "NH1" <-> "NH2" Residue "g TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 106": "OE1" <-> "OE2" Residue "g GLU 129": "OE1" <-> "OE2" Residue "g ASP 140": "OD1" <-> "OD2" Residue "g GLU 146": "OE1" <-> "OE2" Residue "h ASP 5": "OD1" <-> "OD2" Residue "h ASP 9": "OD1" <-> "OD2" Residue "h GLU 43": "OE1" <-> "OE2" Residue "h PHE 49": "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 89": "OE1" <-> "OE2" Residue "i GLU 97": "OE1" <-> "OE2" Residue "i ARG 99": "NH1" <-> "NH2" Residue "i GLU 112": "OE1" <-> "OE2" Residue "i ARG 124": "NH1" <-> "NH2" Residue "j ASP 14": "OD1" <-> "OD2" Residue "j ASP 19": "OD1" <-> "OD2" Residue "j ASP 60": "OD1" <-> "OD2" Residue "j ARG 68": "NH1" <-> "NH2" Residue "j GLU 78": "OE1" <-> "OE2" Residue "j GLU 81": "OE1" <-> "OE2" Residue "j ASP 85": "OD1" <-> "OD2" Residue "j ASP 91": "OD1" <-> "OD2" Residue "k PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 93": "NH1" <-> "NH2" Residue "k GLU 94": "OE1" <-> "OE2" Residue "k ASP 112": "OD1" <-> "OD2" Residue "l ARG 9": "NH1" <-> "NH2" Residue "l ARG 14": "NH1" <-> "NH2" Residue "l GLU 25": "OE1" <-> "OE2" Residue "l ARG 50": "NH1" <-> "NH2" Residue "l ARG 56": "NH1" <-> "NH2" Residue "l PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 76": "OE1" <-> "OE2" Residue "l ARG 83": "NH1" <-> "NH2" Residue "l ASP 89": "OD1" <-> "OD2" Residue "m ASP 11": "OD1" <-> "OD2" Residue "m TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 42": "OD1" <-> "OD2" Residue "m GLU 50": "OE1" <-> "OE2" Residue "m ASP 58": "OD1" <-> "OD2" Residue "m GLU 59": "OE1" <-> "OE2" Residue "m PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 10": "OE1" <-> "OE2" Residue "n ASP 18": "OD1" <-> "OD2" Residue "n TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 26": "OE1" <-> "OE2" Residue "n ASP 33": "OD1" <-> "OD2" Residue "n ASP 40": "OD1" <-> "OD2" Residue "n ARG 90": "NH1" <-> "NH2" Residue "p ARG 8": "NH1" <-> "NH2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "p PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 47": "OE1" <-> "OE2" Residue "p GLU 48": "OE1" <-> "OE2" Residue "p ASP 55": "OD1" <-> "OD2" Residue "p GLU 77": "OE1" <-> "OE2" Residue "q ARG 11": "NH1" <-> "NH2" Residue "q ARG 27": "NH1" <-> "NH2" Residue "q PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 48": "OD1" <-> "OD2" Residue "q ASP 57": "OD1" <-> "OD2" Residue "q GLU 63": "OE1" <-> "OE2" Residue "q GLU 80": "OE1" <-> "OE2" Residue "r ARG 12": "NH1" <-> "NH2" Residue "r GLU 16": "OE1" <-> "OE2" Residue "r TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 61": "NH1" <-> "NH2" Residue "r TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 72": "OD1" <-> "OD2" Residue "s GLU 20": "OE1" <-> "OE2" Residue "s GLU 24": "OE1" <-> "OE2" Residue "s ARG 32": "NH1" <-> "NH2" Residue "s GLU 73": "OE1" <-> "OE2" Residue "t ARG 24": "NH1" <-> "NH2" Residue "t ASP 43": "OD1" <-> "OD2" Residue "t GLU 53": "OE1" <-> "OE2" Residue "t ARG 60": "NH1" <-> "NH2" Residue "t ARG 74": "NH1" <-> "NH2" Residue "u PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 33": "NH1" <-> "NH2" Residue "u GLU 39": "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" 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: 146158 Number of models: 1 Model: "" Number of chains: 57 Chain: "A" Number of atoms: 62320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62320 Classifications: {'RNA': 2903} Modifications used: {'rna2p_pur': 250, 'rna2p_pyr': 130, 'rna3p_pur': 1424, 'rna3p_pyr': 1099} Link IDs: {'rna2p': 380, 'rna3p': 2522} 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': 5, 'rna3p_pur': 59, 'rna3p_pyr': 51} Link IDs: {'rna2p': 10, 'rna3p': 109} Chain: "C" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1304 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 8, 'TRANS': 165} Chain: "H" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 709 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "0" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 434 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "1" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "3" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "4" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "5" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 514 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "6" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 123 Classifications: {'RNA': 6} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 1, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "7" Number of atoms: 61 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 6, 50 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Conformer: "B" Number of residues, atoms: 6, 50 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} bond proxies already assigned to first conformer: 38 Chain: "8" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1861 Classifications: {'RNA': 87} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 39, 'rna3p_pyr': 34} Link IDs: {'rna2p': 13, 'rna3p': 73} Chain: "a" Number of atoms: 33037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1540, 33037 Classifications: {'RNA': 1540} Modifications used: {'rna2p_pur': 109, 'rna2p_pyr': 67, 'rna3p_pur': 766, 'rna3p_pyr': 598} Link IDs: {'rna2p': 176, 'rna3p': 1363} 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: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1643 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 3, 'rna3p_pur': 32, 'rna3p_pyr': 34} Link IDs: {'rna2p': 10, 'rna3p': 66} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 58 Unusual residues: {'TEL': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG 7 6 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG 7 6 " occ=0.50 Time building chain proxies: 56.38, per 1000 atoms: 0.39 Number of scatterers: 146158 At special positions: 0 Unit cell: (267.028, 273.676, 228.248, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 148 16.00 P 4733 15.00 O 40822 8.00 N 27228 7.00 C 73227 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS 4 11 " - pdb=" SG CYS 4 14 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 11 " - pdb=" SG CYS 4 27 " distance=2.05 Simple disulfide: pdb=" SG CYS 5 16 " - pdb=" SG CYS 5 37 " distance=2.04 Simple disulfide: pdb=" SG CYS 5 18 " - pdb=" SG CYS 5 40 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 53801 O4' U A2506 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 55.75 Conformation dependent library (CDL) restraints added in 6.6 seconds 11184 Ramachandran restraints generated. 5592 Oldfield, 0 Emsley, 5592 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10456 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 173 helices and 69 sheets defined 39.2% alpha, 19.2% beta 1544 base pairs and 2749 stacking pairs defined. Time for finding SS restraints: 72.83 Creating SS restraints... Processing helix chain 'C' and resid 10 through 16 removed outlier: 4.472A pdb=" N VAL C 16 " --> pdb=" O GLY C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.772A pdb=" N LEU C 34 " --> pdb=" O PHE C 30 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N GLU C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 30 through 35' Processing helix chain 'C' and resid 131 through 136 removed outlier: 3.775A pdb=" N ILE C 135 " --> pdb=" O PRO C 131 " (cutoff:3.500A) Proline residue: C 136 - end of helix No H-bonds generated for 'chain 'C' and resid 131 through 136' Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.937A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 3.760A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ASN C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 260 through 268 removed outlier: 6.217A pdb=" N ASP C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LYS C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N PHE C 266 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N VAL C 268 " --> pdb=" O ASP C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 260 through 268' Processing helix chain 'C' and resid 197 through 202 removed outlier: 4.452A pdb=" N MET C 201 " --> pdb=" O ALA C 198 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C 202 " --> pdb=" O GLU C 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 72 removed outlier: 4.326A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY D 72 " --> pdb=" O PHE D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 105 removed outlier: 3.744A pdb=" N ALA D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LYS D 105 " --> pdb=" O PHE D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 41 removed outlier: 3.505A pdb=" N VAL E 28 " --> pdb=" O ASN E 24 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N GLN E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 removed outlier: 3.808A pdb=" N ASP E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 142 removed outlier: 3.826A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 163 removed outlier: 3.541A pdb=" N ALA E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG E 162 " --> pdb=" O PHE E 158 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 184 removed outlier: 3.508A pdb=" N PHE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ASP E 184 " --> pdb=" O LEU E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 201 Processing helix chain 'F' and resid 2 through 20 removed outlier: 4.970A pdb=" N VAL F 13 " --> pdb=" O LYS F 9 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE F 20 " --> pdb=" O LEU F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 61 removed outlier: 5.185A pdb=" N LEU F 50 " --> pdb=" O ASP F 46 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA F 55 " --> pdb=" O ASP F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 111 removed outlier: 3.742A pdb=" N ALA F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N VAL F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Proline residue: F 109 - end of helix Processing helix chain 'F' and resid 162 through 174 removed outlier: 3.787A pdb=" N PHE F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP F 174 " --> pdb=" O LEU F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 removed outlier: 5.468A pdb=" N ALA F 43 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE F 44 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA F 45 " --> pdb=" O GLU F 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 40 through 45' Processing helix chain 'F' and resid 134 through 139 removed outlier: 3.809A pdb=" N ILE F 137 " --> pdb=" O GLU F 134 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE F 138 " --> pdb=" O GLN F 135 " (cutoff:3.500A) Proline residue: F 139 - end of helix No H-bonds generated for 'chain 'F' and resid 134 through 139' Processing helix chain 'G' and resid 2 through 7 removed outlier: 4.513A pdb=" N ALA G 7 " --> pdb=" O ARG G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 81 Processing helix chain 'G' and resid 137 through 153 removed outlier: 4.255A pdb=" N ARG G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 Processing helix chain 'H' and resid 40 through 50 removed outlier: 5.894A pdb=" N ILE H 44 " --> pdb=" O THR H 40 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N GLU H 45 " --> pdb=" O LYS H 41 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ALA H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG H 50 " --> pdb=" O PHE H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 73 removed outlier: 4.954A pdb=" N ALA H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LYS H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASN H 73 " --> pdb=" O ALA H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 Processing helix chain 'H' and resid 111 through 116 removed outlier: 4.240A pdb=" N VAL H 115 " --> pdb=" O ALA H 111 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ARG H 116 " --> pdb=" O LYS H 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 111 through 116' Processing helix chain 'J' and resid 24 through 38 Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.315A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 123 removed outlier: 4.110A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LYS J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 removed outlier: 4.577A pdb=" N LYS J 72 " --> pdb=" O ASN J 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 67 through 72' Processing helix chain 'K' and resid 110 through 120 removed outlier: 4.236A pdb=" N LEU K 118 " --> pdb=" O LYS K 114 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA K 119 " --> pdb=" O ILE K 115 " (cutoff:3.500A) Proline residue: K 120 - end of helix Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.781A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 37 through 42' Processing helix chain 'L' and resid 56 through 62 removed outlier: 3.685A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 4.386A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 68 through 75' Processing helix chain 'L' and resid 78 through 85 removed outlier: 3.764A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 85' Processing helix chain 'L' and resid 91 through 99 removed outlier: 3.654A pdb=" N LEU L 95 " --> pdb=" O ASP L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 139 Processing helix chain 'M' and resid 42 through 58 Processing helix chain 'M' and resid 109 through 125 removed outlier: 4.635A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 58 Proline residue: N 50 - end of helix removed outlier: 3.662A pdb=" N LYS N 56 " --> pdb=" O ILE N 52 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASP N 58 " --> pdb=" O LEU N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 Processing helix chain 'N' and resid 72 through 88 removed outlier: 5.194A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix Processing helix chain 'O' and resid 2 through 22 removed outlier: 3.812A pdb=" N ALA O 6 " --> pdb=" O ASP O 2 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG O 7 " --> pdb=" O LYS O 3 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG O 9 " --> pdb=" O SER O 5 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG O 10 " --> pdb=" O ALA O 6 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG O 16 " --> pdb=" O THR O 12 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS O 17 " --> pdb=" O ARG O 13 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 4.612A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 Processing helix chain 'O' and resid 101 through 114 removed outlier: 4.320A pdb=" N ALA O 105 " --> pdb=" O GLY O 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 13 Processing helix chain 'P' and resid 97 through 104 removed outlier: 4.098A pdb=" N ARG P 101 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N THR P 104 " --> pdb=" O LEU P 100 " (cutoff:3.500A) Processing helix chain 'Q' and resid 6 through 22 removed outlier: 3.571A pdb=" N ALA Q 10 " --> pdb=" O ARG Q 6 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE Q 17 " --> pdb=" O ARG Q 13 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LYS Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 3.852A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 37 Processing helix chain 'Q' and resid 39 through 73 removed outlier: 3.905A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 removed outlier: 3.518A pdb=" N SER Q 87 " --> pdb=" O LEU Q 83 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 101 Processing helix chain 'Q' and resid 102 through 118 removed outlier: 3.880A pdb=" N ALA Q 118 " --> pdb=" O LYS Q 114 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 4.126A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 Processing helix chain 'S' and resid 41 through 61 Processing helix chain 'S' and resid 65 through 70 removed outlier: 3.906A pdb=" N LEU S 69 " --> pdb=" O ASP S 65 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LYS S 70 " --> pdb=" O ILE S 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 65 through 70' Processing helix chain 'T' and resid 2 through 11 removed outlier: 4.255A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 Processing helix chain 'T' and resid 39 through 51 Processing helix chain 'U' and resid 66 through 71 removed outlier: 3.739A pdb=" N VAL U 70 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ALA U 71 " --> pdb=" O VAL U 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 66 through 71' Processing helix chain 'V' and resid 13 through 24 removed outlier: 4.024A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 54 removed outlier: 3.702A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ALA V 54 " --> pdb=" O MET V 50 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 63 removed outlier: 4.075A pdb=" N GLY X 63 " --> pdb=" O ILE X 59 " (cutoff:3.500A) Processing helix chain 'X' and resid 64 through 75 Processing helix chain 'Y' and resid 2 through 10 removed outlier: 4.363A pdb=" N LEU Y 6 " --> pdb=" O LYS Y 2 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N SER Y 10 " --> pdb=" O LEU Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 35 Processing helix chain 'Y' and resid 40 through 61 removed outlier: 4.088A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 28 Processing helix chain 'Z' and resid 41 through 52 Processing helix chain '0' and resid 9 through 21 removed outlier: 4.513A pdb=" N HIS 0 19 " --> pdb=" O MET 0 15 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASP 0 20 " --> pdb=" O ARG 0 16 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA 0 21 " --> pdb=" O ARG 0 17 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 17 through 25 removed outlier: 4.052A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LYS 2 25 " --> pdb=" O ARG 2 21 " (cutoff:3.500A) Processing helix chain '2' and resid 26 through 38 Processing helix chain '3' and resid 7 through 14 Processing helix chain '3' and resid 32 through 37 removed outlier: 4.477A pdb=" N LYS 3 36 " --> pdb=" O ILE 3 32 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ALA 3 37 " --> pdb=" O LEU 3 33 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 32 through 37' Processing helix chain '3' and resid 38 through 46 removed outlier: 3.574A pdb=" N ARG 3 45 " --> pdb=" O LYS 3 41 " (cutoff:3.500A) Proline residue: 3 46 - end of helix Processing helix chain '3' and resid 52 through 63 removed outlier: 3.889A pdb=" N ALA 3 60 " --> pdb=" O GLY 3 56 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS 3 61 " --> pdb=" O LEU 3 57 " (cutoff:3.500A) Proline residue: 3 63 - end of helix Processing helix chain '5' and resid 41 through 46 removed outlier: 3.589A pdb=" N THR 5 45 " --> pdb=" O HIS 5 41 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLY 5 46 " --> pdb=" O PRO 5 42 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 41 through 46' Processing helix chain '5' and resid 55 through 64 Processing helix chain 'b' and resid 5 through 13 removed outlier: 3.804A pdb=" N MET b 9 " --> pdb=" O SER b 5 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 29 removed outlier: 4.027A pdb=" N LYS b 28 " --> pdb=" O ASN b 24 " (cutoff:3.500A) Proline residue: b 29 - end of helix No H-bonds generated for 'chain 'b' and resid 24 through 29' Processing helix chain 'b' and resid 42 through 64 Proline residue: b 48 - end of helix removed outlier: 4.140A pdb=" N ARG b 63 " --> pdb=" O LYS b 59 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS b 64 " --> pdb=" O ILE b 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 74 through 88 removed outlier: 4.158A pdb=" N GLU b 78 " --> pdb=" O ARG b 74 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA b 79 " --> pdb=" O ALA b 75 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N CYS b 87 " --> pdb=" O ALA b 83 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP b 88 " --> pdb=" O ALA b 84 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 122 Processing helix chain 'b' and resid 130 through 148 removed outlier: 6.248A pdb=" N ALA b 134 " --> pdb=" O THR b 130 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ARG b 139 " --> pdb=" O LEU b 135 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLU b 140 " --> pdb=" O MET b 136 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER b 147 " --> pdb=" O LYS b 143 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU b 148 " --> pdb=" O LEU b 144 " (cutoff:3.500A) Processing helix chain 'b' and resid 165 through 170 removed outlier: 3.684A pdb=" N HIS b 170 " --> pdb=" O ALA b 166 " (cutoff:3.500A) Processing helix chain 'b' and resid 171 through 180 Processing helix chain 'b' and resid 206 through 227 removed outlier: 3.678A pdb=" N GLN b 227 " --> pdb=" O GLU b 223 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 15 removed outlier: 5.159A pdb=" N GLY c 13 " --> pdb=" O GLY c 9 " (cutoff:3.500A) Processing helix chain 'c' and resid 25 through 48 removed outlier: 5.140A pdb=" N ALA c 30 " --> pdb=" O THR c 26 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASP c 31 " --> pdb=" O LYS c 27 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS c 45 " --> pdb=" O GLN c 41 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU c 46 " --> pdb=" O TYR c 42 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 78 Processing helix chain 'c' and resid 81 through 96 removed outlier: 3.568A pdb=" N GLU c 85 " --> pdb=" O GLY c 81 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ASP c 93 " --> pdb=" O LYS c 89 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY c 96 " --> pdb=" O ALA c 92 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 113 removed outlier: 4.257A pdb=" N ASP c 112 " --> pdb=" O LYS c 108 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ALA c 113 " --> pdb=" O PRO c 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 108 through 113' Processing helix chain 'c' and resid 114 through 127 Processing helix chain 'c' and resid 129 through 145 Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.054A pdb=" N LEU d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU d 15 " --> pdb=" O LEU d 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 32 removed outlier: 4.082A pdb=" N CYS d 32 " --> pdb=" O ILE d 28 " (cutoff:3.500A) Processing helix chain 'd' and resid 49 through 66 removed outlier: 3.542A pdb=" N TYR d 65 " --> pdb=" O VAL d 61 " (cutoff:3.500A) Processing helix chain 'd' and resid 68 through 83 removed outlier: 4.128A pdb=" N LEU d 82 " --> pdb=" O GLU d 78 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LYS d 83 " --> pdb=" O ALA d 79 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 97 removed outlier: 3.608A pdb=" N ARG d 97 " --> pdb=" O LEU d 93 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 106 Processing helix chain 'd' and resid 110 through 121 Processing helix chain 'd' and resid 146 through 151 removed outlier: 4.393A pdb=" N LYS d 151 " --> pdb=" O GLU d 147 " (cutoff:3.500A) Processing helix chain 'd' and resid 152 through 166 removed outlier: 3.634A pdb=" N LYS d 156 " --> pdb=" O GLN d 152 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU d 166 " --> pdb=" O ALA d 162 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 192 removed outlier: 4.028A pdb=" N LEU d 191 " --> pdb=" O GLU d 187 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N SER d 192 " --> pdb=" O ARG d 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 187 through 192' Processing helix chain 'd' and resid 196 through 206 removed outlier: 4.373A pdb=" N ILE d 200 " --> pdb=" O ASN d 196 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS d 206 " --> pdb=" O GLU d 202 " (cutoff:3.500A) Processing helix chain 'e' and resid 55 through 71 removed outlier: 3.776A pdb=" N ARG e 69 " --> pdb=" O GLU e 65 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N MET e 71 " --> pdb=" O ALA e 67 " (cutoff:3.500A) Processing helix chain 'e' and resid 109 through 119 Processing helix chain 'e' and resid 132 through 148 removed outlier: 5.520A pdb=" N ASN e 148 " --> pdb=" O LEU e 144 " (cutoff:3.500A) Processing helix chain 'e' and resid 149 through 158 Processing helix chain 'e' and resid 160 through 166 removed outlier: 3.853A pdb=" N ILE e 164 " --> pdb=" O SER e 160 " (cutoff:3.500A) Processing helix chain 'f' and resid 14 through 33 removed outlier: 4.079A pdb=" N VAL f 18 " --> pdb=" O GLN f 14 " (cutoff:3.500A) Proline residue: f 19 - end of helix removed outlier: 4.121A pdb=" N GLY f 31 " --> pdb=" O ALA f 27 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ALA f 32 " --> pdb=" O ALA f 28 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU f 33 " --> pdb=" O ILE f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 81 removed outlier: 3.812A pdb=" N ILE f 71 " --> pdb=" O PRO f 67 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 Processing helix chain 'g' and resid 35 through 55 removed outlier: 3.717A pdb=" N ALA g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR g 49 " --> pdb=" O SER g 45 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA g 51 " --> pdb=" O LEU g 47 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLN g 52 " --> pdb=" O GLU g 48 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ARG g 53 " --> pdb=" O THR g 49 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 6.039A pdb=" N ASN g 68 " --> pdb=" O VAL g 64 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG g 70 " --> pdb=" O LEU g 66 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 112 removed outlier: 3.675A pdb=" N ALA g 98 " --> pdb=" O VAL g 94 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYS g 110 " --> pdb=" O GLU g 106 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ARG g 111 " --> pdb=" O ALA g 107 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLY g 112 " --> pdb=" O ALA g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 removed outlier: 3.691A pdb=" N SER g 125 " --> pdb=" O ALA g 121 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 149 removed outlier: 3.970A pdb=" N LYS g 149 " --> pdb=" O ALA g 145 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 Processing helix chain 'h' and resid 30 through 44 Processing helix chain 'h' and resid 112 through 120 Processing helix chain 'i' and resid 34 through 39 Processing helix chain 'i' and resid 41 through 54 removed outlier: 4.343A pdb=" N ARG i 45 " --> pdb=" O ARG i 41 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET i 46 " --> pdb=" O GLU i 42 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL i 47 " --> pdb=" O THR i 43 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N VAL i 48 " --> pdb=" O ALA i 44 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ARG i 49 " --> pdb=" O ARG i 45 " (cutoff:3.500A) Proline residue: i 51 - end of helix Processing helix chain 'i' and resid 57 through 62 removed outlier: 3.995A pdb=" N LEU i 61 " --> pdb=" O MET i 57 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ASP i 62 " --> pdb=" O VAL i 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 57 through 62' Processing helix chain 'i' and resid 71 through 92 removed outlier: 3.912A pdb=" N GLN i 75 " --> pdb=" O GLY i 71 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR i 90 " --> pdb=" O ALA i 86 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP i 91 " --> pdb=" O LEU i 87 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLU i 92 " --> pdb=" O MET i 88 " (cutoff:3.500A) Processing helix chain 'i' and resid 93 through 102 removed outlier: 4.336A pdb=" N LYS i 100 " --> pdb=" O SER i 96 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ALA i 101 " --> pdb=" O GLU i 97 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY i 102 " --> pdb=" O LEU i 98 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 3.644A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLY j 33 " --> pdb=" O ALA j 29 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 3.991A pdb=" N LEU j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 46 through 51 removed outlier: 3.523A pdb=" N SER k 50 " --> pdb=" O THR k 46 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLY k 51 " --> pdb=" O ALA k 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 46 through 51' Processing helix chain 'k' and resid 54 through 60 removed outlier: 4.221A pdb=" N SER k 58 " --> pdb=" O GLY k 54 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR k 59 " --> pdb=" O SER k 55 " (cutoff:3.500A) Proline residue: k 60 - end of helix No H-bonds generated for 'chain 'k' and resid 54 through 60' Processing helix chain 'k' and resid 61 through 76 removed outlier: 3.543A pdb=" N VAL k 74 " --> pdb=" O CYS k 70 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS k 75 " --> pdb=" O ALA k 71 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLU k 76 " --> pdb=" O ASP k 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 104 removed outlier: 3.609A pdb=" N THR k 96 " --> pdb=" O GLY k 92 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN k 101 " --> pdb=" O ILE k 97 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY k 104 " --> pdb=" O LEU k 100 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 Processing helix chain 'l' and resid 113 through 118 removed outlier: 3.720A pdb=" N TYR l 117 " --> pdb=" O ALA l 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 22 removed outlier: 3.736A pdb=" N SER m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ILE m 22 " --> pdb=" O ALA m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 Processing helix chain 'm' and resid 44 through 49 removed outlier: 4.018A pdb=" N LEU m 48 " --> pdb=" O LYS m 44 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N SER m 49 " --> pdb=" O ILE m 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 44 through 49' Processing helix chain 'm' and resid 50 through 64 removed outlier: 4.122A pdb=" N GLU m 59 " --> pdb=" O THR m 55 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE m 63 " --> pdb=" O GLU m 59 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N VAL m 64 " --> pdb=" O VAL m 60 " (cutoff:3.500A) Processing helix chain 'm' and resid 66 through 84 removed outlier: 3.540A pdb=" N GLY m 84 " --> pdb=" O LEU m 80 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 94 Processing helix chain 'm' and resid 106 through 111 removed outlier: 3.792A pdb=" N GLY m 111 " --> pdb=" O ARG m 107 " (cutoff:3.500A) Processing helix chain 'n' and resid 7 through 25 removed outlier: 4.176A pdb=" N LYS n 19 " --> pdb=" O ALA n 15 " (cutoff:3.500A) Processing helix chain 'n' and resid 37 through 51 removed outlier: 3.621A pdb=" N ARG n 41 " --> pdb=" O SER n 37 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU n 51 " --> pdb=" O LYS n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 80 through 91 Processing helix chain 'o' and resid 4 through 16 removed outlier: 3.621A pdb=" N GLU o 14 " --> pdb=" O LYS o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 44 Processing helix chain 'o' and resid 49 through 74 Processing helix chain 'o' and resid 75 through 86 Processing helix chain 'p' and resid 53 through 64 removed outlier: 3.895A pdb=" N ILE p 57 " --> pdb=" O ASP p 53 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 82 Processing helix chain 'r' and resid 11 through 17 removed outlier: 3.770A pdb=" N ALA r 15 " --> pdb=" O CYS r 11 " (cutoff:3.500A) Processing helix chain 'r' and resid 25 through 34 removed outlier: 3.633A pdb=" N LEU r 29 " --> pdb=" O ASP r 25 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N THR r 34 " --> pdb=" O LYS r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 46 removed outlier: 3.557A pdb=" N THR r 45 " --> pdb=" O PRO r 41 " (cutoff:3.500A) Processing helix chain 'r' and resid 48 through 66 removed outlier: 3.662A pdb=" N SER r 66 " --> pdb=" O ALA r 62 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 26 Processing helix chain 's' and resid 70 through 76 removed outlier: 4.484A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) Proline residue: s 76 - end of helix No H-bonds generated for 'chain 's' and resid 70 through 76' Processing helix chain 't' and resid 4 through 41 Processing helix chain 't' and resid 44 through 65 Proline residue: t 56 - end of helix Processing helix chain 't' and resid 68 through 87 removed outlier: 4.242A pdb=" N ALA t 87 " --> pdb=" O ILE t 83 " (cutoff:3.500A) Processing helix chain 'u' and resid 11 through 27 removed outlier: 3.556A pdb=" N ALA u 15 " --> pdb=" O PRO u 11 " (cutoff:3.500A) Processing helix chain 'u' and resid 28 through 37 removed outlier: 3.572A pdb=" N GLU u 36 " --> pdb=" O VAL u 32 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N PHE u 37 " --> pdb=" O ARG u 33 " (cutoff:3.500A) Processing helix chain 'u' and resid 40 through 68 removed outlier: 4.026A pdb=" N ASN u 64 " --> pdb=" O LEU u 60 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG u 66 " --> pdb=" O ARG u 62 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ARG u 67 " --> pdb=" O GLU u 63 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N THR u 68 " --> pdb=" O ASN u 64 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'C' and resid 2 through 5 Processing sheet with id= 2, first strand: chain 'C' and resid 80 through 83 removed outlier: 3.501A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE C 74 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N SER C 118 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASP C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N GLY C 127 " --> pdb=" O GLN C 115 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N GLN C 117 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 138 through 142 removed outlier: 4.370A pdb=" N SER C 139 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR C 173 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 91 through 96 removed outlier: 4.388A pdb=" N GLU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 3 through 8 removed outlier: 4.691A pdb=" N SER D 199 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'D' and resid 11 through 16 removed outlier: 4.348A pdb=" N VAL D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG D 179 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 36 through 39 removed outlier: 4.231A pdb=" N GLN D 94 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 47 through 51 Processing sheet with id= 9, first strand: chain 'E' and resid 1 through 6 removed outlier: 4.361A pdb=" N SER E 10 " --> pdb=" O LEU E 5 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'E' and resid 117 through 120 removed outlier: 3.519A pdb=" N ASP E 168 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'F' and resid 65 through 69 removed outlier: 5.260A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'G' and resid 16 through 19 removed outlier: 4.257A pdb=" N ASP G 16 " --> pdb=" O LYS G 27 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS G 27 " --> pdb=" O ASP G 16 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= 14, first strand: chain 'G' and resid 82 through 89 removed outlier: 5.765A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'G' and resid 94 through 98 Processing sheet with id= 16, first strand: chain 'H' and resid 3 through 6 removed outlier: 7.359A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'H' and resid 76 through 81 removed outlier: 8.744A pdb=" N GLU H 76 " --> pdb=" O LYS H 141 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE H 143 " --> pdb=" O GLU H 76 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL H 78 " --> pdb=" O ILE H 143 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE H 80 " --> pdb=" O ASN H 145 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL H 147 " --> pdb=" O ILE H 80 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA H 140 " --> pdb=" O PHE H 132 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE H 132 " --> pdb=" O ALA H 140 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'J' and resid 52 through 57 removed outlier: 4.713A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'J' and resid 74 through 78 removed outlier: 7.387A pdb=" N GLY J 83 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'K' and resid 56 through 61 removed outlier: 4.709A pdb=" N ASP K 56 " --> pdb=" O ILE K 43 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLY K 81 " --> pdb=" O LYS K 66 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS K 66 " --> pdb=" O GLY K 81 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'K' and resid 68 through 71 removed outlier: 3.813A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'M' and resid 37 through 40 No H-bonds generated for sheet with id= 22 Processing sheet with id= 23, first strand: chain 'M' and resid 62 through 65 removed outlier: 6.512A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'M' and resid 30 through 36 removed outlier: 7.415A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.763A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'O' and resid 49 through 52 removed outlier: 3.625A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'P' and resid 38 through 45 removed outlier: 6.502A pdb=" N THR P 25 " --> pdb=" O LYS P 87 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'P' and resid 49 through 53 removed outlier: 3.741A pdb=" N ALA P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARG P 53 " --> pdb=" O HIS P 56 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N HIS P 56 " --> pdb=" O ARG P 53 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N SER P 57 " --> pdb=" O THR P 76 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'R' and resid 11 through 15 removed outlier: 6.604A pdb=" N LEU R 39 " --> pdb=" O GLY R 50 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'R' and resid 17 through 22 removed outlier: 4.477A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'R' and resid 65 through 76 removed outlier: 3.620A pdb=" N ALA R 65 " --> pdb=" O ASP R 95 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY R 67 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N GLN R 91 " --> pdb=" O GLY R 69 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LYS R 71 " --> pdb=" O HIS R 89 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N HIS R 89 " --> pdb=" O LYS R 71 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LYS R 73 " --> pdb=" O GLN R 87 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLN R 87 " --> pdb=" O LYS R 73 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL R 75 " --> pdb=" O LYS R 85 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LYS R 85 " --> pdb=" O VAL R 75 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'S' and resid 2 through 8 removed outlier: 4.420A pdb=" N THR S 3 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL S 107 " --> pdb=" O THR S 3 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'S' and resid 81 through 88 removed outlier: 4.226A pdb=" N ARG S 92 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'T' and resid 29 through 33 removed outlier: 5.209A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'U' and resid 40 through 45 removed outlier: 5.138A pdb=" N ASN U 40 " --> pdb=" O ALA U 63 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'U' and resid 82 through 87 removed outlier: 5.102A pdb=" N ARG U 82 " --> pdb=" O LYS U 97 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ARG U 94 " --> pdb=" O ILE U 103 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU U 101 " --> pdb=" O PHE U 96 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'V' and resid 69 through 72 removed outlier: 3.621A pdb=" N THR V 62 " --> pdb=" O PHE V 2 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU V 38 " --> pdb=" O ILE V 30 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'W' and resid 51 through 54 removed outlier: 4.288A pdb=" N THR W 58 " --> pdb=" O GLY W 54 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'W' and resid 66 through 71 Processing sheet with id= 40, first strand: chain 'X' and resid 12 through 19 removed outlier: 3.651A pdb=" N SER X 19 " --> pdb=" O ASN X 23 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASN X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'X' and resid 35 through 41 Processing sheet with id= 42, first strand: chain 'Z' and resid 35 through 39 removed outlier: 6.158A pdb=" N LYS Z 6 " --> pdb=" O GLU Z 58 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N MET Z 54 " --> pdb=" O THR Z 10 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain '0' and resid 28 through 31 removed outlier: 6.428A pdb=" N SER 0 29 " --> pdb=" O LYS 0 37 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS 0 37 " --> pdb=" O SER 0 29 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ASP 0 31 " --> pdb=" O GLY 0 35 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain '1' and resid 20 through 26 removed outlier: 4.011A pdb=" N TYR 1 49 " --> pdb=" O LEU 1 36 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU 1 36 " --> pdb=" O TYR 1 49 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU 1 51 " --> pdb=" O LEU 1 34 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU 1 34 " --> pdb=" O GLU 1 51 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain '3' and resid 22 through 25 No H-bonds generated for sheet with id= 45 Processing sheet with id= 46, first strand: chain '4' and resid 13 through 18 removed outlier: 8.168A pdb=" N ASN 4 13 " --> pdb=" O SER 4 28 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER 4 28 " --> pdb=" O ASN 4 13 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain '5' and resid 11 through 16 removed outlier: 4.084A pdb=" N ASN 5 20 " --> pdb=" O CYS 5 16 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'b' and resid 89 through 92 removed outlier: 3.679A pdb=" N LEU b 68 " --> pdb=" O ALA b 160 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA b 185 " --> pdb=" O PHE b 198 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'c' and resid 54 through 59 removed outlier: 3.629A pdb=" N ARG c 54 " --> pdb=" O HIS c 69 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'c' and resid 164 through 170 removed outlier: 6.807A pdb=" N ASP c 181 " --> pdb=" O LYS c 204 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'd' and resid 141 through 144 removed outlier: 3.510A pdb=" N ASP d 141 " --> pdb=" O PHE d 182 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU d 179 " --> pdb=" O ASP d 174 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'e' and resid 11 through 16 removed outlier: 6.695A pdb=" N LEU e 36 " --> pdb=" O ILE e 16 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'e' and resid 84 through 88 removed outlier: 4.048A pdb=" N TYR e 128 " --> pdb=" O ARG e 93 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'e' and resid 32 through 41 removed outlier: 6.894A pdb=" N ARG e 45 " --> pdb=" O ASP e 41 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'f' and resid 38 through 43 removed outlier: 3.723A pdb=" N ARG f 38 " --> pdb=" O ASN f 63 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N HIS f 3 " --> pdb=" O THR f 92 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG f 86 " --> pdb=" O MET f 9 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'f' and resid 44 through 47 removed outlier: 5.820A pdb=" N LEU f 47 " --> pdb=" O HIS f 55 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N HIS f 55 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'g' and resid 72 through 77 removed outlier: 6.733A pdb=" N THR g 72 " --> pdb=" O VAL g 91 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'h' and resid 23 through 29 removed outlier: 6.778A pdb=" N ALA h 23 " --> pdb=" O LEU h 63 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLU h 58 " --> pdb=" O GLU h 52 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP h 48 " --> pdb=" O THR h 62 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'h' and resid 74 through 77 removed outlier: 3.708A pdb=" N CYS h 127 " --> pdb=" O VAL h 103 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL h 103 " --> pdb=" O ILE h 126 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'i' and resid 5 through 11 Processing sheet with id= 61, first strand: chain 'j' and resid 39 through 42 removed outlier: 3.966A pdb=" N LEU j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'j' and resid 44 through 52 Processing sheet with id= 63, first strand: chain 'k' and resid 42 through 45 removed outlier: 4.125A pdb=" N ASN k 29 " --> pdb=" O SER k 26 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'l' and resid 29 through 33 removed outlier: 4.887A pdb=" N LEU l 81 " --> pdb=" O VAL l 98 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N HIS l 96 " --> pdb=" O ARG l 83 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'l' and resid 36 through 41 removed outlier: 5.251A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE l 61 " --> pdb=" O LEU l 57 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'p' and resid 4 through 10 Processing sheet with id= 67, first strand: chain 'q' and resid 7 through 11 removed outlier: 6.874A pdb=" N GLU q 60 " --> pdb=" O VAL q 76 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'q' and resid 19 through 30 No H-bonds generated for sheet with id= 68 Processing sheet with id= 69, first strand: chain 's' and resid 30 through 33 removed outlier: 3.666A pdb=" N LEU s 31 " --> pdb=" O THR s 48 " (cutoff:3.500A) 1837 hydrogen bonds defined for protein. 5448 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3885 hydrogen bonds 6084 hydrogen bond angles 0 basepair planarities 1544 basepair parallelities 2749 stacking parallelities Total time for adding SS restraints: 245.35 Time building geometry restraints manager: 60.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 14982 1.31 - 1.45: 73792 1.45 - 1.59: 62018 1.59 - 1.72: 7888 1.72 - 1.86: 264 Bond restraints: 158944 Sorted by residual: bond pdb=" C40 TEL A9000 " pdb=" C43 TEL A9000 " ideal model delta sigma weight residual 1.538 1.323 0.215 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C26 TEL A9000 " pdb=" C30 TEL A9000 " ideal model delta sigma weight residual 1.573 1.386 0.187 2.00e-02 2.50e+03 8.74e+01 bond pdb=" C21 TEL A9000 " pdb=" C26 TEL A9000 " ideal model delta sigma weight residual 1.559 1.390 0.169 2.00e-02 2.50e+03 7.16e+01 bond pdb=" C10 TEL A9000 " pdb=" N6 TEL A9000 " ideal model delta sigma weight residual 1.476 1.339 0.137 2.00e-02 2.50e+03 4.67e+01 bond pdb=" C15 TEL A9000 " pdb=" C21 TEL A9000 " ideal model delta sigma weight residual 1.525 1.391 0.134 2.00e-02 2.50e+03 4.47e+01 ... (remaining 158939 not shown) Histogram of bond angle deviations from ideal: 97.05 - 105.48: 24071 105.48 - 113.91: 101697 113.91 - 122.34: 79730 122.34 - 130.76: 30769 130.76 - 139.19: 1782 Bond angle restraints: 238049 Sorted by residual: angle pdb=" C4' G A2505 " pdb=" C3' G A2505 " pdb=" O3' G A2505 " ideal model delta sigma weight residual 113.00 126.31 -13.31 1.50e+00 4.44e-01 7.87e+01 angle pdb=" N ALA g 65 " pdb=" CA ALA g 65 " pdb=" C ALA g 65 " ideal model delta sigma weight residual 114.56 104.11 10.45 1.27e+00 6.20e-01 6.78e+01 angle pdb=" C27 TEL A9000 " pdb=" N31 TEL A9000 " pdb=" C36 TEL A9000 " ideal model delta sigma weight residual 145.99 123.29 22.70 3.00e+00 1.11e-01 5.72e+01 angle pdb=" C27 TEL A9000 " pdb=" N31 TEL A9000 " pdb=" C37 TEL A9000 " ideal model delta sigma weight residual 105.37 128.00 -22.63 3.00e+00 1.11e-01 5.69e+01 angle pdb=" O3' U 6 27 " pdb=" C3' U 6 27 " pdb=" C2' U 6 27 " ideal model delta sigma weight residual 109.50 120.19 -10.69 1.50e+00 4.44e-01 5.08e+01 ... (remaining 238044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 89459 35.83 - 71.65: 11111 71.65 - 107.48: 1255 107.48 - 143.30: 34 143.30 - 179.13: 54 Dihedral angle restraints: 101913 sinusoidal: 85705 harmonic: 16208 Sorted by residual: dihedral pdb=" CA HIS 3 31 " pdb=" C HIS 3 31 " pdb=" N ILE 3 32 " pdb=" CA ILE 3 32 " ideal model delta harmonic sigma weight residual -180.00 -125.86 -54.14 0 5.00e+00 4.00e-02 1.17e+02 dihedral pdb=" CA LYS d 31 " pdb=" C LYS d 31 " pdb=" N CYS d 32 " pdb=" CA CYS d 32 " ideal model delta harmonic sigma weight residual 180.00 126.55 53.45 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA GLY d 39 " pdb=" C GLY d 39 " pdb=" N GLN d 40 " pdb=" CA GLN d 40 " ideal model delta harmonic sigma weight residual -180.00 -128.05 -51.95 0 5.00e+00 4.00e-02 1.08e+02 ... (remaining 101910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.135: 30458 1.135 - 2.270: 0 2.270 - 3.404: 0 3.404 - 4.539: 0 4.539 - 5.674: 1 Chirality restraints: 30459 Sorted by residual: chirality pdb=" C28 TEL A9000 " pdb=" C24 TEL A9000 " pdb=" C33 TEL A9000 " pdb=" C34 TEL A9000 " both_signs ideal model delta sigma weight residual False -2.76 2.91 -5.67 2.00e-01 2.50e+01 8.05e+02 chirality pdb=" C3' U 6 27 " pdb=" C4' U 6 27 " pdb=" O3' U 6 27 " pdb=" C2' U 6 27 " both_signs ideal model delta sigma weight residual False -2.74 -1.94 -0.81 2.00e-01 2.50e+01 1.63e+01 chirality pdb=" C3' G A2505 " pdb=" C4' G A2505 " pdb=" O3' G A2505 " pdb=" C2' G A2505 " both_signs ideal model delta sigma weight residual False -2.48 -1.70 -0.78 2.00e-01 2.50e+01 1.52e+01 ... (remaining 30456 not shown) Planarity restraints: 12565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY d 39 " 0.019 2.00e-02 2.50e+03 3.76e-02 1.41e+01 pdb=" C GLY d 39 " -0.065 2.00e-02 2.50e+03 pdb=" O GLY d 39 " 0.024 2.00e-02 2.50e+03 pdb=" N GLN d 40 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 980 " 0.049 2.00e-02 2.50e+03 2.26e-02 1.40e+01 pdb=" N9 A A 980 " -0.054 2.00e-02 2.50e+03 pdb=" C8 A A 980 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A A 980 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A A 980 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A A 980 " 0.007 2.00e-02 2.50e+03 pdb=" N6 A A 980 " 0.014 2.00e-02 2.50e+03 pdb=" N1 A A 980 " 0.000 2.00e-02 2.50e+03 pdb=" C2 A A 980 " -0.005 2.00e-02 2.50e+03 pdb=" N3 A A 980 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A A 980 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A1517 " -0.024 2.00e-02 2.50e+03 2.10e-02 1.32e+01 pdb=" N9 G A1517 " 0.017 2.00e-02 2.50e+03 pdb=" C8 G A1517 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G A1517 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G A1517 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G A1517 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G A1517 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G A1517 " -0.025 2.00e-02 2.50e+03 pdb=" C2 G A1517 " 0.058 2.00e-02 2.50e+03 pdb=" N2 G A1517 " -0.020 2.00e-02 2.50e+03 pdb=" N3 G A1517 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G A1517 " 0.003 2.00e-02 2.50e+03 ... (remaining 12562 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.11: 8 2.11 - 2.81: 38656 2.81 - 3.51: 183054 3.51 - 4.20: 481514 4.20 - 4.90: 640636 Nonbonded interactions: 1343868 Sorted by model distance: nonbonded pdb=" C LEU 7 7 " pdb=" O3' A 8 87 " model vdw 1.417 3.270 nonbonded pdb=" O4' U A2506 " pdb=" NH2BARG 7 6 " model vdw 1.574 2.520 nonbonded pdb=" OD1 ASN 5 65 " pdb=" OD2 ASP n 38 " model vdw 1.776 3.040 nonbonded pdb=" N2 G v 1 " pdb=" O2 C v 73 " model vdw 1.788 2.496 nonbonded pdb=" O LEU 7 7 " pdb=" O3' A 8 87 " model vdw 1.945 3.040 ... (remaining 1343863 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 15.180 Check model and map are aligned: 1.630 Set scattering table: 1.020 Process input model: 530.850 Find NCS groups from input model: 2.790 Set up NCS constraints: 0.330 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 556.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 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 : 0.007 0.215 158944 Z= 0.454 Angle : 0.990 22.695 238049 Z= 0.511 Chirality : 0.062 5.674 30459 Planarity : 0.007 0.080 12565 Dihedral : 23.630 179.130 91445 Min Nonbonded Distance : 1.417 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.76 % Favored : 92.93 % Rotamer: Outliers : 0.52 % Allowed : 10.20 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.37 % 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: -3.65 (0.09), residues: 5592 helix: -2.67 (0.09), residues: 1836 sheet: -1.52 (0.15), residues: 1039 loop : -2.56 (0.10), residues: 2717 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 0.026 0.003 PHE F 100 TYR 0.028 0.003 TYR S 38 ARG 0.024 0.001 ARG Q 6 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11184 Ramachandran restraints generated. 5592 Oldfield, 0 Emsley, 5592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11184 Ramachandran restraints generated. 5592 Oldfield, 0 Emsley, 5592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1641 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1617 time to evaluate : 6.608 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: C 181 MET cc_start: 0.7720 (mmm) cc_final: 0.7506 (mmm) REVERT: D 1 MET cc_start: 0.5573 (ptp) cc_final: 0.5373 (ptp) REVERT: D 174 SER cc_start: 0.8801 (m) cc_final: 0.8382 (t) REVERT: E 94 GLN cc_start: 0.8576 (pt0) cc_final: 0.8236 (pt0) REVERT: E 117 ARG cc_start: 0.8680 (mtp180) cc_final: 0.8389 (mtm-85) REVERT: E 118 LEU cc_start: 0.8404 (tp) cc_final: 0.7978 (tp) REVERT: E 163 ASN cc_start: 0.8447 (t0) cc_final: 0.8029 (t0) REVERT: F 7 TYR cc_start: 0.7965 (t80) cc_final: 0.7744 (t80) REVERT: F 73 SER cc_start: 0.7755 (p) cc_final: 0.7476 (p) REVERT: F 85 ILE cc_start: 0.8439 (tp) cc_final: 0.8154 (tp) REVERT: G 147 ASP cc_start: 0.6976 (m-30) cc_final: 0.6722 (m-30) REVERT: H 9 VAL cc_start: 0.6839 (t) cc_final: 0.6404 (t) REVERT: H 12 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7020 (pp) REVERT: J 1 MET cc_start: 0.4239 (ptt) cc_final: 0.3653 (ptt) REVERT: K 5 GLN cc_start: 0.8410 (mm110) cc_final: 0.8167 (mm-40) REVERT: K 98 ARG cc_start: 0.7717 (mtp-110) cc_final: 0.7453 (ptm160) REVERT: K 105 ARG cc_start: 0.7470 (tpp-160) cc_final: 0.7114 (tpp-160) REVERT: L 1 MET cc_start: 0.6959 (pmm) cc_final: 0.6265 (pmm) REVERT: O 104 GLN cc_start: 0.8460 (tt0) cc_final: 0.8219 (tt0) REVERT: O 115 LEU cc_start: 0.8081 (tp) cc_final: 0.7698 (mp) REVERT: P 102 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.6092 (mp0) REVERT: R 13 ARG cc_start: 0.8335 (ttp-170) cc_final: 0.8014 (ttp80) REVERT: S 52 GLU cc_start: 0.7501 (tp30) cc_final: 0.7176 (tp30) REVERT: T 1 MET cc_start: 0.2230 (ptp) cc_final: 0.1541 (ptp) REVERT: T 48 GLN cc_start: 0.7613 (mt0) cc_final: 0.7308 (mt0) REVERT: U 81 ASP cc_start: 0.7373 (m-30) cc_final: 0.7120 (m-30) REVERT: V 9 ARG cc_start: 0.8376 (mtp180) cc_final: 0.8154 (mtp180) REVERT: W 20 ARG cc_start: 0.8678 (mmt-90) cc_final: 0.8475 (mpt180) REVERT: 0 22 LEU cc_start: 0.9118 (mt) cc_final: 0.8904 (mt) REVERT: 0 37 LYS cc_start: 0.8471 (mmtp) cc_final: 0.8267 (mmmt) REVERT: 1 44 ARG cc_start: 0.7155 (mmm-85) cc_final: 0.6854 (mmm-85) REVERT: 5 44 PHE cc_start: 0.8037 (m-10) cc_final: 0.7776 (m-80) REVERT: b 21 ARG cc_start: 0.8031 (ptp-170) cc_final: 0.7799 (ptp-170) REVERT: b 28 LYS cc_start: 0.7868 (tttp) cc_final: 0.7638 (ttmm) REVERT: b 145 GLU cc_start: 0.5865 (mm-30) cc_final: 0.5515 (mm-30) REVERT: c 19 ASN cc_start: 0.8503 (m-40) cc_final: 0.8089 (m-40) REVERT: c 129 MET cc_start: 0.7400 (mtt) cc_final: 0.7151 (mtt) REVERT: c 132 ARG cc_start: 0.7350 (mmm160) cc_final: 0.6924 (mtt90) REVERT: d 34 ILE cc_start: 0.8276 (mm) cc_final: 0.7916 (mm) REVERT: d 47 ARG cc_start: 0.6618 (tpp-160) cc_final: 0.5606 (ttp-170) REVERT: d 113 GLU cc_start: 0.7906 (tt0) cc_final: 0.7498 (tt0) REVERT: e 147 MET cc_start: 0.8633 (ttp) cc_final: 0.8350 (ttp) REVERT: f 45 ARG cc_start: 0.7919 (ptp-170) cc_final: 0.7693 (ptm160) REVERT: f 79 ARG cc_start: 0.7543 (tpp80) cc_final: 0.7182 (tpp-160) REVERT: h 66 PHE cc_start: 0.7159 (t80) cc_final: 0.6839 (t80) REVERT: i 5 GLN cc_start: 0.7505 (mm110) cc_final: 0.5665 (pm20) REVERT: j 45 ARG cc_start: 0.7733 (ttt180) cc_final: 0.7456 (ttt180) REVERT: k 56 ARG cc_start: 0.7400 (mtp180) cc_final: 0.7016 (mtm180) REVERT: n 47 LYS cc_start: 0.7519 (tppp) cc_final: 0.7202 (tptm) REVERT: q 61 ILE cc_start: 0.8041 (mt) cc_final: 0.7818 (mm) REVERT: q 74 THR cc_start: 0.8555 (m) cc_final: 0.8287 (m) REVERT: r 60 LYS cc_start: 0.8773 (mttt) cc_final: 0.8534 (mttp) REVERT: t 54 MET cc_start: 0.8280 (ppp) cc_final: 0.7742 (ttp) REVERT: u 33 ARG cc_start: 0.6553 (ttm110) cc_final: 0.5920 (mtp85) outliers start: 24 outliers final: 7 residues processed: 1636 average time/residue: 1.4054 time to fit residues: 3825.3666 Evaluate side-chains 1319 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1310 time to evaluate : 7.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain 3 residue 32 ILE Chi-restraints excluded: chain 4 residue 14 CYS Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain m residue 68 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 857 optimal weight: 0.9990 chunk 770 optimal weight: 10.0000 chunk 427 optimal weight: 1.9990 chunk 263 optimal weight: 7.9990 chunk 519 optimal weight: 10.0000 chunk 411 optimal weight: 0.0070 chunk 796 optimal weight: 9.9990 chunk 308 optimal weight: 2.9990 chunk 484 optimal weight: 3.9990 chunk 592 optimal weight: 2.9990 chunk 922 optimal weight: 0.0870 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 251 GLN ** C 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN D 150 GLN D 164 GLN G 22 GLN G 64 GLN G 73 ASN G 88 GLN ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 40 HIS J 80 HIS J 128 ASN K 9 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 GLN Q 20 GLN Q 37 GLN Q 71 GLN R 89 HIS R 91 GLN S 15 GLN S 57 ASN ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 46 GLN ** U 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 12 ASN Y 20 ASN Y 58 ASN ** 0 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 6 ASN 1 19 HIS 1 45 GLN 3 28 ASN ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 30 HIS ** b 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 ASN b 190 ASN b 227 GLN c 176 HIS c 190 HIS d 131 ASN d 152 GLN e 121 HIS h 118 GLN i 37 GLN j 58 ASN n 49 GLN o 35 GLN o 46 HIS q 31 HIS q 47 HIS q 50 ASN r 54 GLN ** r 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 52 HIS u 56 HIS Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 158944 Z= 0.154 Angle : 0.589 28.694 238049 Z= 0.307 Chirality : 0.037 2.326 30459 Planarity : 0.005 0.066 12565 Dihedral : 23.802 179.791 80245 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.90 % Favored : 93.88 % Rotamer: Outliers : 3.42 % Allowed : 16.35 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.10), residues: 5592 helix: -0.66 (0.11), residues: 1898 sheet: -1.04 (0.15), residues: 1033 loop : -2.22 (0.10), residues: 2661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 213 HIS 0.009 0.001 HIS r 74 PHE 0.019 0.001 PHE 5 43 TYR 0.016 0.001 TYR Q 47 ARG 0.006 0.000 ARG F 178 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11184 Ramachandran restraints generated. 5592 Oldfield, 0 Emsley, 5592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11184 Ramachandran restraints generated. 5592 Oldfield, 0 Emsley, 5592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1601 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1442 time to evaluate : 6.305 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: C 95 LEU cc_start: 0.8651 (tp) cc_final: 0.8445 (tp) REVERT: C 96 TYR cc_start: 0.8789 (m-80) cc_final: 0.8554 (m-80) REVERT: C 125 LYS cc_start: 0.8480 (mtmt) cc_final: 0.8231 (mtmt) REVERT: D 1 MET cc_start: 0.5461 (ptp) cc_final: 0.4783 (tpp) REVERT: E 110 SER cc_start: 0.8868 (t) cc_final: 0.8667 (t) REVERT: E 118 LEU cc_start: 0.8270 (tp) cc_final: 0.8054 (tp) REVERT: E 136 GLN cc_start: 0.8049 (tp40) cc_final: 0.7403 (tp-100) REVERT: E 200 LEU cc_start: 0.7145 (OUTLIER) cc_final: 0.6745 (tp) REVERT: F 73 SER cc_start: 0.7698 (p) cc_final: 0.7431 (p) REVERT: F 85 ILE cc_start: 0.8391 (tp) cc_final: 0.8099 (tp) REVERT: F 113 ASP cc_start: 0.6858 (t0) cc_final: 0.6546 (t0) REVERT: F 135 GLN cc_start: 0.8470 (pp30) cc_final: 0.7320 (pp30) REVERT: H 12 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6856 (pp) REVERT: H 19 VAL cc_start: 0.7272 (OUTLIER) cc_final: 0.7054 (p) REVERT: J 1 MET cc_start: 0.4336 (ptt) cc_final: 0.3652 (ptt) REVERT: K 105 ARG cc_start: 0.7745 (tpp-160) cc_final: 0.7396 (tpp-160) REVERT: L 1 MET cc_start: 0.6424 (pmm) cc_final: 0.6102 (pmm) REVERT: L 14 LYS cc_start: 0.7177 (mtpp) cc_final: 0.6935 (mttt) REVERT: L 42 SER cc_start: 0.8895 (OUTLIER) cc_final: 0.8634 (t) REVERT: N 110 MET cc_start: 0.7715 (mmt) cc_final: 0.7477 (mmt) REVERT: P 102 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.6234 (mp0) REVERT: R 13 ARG cc_start: 0.8281 (ttp-170) cc_final: 0.7951 (ttp80) REVERT: R 31 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6193 (tp30) REVERT: S 52 GLU cc_start: 0.7580 (tp30) cc_final: 0.7260 (mm-30) REVERT: T 1 MET cc_start: 0.2622 (ptp) cc_final: 0.1814 (mtm) REVERT: T 49 LYS cc_start: 0.8545 (tppp) cc_final: 0.8272 (tttt) REVERT: V 9 ARG cc_start: 0.8446 (mtp180) cc_final: 0.8150 (mtp180) REVERT: W 20 ARG cc_start: 0.8660 (mmt-90) cc_final: 0.8457 (mpt180) REVERT: Y 55 THR cc_start: 0.8719 (m) cc_final: 0.8499 (m) REVERT: 0 37 LYS cc_start: 0.8424 (mmtp) cc_final: 0.8064 (mmtt) REVERT: 0 50 ARG cc_start: 0.8464 (mtp180) cc_final: 0.8262 (mtm180) REVERT: 3 28 ASN cc_start: 0.8891 (OUTLIER) cc_final: 0.8614 (m-40) REVERT: 5 25 ARG cc_start: 0.7567 (mtp85) cc_final: 0.7224 (mtm180) REVERT: b 26 LYS cc_start: 0.7642 (mmmt) cc_final: 0.7419 (mmmt) REVERT: b 145 GLU cc_start: 0.5939 (mm-30) cc_final: 0.5347 (mm-30) REVERT: b 201 PRO cc_start: 0.8772 (Cg_endo) cc_final: 0.8461 (Cg_exo) REVERT: c 19 ASN cc_start: 0.8461 (m-40) cc_final: 0.8147 (m-40) REVERT: c 41 GLN cc_start: 0.8542 (pp30) cc_final: 0.8189 (pp30) REVERT: d 47 ARG cc_start: 0.6698 (tpp-160) cc_final: 0.5656 (ttp-170) REVERT: d 113 GLU cc_start: 0.7732 (tt0) cc_final: 0.7318 (tt0) REVERT: e 12 GLN cc_start: 0.7974 (pt0) cc_final: 0.7627 (tt0) REVERT: g 21 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7468 (mp0) REVERT: g 30 LEU cc_start: 0.8889 (tp) cc_final: 0.8668 (tp) REVERT: h 66 PHE cc_start: 0.7190 (t80) cc_final: 0.6891 (t80) REVERT: h 89 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7743 (ptpt) REVERT: i 5 GLN cc_start: 0.7289 (mm110) cc_final: 0.5439 (pm20) REVERT: i 30 ILE cc_start: 0.8145 (tt) cc_final: 0.7891 (mt) REVERT: i 65 ILE cc_start: 0.8341 (mp) cc_final: 0.8086 (mt) REVERT: k 35 THR cc_start: 0.8569 (p) cc_final: 0.8339 (t) REVERT: n 46 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8814 (mm) REVERT: n 47 LYS cc_start: 0.7534 (tppp) cc_final: 0.7212 (tptm) REVERT: q 74 THR cc_start: 0.8568 (m) cc_final: 0.8367 (m) REVERT: s 73 GLU cc_start: 0.6981 (tt0) cc_final: 0.6710 (tt0) REVERT: t 32 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8772 (mp) REVERT: t 82 GLN cc_start: 0.7882 (mm-40) cc_final: 0.7647 (mm110) outliers start: 159 outliers final: 90 residues processed: 1522 average time/residue: 1.4467 time to fit residues: 3776.2903 Evaluate side-chains 1405 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1305 time to evaluate : 5.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain Z residue 7 ILE Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain 0 residue 6 ASN Chi-restraints excluded: chain 1 residue 48 ILE Chi-restraints excluded: chain 3 residue 28 ASN Chi-restraints excluded: chain 3 residue 32 ILE Chi-restraints excluded: chain 4 residue 14 CYS Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 63 SER Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 35 GLU Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain e residue 123 VAL Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain h residue 10 MET Chi-restraints excluded: chain h residue 79 SER Chi-restraints excluded: chain h residue 89 LYS Chi-restraints excluded: chain h residue 90 ASP Chi-restraints excluded: chain i residue 58 VAL Chi-restraints excluded: chain i residue 91 ASP Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 109 ASN Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain n residue 46 LEU Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain p residue 57 ILE Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain q residue 13 VAL Chi-restraints excluded: chain q residue 14 SER Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain s residue 44 MET Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain t residue 32 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 512 optimal weight: 5.9990 chunk 286 optimal weight: 10.0000 chunk 767 optimal weight: 10.0000 chunk 628 optimal weight: 10.0000 chunk 254 optimal weight: 8.9990 chunk 924 optimal weight: 9.9990 chunk 998 optimal weight: 10.0000 chunk 823 optimal weight: 9.9990 chunk 916 optimal weight: 1.9990 chunk 315 optimal weight: 9.9990 chunk 741 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 46 ASN C 117 GLN C 142 HIS C 153 GLN ** C 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN G 22 GLN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 GLN Q 71 GLN ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 91 GLN S 15 GLN S 57 ASN S 61 ASN T 15 HIS T 70 HIS U 69 ASN U 74 ASN V 49 ASN ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 16 ASN Y 20 ASN 0 4 GLN 1 45 GLN 3 28 ASN 4 13 ASN ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 31 ASN i 37 GLN l 112 GLN n 49 GLN o 35 GLN p 26 ASN t 13 GLN ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.107 158944 Z= 0.539 Angle : 0.820 29.195 238049 Z= 0.411 Chirality : 0.048 2.115 30459 Planarity : 0.006 0.093 12565 Dihedral : 23.830 179.820 80245 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.44 % Favored : 92.31 % Rotamer: Outliers : 6.12 % Allowed : 19.14 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.10), residues: 5592 helix: -0.24 (0.11), residues: 1889 sheet: -0.98 (0.15), residues: 1045 loop : -2.17 (0.11), residues: 2658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 213 HIS 0.014 0.002 HIS r 74 PHE 0.020 0.002 PHE b 198 TYR 0.022 0.003 TYR V 82 ARG 0.010 0.001 ARG f 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11184 Ramachandran restraints generated. 5592 Oldfield, 0 Emsley, 5592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11184 Ramachandran restraints generated. 5592 Oldfield, 0 Emsley, 5592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1593 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 1308 time to evaluate : 6.520 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: D 167 ASN cc_start: 0.8594 (t0) cc_final: 0.8302 (t0) REVERT: E 94 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8049 (pm20) REVERT: E 136 GLN cc_start: 0.7991 (tp40) cc_final: 0.7457 (tp-100) REVERT: E 163 ASN cc_start: 0.8562 (t0) cc_final: 0.8082 (t0) REVERT: F 85 ILE cc_start: 0.8510 (tp) cc_final: 0.8234 (tp) REVERT: G 128 GLN cc_start: 0.7213 (mm-40) cc_final: 0.6992 (mm-40) REVERT: H 12 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7193 (pp) REVERT: J 1 MET cc_start: 0.4175 (ptt) cc_final: 0.3636 (ptt) REVERT: K 105 ARG cc_start: 0.7730 (tpp-160) cc_final: 0.7287 (tpp-160) REVERT: L 14 LYS cc_start: 0.7469 (mtpp) cc_final: 0.7145 (ttpt) REVERT: L 27 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8907 (pp) REVERT: N 4 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7999 (tpp80) REVERT: P 102 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6116 (mp0) REVERT: R 13 ARG cc_start: 0.8308 (ttp-170) cc_final: 0.8070 (ttp80) REVERT: S 52 GLU cc_start: 0.7530 (tp30) cc_final: 0.7319 (tp30) REVERT: S 78 GLU cc_start: 0.7737 (pm20) cc_final: 0.7422 (pm20) REVERT: T 1 MET cc_start: 0.2618 (ptp) cc_final: 0.2057 (mtm) REVERT: V 5 ASN cc_start: 0.8054 (OUTLIER) cc_final: 0.7847 (m-40) REVERT: V 9 ARG cc_start: 0.8585 (mtp180) cc_final: 0.8310 (mtp180) REVERT: Y 9 LYS cc_start: 0.8542 (mtpt) cc_final: 0.8281 (tttm) REVERT: Y 60 LYS cc_start: 0.6645 (ttmt) cc_final: 0.6326 (tttt) REVERT: 0 6 ASN cc_start: 0.8357 (OUTLIER) cc_final: 0.7999 (p0) REVERT: 2 13 ASN cc_start: 0.8671 (m-40) cc_final: 0.8464 (m-40) REVERT: 5 20 ASN cc_start: 0.7177 (t0) cc_final: 0.6838 (t0) REVERT: b 28 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7447 (ttmt) REVERT: b 145 GLU cc_start: 0.6235 (mm-30) cc_final: 0.5934 (mm-30) REVERT: b 186 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8247 (mp) REVERT: c 84 VAL cc_start: 0.8203 (OUTLIER) cc_final: 0.7996 (p) REVERT: d 47 ARG cc_start: 0.6804 (tpp-160) cc_final: 0.5676 (ttp-170) REVERT: d 113 GLU cc_start: 0.7903 (tt0) cc_final: 0.7515 (tt0) REVERT: d 165 ARG cc_start: 0.6476 (mtm110) cc_final: 0.6165 (ttm110) REVERT: e 78 ASN cc_start: 0.7472 (OUTLIER) cc_final: 0.7227 (p0) REVERT: g 30 LEU cc_start: 0.8999 (tp) cc_final: 0.8794 (tp) REVERT: g 48 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6695 (mm-30) REVERT: g 101 MET cc_start: 0.8058 (mtm) cc_final: 0.7855 (mtm) REVERT: h 3 MET cc_start: 0.8494 (tpp) cc_final: 0.8147 (mmm) REVERT: h 66 PHE cc_start: 0.7378 (t80) cc_final: 0.6961 (t80) REVERT: i 30 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8140 (mt) REVERT: i 62 ASP cc_start: 0.6743 (OUTLIER) cc_final: 0.6324 (p0) REVERT: i 65 ILE cc_start: 0.8429 (mp) cc_final: 0.8201 (mt) REVERT: l 65 SER cc_start: 0.8770 (t) cc_final: 0.8459 (m) REVERT: o 59 MET cc_start: 0.7893 (ptp) cc_final: 0.7576 (mtm) REVERT: p 1 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7224 (ptm) REVERT: s 73 GLU cc_start: 0.7293 (tt0) cc_final: 0.7058 (tt0) REVERT: t 82 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7704 (mm110) REVERT: u 33 ARG cc_start: 0.6455 (ttm110) cc_final: 0.5716 (mtt180) outliers start: 285 outliers final: 214 residues processed: 1470 average time/residue: 1.2829 time to fit residues: 3257.6676 Evaluate side-chains 1494 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 1266 time to evaluate : 6.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 153 GLN Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain N residue 4 ARG Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 99 LYS Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 65 ILE Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 82 ILE Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Z residue 7 ILE Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain 0 residue 6 ASN Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 48 ILE Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 3 residue 32 ILE Chi-restraints excluded: chain 3 residue 61 CYS Chi-restraints excluded: chain 4 residue 11 CYS Chi-restraints excluded: chain 4 residue 14 CYS Chi-restraints excluded: chain 4 residue 17 VAL Chi-restraints excluded: chain 5 residue 5 ILE Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 28 LYS Chi-restraints excluded: chain b residue 51 ASN Chi-restraints excluded: chain b residue 63 ARG Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain b residue 191 SER Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain b residue 220 THR Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 46 GLU Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain c residue 63 SER Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain d residue 35 GLU Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain d residue 171 LEU Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain e residue 78 ASN Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 100 SER Chi-restraints excluded: chain e residue 145 GLU Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 104 ILE Chi-restraints excluded: chain g residue 146 GLU Chi-restraints excluded: chain h residue 10 MET Chi-restraints excluded: chain h residue 79 SER Chi-restraints excluded: chain h residue 90 ASP Chi-restraints excluded: chain h residue 104 VAL Chi-restraints excluded: chain h residue 105 SER Chi-restraints excluded: chain i residue 29 VAL Chi-restraints excluded: chain i residue 30 ILE Chi-restraints excluded: chain i residue 55 VAL Chi-restraints excluded: chain i residue 58 VAL Chi-restraints excluded: chain i residue 62 ASP Chi-restraints excluded: chain i residue 91 ASP Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain i residue 112 GLU Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 63 ASP Chi-restraints excluded: chain j residue 83 THR Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 109 ASN Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain m residue 7 ILE Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 19 LEU Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 45 ILE Chi-restraints excluded: chain m residue 56 LEU Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain o residue 61 SER Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 57 ILE Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain p residue 75 ILE Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 13 VAL Chi-restraints excluded: chain q residue 14 SER Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain r residue 40 VAL Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 44 MET Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 67 VAL Chi-restraints excluded: chain t residue 30 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 913 optimal weight: 0.7980 chunk 694 optimal weight: 10.0000 chunk 479 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 441 optimal weight: 7.9990 chunk 620 optimal weight: 10.0000 chunk 927 optimal weight: 3.9990 chunk 982 optimal weight: 0.8980 chunk 484 optimal weight: 7.9990 chunk 879 optimal weight: 4.9990 chunk 264 optimal weight: 5.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 153 GLN ** C 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 GLN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** O 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 GLN Q 37 GLN Q 71 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN U 46 GLN U 74 ASN V 49 ASN ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN 1 19 HIS 1 45 GLN ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 121 HIS i 37 GLN l 5 ASN n 49 GLN o 35 GLN ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 158944 Z= 0.233 Angle : 0.616 28.059 238049 Z= 0.319 Chirality : 0.039 2.121 30459 Planarity : 0.005 0.062 12565 Dihedral : 23.720 178.678 80245 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.55 % Favored : 93.24 % Rotamer: Outliers : 5.41 % Allowed : 21.98 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.16 % 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: -1.44 (0.11), residues: 5592 helix: 0.35 (0.12), residues: 1894 sheet: -0.86 (0.15), residues: 1062 loop : -2.00 (0.11), residues: 2636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 213 HIS 0.008 0.001 HIS r 74 PHE 0.017 0.001 PHE i 39 TYR 0.018 0.002 TYR S 38 ARG 0.010 0.000 ARG f 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11184 Ramachandran restraints generated. 5592 Oldfield, 0 Emsley, 5592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11184 Ramachandran restraints generated. 5592 Oldfield, 0 Emsley, 5592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1560 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 1308 time to evaluate : 6.470 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: E 35 TYR cc_start: 0.8145 (t80) cc_final: 0.6801 (t80) REVERT: E 136 GLN cc_start: 0.7948 (tp40) cc_final: 0.7410 (tp-100) REVERT: E 140 ASP cc_start: 0.7506 (p0) cc_final: 0.7257 (p0) REVERT: E 143 LEU cc_start: 0.8059 (mt) cc_final: 0.7813 (mt) REVERT: E 163 ASN cc_start: 0.8436 (t0) cc_final: 0.7897 (t0) REVERT: F 85 ILE cc_start: 0.8447 (tp) cc_final: 0.8187 (tp) REVERT: F 94 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.6411 (tm-30) REVERT: F 135 GLN cc_start: 0.8268 (pp30) cc_final: 0.7203 (pp30) REVERT: G 128 GLN cc_start: 0.7122 (mm-40) cc_final: 0.6912 (mm-40) REVERT: H 12 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7135 (pp) REVERT: J 1 MET cc_start: 0.4291 (ptt) cc_final: 0.3732 (ptt) REVERT: J 106 LYS cc_start: 0.8353 (ttmt) cc_final: 0.7910 (mttp) REVERT: K 105 ARG cc_start: 0.7710 (tpp-160) cc_final: 0.7241 (tpp-160) REVERT: L 14 LYS cc_start: 0.7452 (mtpp) cc_final: 0.7224 (ttpt) REVERT: L 27 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8939 (pp) REVERT: N 4 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7905 (tpp80) REVERT: P 102 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.6105 (mp0) REVERT: R 13 ARG cc_start: 0.8265 (ttp-170) cc_final: 0.7986 (ttp80) REVERT: S 52 GLU cc_start: 0.7534 (tp30) cc_final: 0.7262 (tp30) REVERT: T 1 MET cc_start: 0.2688 (ptp) cc_final: 0.2034 (mtm) REVERT: T 28 ASN cc_start: 0.8141 (t0) cc_final: 0.7932 (t0) REVERT: T 49 LYS cc_start: 0.8608 (tppp) cc_final: 0.8227 (tttt) REVERT: V 9 ARG cc_start: 0.8494 (mtp180) cc_final: 0.8165 (mtm180) REVERT: Y 9 LYS cc_start: 0.8338 (mtpt) cc_final: 0.8118 (tttm) REVERT: Y 20 ASN cc_start: 0.8437 (m-40) cc_final: 0.8193 (m110) REVERT: Y 60 LYS cc_start: 0.6619 (ttmt) cc_final: 0.6306 (tttt) REVERT: 0 50 ARG cc_start: 0.8455 (mtp180) cc_final: 0.8228 (mtm180) REVERT: b 145 GLU cc_start: 0.6075 (mm-30) cc_final: 0.5853 (mm-30) REVERT: b 221 VAL cc_start: 0.7896 (m) cc_final: 0.7690 (t) REVERT: c 185 ASN cc_start: 0.8603 (m-40) cc_final: 0.8375 (t0) REVERT: d 47 ARG cc_start: 0.6537 (tpp-160) cc_final: 0.5471 (ttp-170) REVERT: d 113 GLU cc_start: 0.7784 (tt0) cc_final: 0.7317 (tt0) REVERT: d 165 ARG cc_start: 0.6437 (mtm110) cc_final: 0.6074 (ttm110) REVERT: d 202 GLU cc_start: 0.6895 (mt-10) cc_final: 0.6523 (tt0) REVERT: g 30 LEU cc_start: 0.8932 (tp) cc_final: 0.8729 (tp) REVERT: h 3 MET cc_start: 0.8351 (tpp) cc_final: 0.7995 (mmm) REVERT: h 60 GLU cc_start: 0.7107 (mp0) cc_final: 0.6901 (mp0) REVERT: j 7 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7707 (mtm180) REVERT: n 47 LYS cc_start: 0.7708 (tppp) cc_final: 0.7421 (tptm) REVERT: p 1 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.7435 (ptm) REVERT: s 73 GLU cc_start: 0.7246 (tt0) cc_final: 0.6991 (tt0) REVERT: t 54 MET cc_start: 0.8381 (ttp) cc_final: 0.7884 (ttp) REVERT: t 82 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7686 (mm110) REVERT: u 33 ARG cc_start: 0.6392 (ttm110) cc_final: 0.5706 (mtt180) outliers start: 252 outliers final: 195 residues processed: 1443 average time/residue: 1.3218 time to fit residues: 3274.3236 Evaluate side-chains 1466 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1264 time to evaluate : 6.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain N residue 4 ARG Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 99 LYS Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 27 GLU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 65 ILE Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 82 ILE Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain Z residue 7 ILE Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 48 ILE Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 3 residue 28 ASN Chi-restraints excluded: chain 3 residue 32 ILE Chi-restraints excluded: chain 3 residue 33 LEU Chi-restraints excluded: chain 3 residue 61 CYS Chi-restraints excluded: chain 4 residue 14 CYS Chi-restraints excluded: chain 4 residue 17 VAL Chi-restraints excluded: chain 5 residue 5 ILE Chi-restraints excluded: chain 5 residue 51 VAL Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 46 THR Chi-restraints excluded: chain b residue 63 ARG Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain c residue 63 SER Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain d residue 34 ILE Chi-restraints excluded: chain d residue 35 GLU Chi-restraints excluded: chain d residue 40 GLN Chi-restraints excluded: chain d residue 123 ILE Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain d residue 145 ILE Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain d residue 171 LEU Chi-restraints excluded: chain d residue 195 ILE Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 90 THR Chi-restraints excluded: chain e residue 100 SER Chi-restraints excluded: chain e residue 117 VAL Chi-restraints excluded: chain e residue 122 ASN Chi-restraints excluded: chain e residue 123 VAL Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain e residue 145 GLU Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 104 ILE Chi-restraints excluded: chain h residue 10 MET Chi-restraints excluded: chain h residue 74 SER Chi-restraints excluded: chain h residue 79 SER Chi-restraints excluded: chain h residue 90 ASP Chi-restraints excluded: chain h residue 104 VAL Chi-restraints excluded: chain i residue 18 ARG Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 58 VAL Chi-restraints excluded: chain i residue 91 ASP Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain j residue 7 ARG Chi-restraints excluded: chain j residue 40 ILE 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 k residue 46 THR Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 109 ASN Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain m residue 7 ILE Chi-restraints excluded: chain m residue 19 LEU Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain o residue 61 SER Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 57 ILE Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 13 VAL Chi-restraints excluded: chain q residue 14 SER Chi-restraints excluded: chain q residue 18 GLU Chi-restraints excluded: chain q residue 19 LYS Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 44 MET Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 67 VAL Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 27 MET Chi-restraints excluded: chain t residue 30 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 817 optimal weight: 6.9990 chunk 557 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 731 optimal weight: 7.9990 chunk 405 optimal weight: 3.9990 chunk 838 optimal weight: 9.9990 chunk 678 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 501 optimal weight: 0.0670 chunk 881 optimal weight: 9.9990 chunk 247 optimal weight: 10.0000 overall best weight: 5.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 117 GLN C 153 GLN ** C 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN G 22 GLN G 64 GLN G 101 ASN G 116 GLN ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS J 128 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 GLN Q 71 GLN R 6 GLN ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 74 ASN ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 45 GLN ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 93 ASN b 146 ASN ** b 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 118 GLN i 37 GLN j 58 ASN l 5 ASN l 112 GLN n 49 GLN o 35 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 158944 Z= 0.430 Angle : 0.733 28.277 238049 Z= 0.372 Chirality : 0.045 2.106 30459 Planarity : 0.006 0.071 12565 Dihedral : 23.741 179.361 80245 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.62 % Favored : 92.16 % Rotamer: Outliers : 7.11 % Allowed : 21.80 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.16 % 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: -1.49 (0.11), residues: 5592 helix: 0.26 (0.12), residues: 1902 sheet: -0.85 (0.15), residues: 1048 loop : -2.00 (0.11), residues: 2642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 213 HIS 0.010 0.001 HIS r 74 PHE 0.020 0.002 PHE i 39 TYR 0.023 0.002 TYR S 38 ARG 0.012 0.001 ARG f 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11184 Ramachandran restraints generated. 5592 Oldfield, 0 Emsley, 5592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11184 Ramachandran restraints generated. 5592 Oldfield, 0 Emsley, 5592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1602 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 331 poor density : 1271 time to evaluate : 6.309 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: D 4 LEU cc_start: 0.8408 (mt) cc_final: 0.8207 (mp) REVERT: D 167 ASN cc_start: 0.8508 (t0) cc_final: 0.8177 (t0) REVERT: E 35 TYR cc_start: 0.8225 (t80) cc_final: 0.6986 (t80) REVERT: E 94 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8064 (pm20) REVERT: E 136 GLN cc_start: 0.7993 (tp40) cc_final: 0.7719 (tp40) REVERT: E 163 ASN cc_start: 0.8514 (t0) cc_final: 0.8028 (t0) REVERT: F 85 ILE cc_start: 0.8492 (tp) cc_final: 0.8266 (tp) REVERT: H 12 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7252 (pp) REVERT: J 1 MET cc_start: 0.4294 (ptt) cc_final: 0.3876 (ptt) REVERT: K 105 ARG cc_start: 0.7740 (tpp-160) cc_final: 0.7185 (tpp-160) REVERT: L 1 MET cc_start: 0.6640 (pmm) cc_final: 0.6116 (pmm) REVERT: L 14 LYS cc_start: 0.7596 (mtpp) cc_final: 0.7266 (ttpt) REVERT: L 27 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8913 (pp) REVERT: N 4 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.8021 (tpp80) REVERT: P 102 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6126 (mp0) REVERT: R 11 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8676 (mp10) REVERT: S 52 GLU cc_start: 0.7528 (tp30) cc_final: 0.7280 (tp30) REVERT: T 1 MET cc_start: 0.2654 (ptp) cc_final: 0.2059 (mtm) REVERT: T 28 ASN cc_start: 0.8193 (t0) cc_final: 0.7937 (t0) REVERT: U 96 PHE cc_start: 0.8208 (m-10) cc_final: 0.7926 (m-10) REVERT: U 101 GLU cc_start: 0.6963 (mp0) cc_final: 0.6429 (mp0) REVERT: V 9 ARG cc_start: 0.8602 (mtp180) cc_final: 0.8214 (mtm180) REVERT: Y 9 LYS cc_start: 0.8477 (mtpt) cc_final: 0.8179 (tttm) REVERT: Y 60 LYS cc_start: 0.6774 (ttmt) cc_final: 0.6471 (tttt) REVERT: b 28 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7415 (ttmt) REVERT: b 186 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8247 (mp) REVERT: c 185 ASN cc_start: 0.8635 (m-40) cc_final: 0.8431 (t0) REVERT: d 47 ARG cc_start: 0.6526 (tpp-160) cc_final: 0.5394 (ttp-170) REVERT: d 113 GLU cc_start: 0.7824 (tt0) cc_final: 0.7516 (tt0) REVERT: d 165 ARG cc_start: 0.6453 (mtm110) cc_final: 0.6092 (ttm110) REVERT: d 202 GLU cc_start: 0.6942 (mt-10) cc_final: 0.6578 (tt0) REVERT: h 3 MET cc_start: 0.8479 (tpp) cc_final: 0.8171 (mmm) REVERT: h 50 LYS cc_start: 0.7680 (mmmt) cc_final: 0.7445 (mmtt) REVERT: i 62 ASP cc_start: 0.6838 (OUTLIER) cc_final: 0.6464 (p0) REVERT: j 7 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7704 (mtm180) REVERT: n 47 LYS cc_start: 0.7803 (tppp) cc_final: 0.7528 (tptm) REVERT: o 57 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8024 (mm) REVERT: p 1 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7341 (ptm) REVERT: r 25 ASP cc_start: 0.7660 (p0) cc_final: 0.7429 (p0) REVERT: s 73 GLU cc_start: 0.7287 (tt0) cc_final: 0.7053 (tt0) REVERT: t 54 MET cc_start: 0.8479 (ttp) cc_final: 0.7960 (ttp) REVERT: u 33 ARG cc_start: 0.6464 (ttm110) cc_final: 0.5761 (mtt180) outliers start: 331 outliers final: 263 residues processed: 1466 average time/residue: 1.3082 time to fit residues: 3296.4167 Evaluate side-chains 1523 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 1248 time to evaluate : 6.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain N residue 4 ARG Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 99 LYS Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 27 GLU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 11 GLN Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 65 ILE Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 82 ILE Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 56 MET Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Z residue 7 ILE Chi-restraints excluded: chain Z residue 40 ASP Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 48 ILE Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 3 residue 32 ILE Chi-restraints excluded: chain 3 residue 33 LEU Chi-restraints excluded: chain 3 residue 61 CYS Chi-restraints excluded: chain 4 residue 14 CYS Chi-restraints excluded: chain 4 residue 17 VAL Chi-restraints excluded: chain 5 residue 5 ILE Chi-restraints excluded: chain 5 residue 9 TYR Chi-restraints excluded: chain 5 residue 37 CYS Chi-restraints excluded: chain 5 residue 51 VAL Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 28 LYS Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 51 ASN Chi-restraints excluded: chain b residue 63 ARG Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 147 SER Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 191 SER Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain b residue 220 THR Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain c residue 63 SER Chi-restraints excluded: chain c residue 101 ILE Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 34 ILE Chi-restraints excluded: chain d residue 35 GLU Chi-restraints excluded: chain d residue 40 GLN Chi-restraints excluded: chain d residue 123 ILE Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain d residue 145 ILE Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain d residue 171 LEU Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 90 THR Chi-restraints excluded: chain e residue 94 VAL Chi-restraints excluded: chain e residue 100 SER Chi-restraints excluded: chain e residue 122 ASN Chi-restraints excluded: chain e residue 123 VAL Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain e residue 145 GLU Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 104 ILE Chi-restraints excluded: chain h residue 10 MET Chi-restraints excluded: chain h residue 31 LYS Chi-restraints excluded: chain h residue 36 ILE Chi-restraints excluded: chain h residue 74 SER Chi-restraints excluded: chain h residue 79 SER Chi-restraints excluded: chain h residue 90 ASP Chi-restraints excluded: chain h residue 104 VAL Chi-restraints excluded: chain h residue 105 SER Chi-restraints excluded: chain i residue 18 ARG Chi-restraints excluded: chain i residue 30 ILE Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 58 VAL Chi-restraints excluded: chain i residue 62 ASP Chi-restraints excluded: chain i residue 84 THR Chi-restraints excluded: chain i residue 91 ASP Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain i residue 112 GLU Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain j residue 7 ARG Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain j residue 83 THR 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 k residue 46 THR Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 72 ASP Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 109 ASN Chi-restraints excluded: chain l residue 4 VAL Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain l residue 102 LEU Chi-restraints excluded: chain m residue 7 ILE Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 19 LEU Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 45 ILE Chi-restraints excluded: chain m residue 65 VAL Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain o residue 61 SER Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 57 ILE Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain p residue 75 ILE Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 13 VAL Chi-restraints excluded: chain q residue 14 SER Chi-restraints excluded: chain q residue 18 GLU Chi-restraints excluded: chain q residue 19 LYS Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 11 ILE Chi-restraints excluded: chain s residue 44 MET Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 67 VAL Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 27 MET Chi-restraints excluded: chain t residue 30 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 330 optimal weight: 2.9990 chunk 884 optimal weight: 7.9990 chunk 194 optimal weight: 6.9990 chunk 576 optimal weight: 5.9990 chunk 242 optimal weight: 7.9990 chunk 983 optimal weight: 0.8980 chunk 816 optimal weight: 6.9990 chunk 455 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 325 optimal weight: 0.8980 chunk 516 optimal weight: 10.0000 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 117 GLN ** C 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** O 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 66 ASN Q 37 GLN Q 71 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 19 HIS 1 45 GLN ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 93 ASN ** b 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 185 ASN ** d 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 121 HIS h 118 GLN i 37 GLN l 5 ASN l 112 GLN o 35 GLN ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 158944 Z= 0.266 Angle : 0.627 27.819 238049 Z= 0.323 Chirality : 0.039 2.120 30459 Planarity : 0.005 0.059 12565 Dihedral : 23.674 179.546 80245 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.94 % Favored : 92.88 % Rotamer: Outliers : 6.57 % Allowed : 22.79 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.11), residues: 5592 helix: 0.56 (0.12), residues: 1901 sheet: -0.81 (0.15), residues: 1045 loop : -1.90 (0.11), residues: 2646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 248 HIS 0.008 0.001 HIS r 74 PHE 0.017 0.002 PHE i 39 TYR 0.018 0.002 TYR S 38 ARG 0.012 0.000 ARG f 44 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11184 Ramachandran restraints generated. 5592 Oldfield, 0 Emsley, 5592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11184 Ramachandran restraints generated. 5592 Oldfield, 0 Emsley, 5592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1603 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 306 poor density : 1297 time to evaluate : 6.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 167 ASN cc_start: 0.8562 (t0) cc_final: 0.8204 (t0) REVERT: E 35 TYR cc_start: 0.8126 (t80) cc_final: 0.7346 (t80) REVERT: E 163 ASN cc_start: 0.8464 (t0) cc_final: 0.7970 (t0) REVERT: F 85 ILE cc_start: 0.8456 (tp) cc_final: 0.8247 (tp) REVERT: F 134 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7333 (mm-30) REVERT: G 166 ASP cc_start: 0.6083 (OUTLIER) cc_final: 0.5406 (m-30) REVERT: H 12 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7129 (pp) REVERT: J 1 MET cc_start: 0.4339 (ptt) cc_final: 0.3949 (ptt) REVERT: J 106 LYS cc_start: 0.8220 (ttmt) cc_final: 0.7982 (mttp) REVERT: K 105 ARG cc_start: 0.7738 (tpp-160) cc_final: 0.7302 (tpp-160) REVERT: L 1 MET cc_start: 0.6612 (pmm) cc_final: 0.5990 (pmm) REVERT: L 14 LYS cc_start: 0.7548 (mtpp) cc_final: 0.7218 (ttpt) REVERT: L 27 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8929 (pp) REVERT: P 66 ASN cc_start: 0.7907 (OUTLIER) cc_final: 0.7691 (p0) REVERT: P 102 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.6098 (mp0) REVERT: R 11 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8816 (mp10) REVERT: R 13 ARG cc_start: 0.8491 (ttp80) cc_final: 0.8025 (ttt90) REVERT: S 52 GLU cc_start: 0.7535 (tp30) cc_final: 0.7207 (tp30) REVERT: T 1 MET cc_start: 0.2713 (ptp) cc_final: 0.2068 (mtm) REVERT: T 28 ASN cc_start: 0.8230 (t0) cc_final: 0.7995 (t0) REVERT: U 96 PHE cc_start: 0.8193 (m-10) cc_final: 0.7901 (m-10) REVERT: V 9 ARG cc_start: 0.8566 (mtp180) cc_final: 0.8171 (mtm180) REVERT: Y 9 LYS cc_start: 0.8372 (mtpt) cc_final: 0.8121 (tttm) REVERT: Y 60 LYS cc_start: 0.6757 (ttmt) cc_final: 0.6461 (tttt) REVERT: b 9 MET cc_start: 0.7338 (mtt) cc_final: 0.7136 (mtt) REVERT: b 186 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8304 (mp) REVERT: b 221 VAL cc_start: 0.7847 (m) cc_final: 0.7636 (t) REVERT: d 47 ARG cc_start: 0.6332 (tpp-160) cc_final: 0.5214 (ttp-170) REVERT: d 88 GLU cc_start: 0.5666 (tt0) cc_final: 0.5287 (tt0) REVERT: d 113 GLU cc_start: 0.7767 (tt0) cc_final: 0.7303 (tt0) REVERT: d 165 ARG cc_start: 0.6399 (mtm110) cc_final: 0.6037 (ttm110) REVERT: d 202 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6540 (tt0) REVERT: h 3 MET cc_start: 0.8304 (tpp) cc_final: 0.8039 (mmm) REVERT: h 67 GLN cc_start: 0.6072 (OUTLIER) cc_final: 0.5072 (mm-40) REVERT: i 123 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7190 (ttt-90) REVERT: j 7 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7733 (mtm180) REVERT: n 47 LYS cc_start: 0.7804 (tppp) cc_final: 0.7491 (tptm) REVERT: o 57 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7967 (mm) REVERT: p 1 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7251 (ptm) REVERT: s 56 GLN cc_start: 0.7732 (pt0) cc_final: 0.7517 (pt0) REVERT: s 73 GLU cc_start: 0.7273 (tt0) cc_final: 0.7017 (tt0) REVERT: t 54 MET cc_start: 0.8451 (ttp) cc_final: 0.7872 (ttp) REVERT: u 33 ARG cc_start: 0.6461 (ttm110) cc_final: 0.5757 (mtt180) outliers start: 306 outliers final: 247 residues processed: 1474 average time/residue: 1.2986 time to fit residues: 3293.1667 Evaluate side-chains 1522 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 1263 time to evaluate : 6.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 99 LYS Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 27 GLU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 66 ASN Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain R residue 11 GLN Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 65 ILE Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 82 ILE Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 56 MET Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 46 ASP Chi-restraints excluded: chain 1 residue 11 LEU Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 48 ILE Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 3 residue 28 ASN Chi-restraints excluded: chain 3 residue 32 ILE Chi-restraints excluded: chain 3 residue 33 LEU Chi-restraints excluded: chain 3 residue 61 CYS Chi-restraints excluded: chain 4 residue 14 CYS Chi-restraints excluded: chain 4 residue 17 VAL Chi-restraints excluded: chain 5 residue 5 ILE Chi-restraints excluded: chain 5 residue 9 TYR Chi-restraints excluded: chain 5 residue 37 CYS Chi-restraints excluded: chain 5 residue 51 VAL Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 147 SER Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 191 SER Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain c residue 63 SER Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 34 ILE Chi-restraints excluded: chain d residue 35 GLU Chi-restraints excluded: chain d residue 40 GLN Chi-restraints excluded: chain d residue 123 ILE Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain d residue 145 ILE Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain d residue 171 LEU Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain e residue 69 ARG Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 90 THR Chi-restraints excluded: chain e residue 94 VAL Chi-restraints excluded: chain e residue 100 SER Chi-restraints excluded: chain e residue 117 VAL Chi-restraints excluded: chain e residue 122 ASN Chi-restraints excluded: chain e residue 123 VAL Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain e residue 145 GLU Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 104 ILE Chi-restraints excluded: chain h residue 10 MET Chi-restraints excluded: chain h residue 31 LYS Chi-restraints excluded: chain h residue 67 GLN Chi-restraints excluded: chain h residue 74 SER Chi-restraints excluded: chain h residue 79 SER Chi-restraints excluded: chain h residue 90 ASP Chi-restraints excluded: chain h residue 104 VAL Chi-restraints excluded: chain h residue 105 SER Chi-restraints excluded: chain i residue 18 ARG Chi-restraints excluded: chain i residue 30 ILE Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 90 TYR Chi-restraints excluded: chain i residue 91 ASP Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 123 ARG Chi-restraints excluded: chain j residue 7 ARG Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain j residue 83 THR Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 72 ASP Chi-restraints excluded: chain k residue 95 SER Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 109 ASN Chi-restraints excluded: chain l residue 4 VAL Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain l residue 102 LEU Chi-restraints excluded: chain l residue 115 SER Chi-restraints excluded: chain m residue 7 ILE Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 19 LEU Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 45 ILE Chi-restraints excluded: chain m residue 65 VAL Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain o residue 61 SER Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain p residue 57 ILE Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain p residue 75 ILE Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 13 VAL Chi-restraints excluded: chain q residue 14 SER Chi-restraints excluded: chain q residue 18 GLU Chi-restraints excluded: chain q residue 19 LYS Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 44 MET Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 67 VAL Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 27 MET Chi-restraints excluded: chain t residue 30 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 947 optimal weight: 0.9980 chunk 110 optimal weight: 30.0000 chunk 560 optimal weight: 9.9990 chunk 717 optimal weight: 10.0000 chunk 556 optimal weight: 4.9990 chunk 827 optimal weight: 0.9980 chunk 548 optimal weight: 5.9990 chunk 979 optimal weight: 7.9990 chunk 612 optimal weight: 4.9990 chunk 597 optimal weight: 8.9990 chunk 452 optimal weight: 2.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 117 GLN ** C 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN F 27 GLN ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS J 128 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 66 ASN Q 37 GLN Q 71 GLN R 6 GLN ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 45 GLN 4 37 GLN ** b 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 185 ASN ** d 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 37 GLN l 5 ASN l 112 GLN o 35 GLN t 13 GLN ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 158944 Z= 0.243 Angle : 0.609 27.860 238049 Z= 0.313 Chirality : 0.038 2.114 30459 Planarity : 0.005 0.059 12565 Dihedral : 23.634 179.618 80245 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.41 % Favored : 92.42 % Rotamer: Outliers : 6.79 % Allowed : 23.46 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.16 % 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: -1.09 (0.11), residues: 5592 helix: 0.74 (0.12), residues: 1895 sheet: -0.75 (0.16), residues: 1052 loop : -1.83 (0.11), residues: 2645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 248 HIS 0.007 0.001 HIS r 74 PHE 0.017 0.001 PHE U 73 TYR 0.017 0.001 TYR Q 47 ARG 0.013 0.000 ARG f 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11184 Ramachandran restraints generated. 5592 Oldfield, 0 Emsley, 5592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11184 Ramachandran restraints generated. 5592 Oldfield, 0 Emsley, 5592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1608 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 316 poor density : 1292 time to evaluate : 6.499 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: D 130 GLN cc_start: 0.8644 (mt0) cc_final: 0.8438 (mt0) REVERT: D 167 ASN cc_start: 0.8559 (t0) cc_final: 0.8198 (t0) REVERT: E 94 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8023 (pm20) REVERT: E 163 ASN cc_start: 0.8519 (t0) cc_final: 0.8024 (t0) REVERT: F 94 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6440 (tm-30) REVERT: G 166 ASP cc_start: 0.5999 (OUTLIER) cc_final: 0.5368 (m-30) REVERT: H 1 MET cc_start: 0.4270 (tmm) cc_final: 0.2761 (mpp) REVERT: H 12 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.7117 (pp) REVERT: J 1 MET cc_start: 0.4218 (ptt) cc_final: 0.3888 (ptt) REVERT: K 105 ARG cc_start: 0.7733 (tpp-160) cc_final: 0.7315 (tpp-160) REVERT: L 1 MET cc_start: 0.6516 (pmm) cc_final: 0.5901 (pmm) REVERT: L 14 LYS cc_start: 0.7495 (mtpp) cc_final: 0.7225 (ttpt) REVERT: L 27 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8975 (pp) REVERT: P 102 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6068 (mp0) REVERT: R 11 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8792 (mp10) REVERT: R 13 ARG cc_start: 0.8520 (ttp80) cc_final: 0.7892 (ttt90) REVERT: R 16 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7590 (mm-30) REVERT: S 52 GLU cc_start: 0.7544 (tp30) cc_final: 0.7238 (tp30) REVERT: T 1 MET cc_start: 0.2770 (ptp) cc_final: 0.2109 (mtm) REVERT: T 28 ASN cc_start: 0.8190 (t0) cc_final: 0.7977 (t0) REVERT: U 96 PHE cc_start: 0.8171 (m-10) cc_final: 0.7889 (m-10) REVERT: V 9 ARG cc_start: 0.8576 (mtp180) cc_final: 0.8204 (mtm180) REVERT: Y 9 LYS cc_start: 0.8364 (mtpt) cc_final: 0.8140 (tttm) REVERT: Y 28 LEU cc_start: 0.8574 (mm) cc_final: 0.8282 (tp) REVERT: Y 60 LYS cc_start: 0.6755 (ttmt) cc_final: 0.6453 (tttt) REVERT: 0 50 ARG cc_start: 0.8577 (mtp180) cc_final: 0.8280 (mtm180) REVERT: b 9 MET cc_start: 0.7331 (mtt) cc_final: 0.7121 (mtt) REVERT: b 28 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7296 (ttmt) REVERT: b 186 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8309 (mp) REVERT: b 221 VAL cc_start: 0.7917 (m) cc_final: 0.7713 (t) REVERT: d 47 ARG cc_start: 0.6120 (tpp-160) cc_final: 0.4988 (ttp-170) REVERT: d 88 GLU cc_start: 0.5714 (tt0) cc_final: 0.5450 (tt0) REVERT: d 113 GLU cc_start: 0.7658 (tt0) cc_final: 0.7255 (tt0) REVERT: d 202 GLU cc_start: 0.6869 (mt-10) cc_final: 0.6496 (tt0) REVERT: e 156 LYS cc_start: 0.8293 (mtmt) cc_final: 0.7955 (ptpt) REVERT: h 3 MET cc_start: 0.8329 (tpp) cc_final: 0.8056 (mmm) REVERT: h 67 GLN cc_start: 0.6035 (OUTLIER) cc_final: 0.5756 (pm20) REVERT: i 123 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7922 (tmt-80) REVERT: j 7 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7704 (mtm180) REVERT: n 47 LYS cc_start: 0.7827 (tppp) cc_final: 0.7499 (tptm) REVERT: o 57 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7900 (mm) REVERT: o 87 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6757 (pp) REVERT: p 1 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7265 (ptm) REVERT: s 56 GLN cc_start: 0.7708 (pt0) cc_final: 0.7477 (pt0) REVERT: s 73 GLU cc_start: 0.7263 (tt0) cc_final: 0.7014 (tt0) REVERT: t 54 MET cc_start: 0.8443 (ttp) cc_final: 0.7844 (ttp) REVERT: u 33 ARG cc_start: 0.6497 (ttm110) cc_final: 0.5781 (mtt180) outliers start: 316 outliers final: 262 residues processed: 1477 average time/residue: 1.2972 time to fit residues: 3296.4390 Evaluate side-chains 1528 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 1251 time to evaluate : 5.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain P residue 27 GLU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain R residue 11 GLN Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 45 GLU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 65 ILE Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 82 ILE Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 56 MET Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 46 ASP Chi-restraints excluded: chain 1 residue 11 LEU Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 48 ILE Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 3 residue 28 ASN Chi-restraints excluded: chain 3 residue 32 ILE Chi-restraints excluded: chain 3 residue 33 LEU Chi-restraints excluded: chain 3 residue 61 CYS Chi-restraints excluded: chain 4 residue 14 CYS Chi-restraints excluded: chain 4 residue 17 VAL Chi-restraints excluded: chain 4 residue 37 GLN Chi-restraints excluded: chain 5 residue 5 ILE Chi-restraints excluded: chain 5 residue 9 TYR Chi-restraints excluded: chain 5 residue 37 CYS Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 8 ASP Chi-restraints excluded: chain b residue 28 LYS Chi-restraints excluded: chain b residue 123 ASP Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 191 SER Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain c residue 63 SER Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 185 ASN Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 34 ILE Chi-restraints excluded: chain d residue 35 GLU Chi-restraints excluded: chain d residue 40 GLN Chi-restraints excluded: chain d residue 123 ILE Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain d residue 145 ILE Chi-restraints excluded: chain d residue 171 LEU Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain e residue 69 ARG Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 90 THR Chi-restraints excluded: chain e residue 100 SER Chi-restraints excluded: chain e residue 117 VAL Chi-restraints excluded: chain e residue 122 ASN Chi-restraints excluded: chain e residue 123 VAL Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain e residue 145 GLU Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 104 ILE Chi-restraints excluded: chain h residue 10 MET Chi-restraints excluded: chain h residue 31 LYS Chi-restraints excluded: chain h residue 67 GLN Chi-restraints excluded: chain h residue 74 SER Chi-restraints excluded: chain h residue 79 SER Chi-restraints excluded: chain h residue 90 ASP Chi-restraints excluded: chain h residue 104 VAL Chi-restraints excluded: chain h residue 105 SER Chi-restraints excluded: chain i residue 18 ARG Chi-restraints excluded: chain i residue 30 ILE Chi-restraints excluded: chain i residue 58 VAL Chi-restraints excluded: chain i residue 90 TYR Chi-restraints excluded: chain i residue 91 ASP Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 123 ARG Chi-restraints excluded: chain j residue 7 ARG Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain j residue 83 THR Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 72 ASP Chi-restraints excluded: chain k residue 95 SER Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 109 ASN Chi-restraints excluded: chain l residue 4 VAL Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain l residue 102 LEU Chi-restraints excluded: chain l residue 115 SER Chi-restraints excluded: chain m residue 7 ILE Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 45 ILE Chi-restraints excluded: chain m residue 65 VAL Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain o residue 61 SER Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain p residue 57 ILE Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain p residue 75 ILE Chi-restraints excluded: chain q residue 13 VAL Chi-restraints excluded: chain q residue 14 SER Chi-restraints excluded: chain q residue 17 MET Chi-restraints excluded: chain q residue 18 GLU Chi-restraints excluded: chain q residue 19 LYS Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain r residue 44 ILE Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 11 ILE Chi-restraints excluded: chain s residue 44 MET Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 67 VAL Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 27 MET Chi-restraints excluded: chain t residue 30 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 605 optimal weight: 0.9980 chunk 391 optimal weight: 3.9990 chunk 584 optimal weight: 0.6980 chunk 294 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 chunk 189 optimal weight: 10.0000 chunk 622 optimal weight: 20.0000 chunk 667 optimal weight: 10.0000 chunk 484 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 769 optimal weight: 10.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 117 GLN ** C 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN F 27 GLN G 48 ASN G 64 GLN ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** O 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 66 ASN Q 37 GLN Q 71 GLN ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 12 GLN ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 45 GLN ** b 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 185 ASN d 131 ASN f 46 GLN i 37 GLN l 5 ASN l 112 GLN n 49 GLN o 35 GLN t 13 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 158944 Z= 0.331 Angle : 0.662 28.038 238049 Z= 0.338 Chirality : 0.041 2.105 30459 Planarity : 0.005 0.067 12565 Dihedral : 23.637 179.372 80245 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.42 % Favored : 92.40 % Rotamer: Outliers : 7.22 % Allowed : 23.78 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.16 % 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: -1.14 (0.11), residues: 5592 helix: 0.64 (0.12), residues: 1896 sheet: -0.69 (0.16), residues: 1032 loop : -1.84 (0.11), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 213 HIS 0.008 0.001 HIS r 74 PHE 0.018 0.002 PHE i 39 TYR 0.024 0.002 TYR d 76 ARG 0.014 0.001 ARG f 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11184 Ramachandran restraints generated. 5592 Oldfield, 0 Emsley, 5592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11184 Ramachandran restraints generated. 5592 Oldfield, 0 Emsley, 5592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1601 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 336 poor density : 1265 time to evaluate : 6.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 167 ASN cc_start: 0.8575 (t0) cc_final: 0.8245 (t0) REVERT: E 61 ARG cc_start: 0.8376 (mtm-85) cc_final: 0.8153 (mtm-85) REVERT: E 94 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8040 (pm20) REVERT: E 163 ASN cc_start: 0.8556 (t0) cc_final: 0.8086 (t0) REVERT: G 166 ASP cc_start: 0.6006 (OUTLIER) cc_final: 0.5369 (m-30) REVERT: H 1 MET cc_start: 0.4366 (tmm) cc_final: 0.2846 (mpp) REVERT: H 12 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7116 (pp) REVERT: J 1 MET cc_start: 0.4270 (ptt) cc_final: 0.3920 (ptt) REVERT: L 1 MET cc_start: 0.6598 (pmm) cc_final: 0.6061 (pmm) REVERT: L 14 LYS cc_start: 0.7563 (mtpp) cc_final: 0.7225 (ttpt) REVERT: L 27 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8957 (pp) REVERT: P 102 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6102 (mp0) REVERT: R 11 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8728 (mp10) REVERT: R 13 ARG cc_start: 0.8548 (ttp80) cc_final: 0.8121 (ttt90) REVERT: S 52 GLU cc_start: 0.7529 (tp30) cc_final: 0.7212 (tp30) REVERT: T 1 MET cc_start: 0.2655 (ptp) cc_final: 0.1997 (mtm) REVERT: T 28 ASN cc_start: 0.8202 (t0) cc_final: 0.7959 (t0) REVERT: U 96 PHE cc_start: 0.8181 (m-10) cc_final: 0.7906 (m-10) REVERT: V 9 ARG cc_start: 0.8600 (mtp180) cc_final: 0.8202 (mtm180) REVERT: Y 9 LYS cc_start: 0.8455 (mtpt) cc_final: 0.8141 (tttm) REVERT: Y 60 LYS cc_start: 0.6791 (ttmt) cc_final: 0.6489 (tttt) REVERT: b 28 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7307 (ttmt) REVERT: b 186 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8214 (mp) REVERT: b 221 VAL cc_start: 0.7917 (m) cc_final: 0.7707 (t) REVERT: d 47 ARG cc_start: 0.6096 (tpp-160) cc_final: 0.4977 (ttp-170) REVERT: d 88 GLU cc_start: 0.5760 (tt0) cc_final: 0.5403 (tt0) REVERT: d 113 GLU cc_start: 0.7703 (tt0) cc_final: 0.7254 (tt0) REVERT: d 202 GLU cc_start: 0.6924 (mt-10) cc_final: 0.6554 (tt0) REVERT: e 156 LYS cc_start: 0.8323 (mtmt) cc_final: 0.7985 (ptpt) REVERT: h 3 MET cc_start: 0.8337 (tpp) cc_final: 0.8047 (mmm) REVERT: h 67 GLN cc_start: 0.6092 (OUTLIER) cc_final: 0.5026 (mm-40) REVERT: i 123 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7995 (tmt-80) REVERT: j 7 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7719 (mtm180) REVERT: k 93 ARG cc_start: 0.6604 (OUTLIER) cc_final: 0.5400 (ptp-170) REVERT: n 47 LYS cc_start: 0.7820 (tppp) cc_final: 0.7502 (tptm) REVERT: o 57 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7942 (mm) REVERT: p 1 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7360 (ptm) REVERT: r 25 ASP cc_start: 0.7790 (p0) cc_final: 0.7557 (p0) REVERT: s 56 GLN cc_start: 0.7766 (pt0) cc_final: 0.7514 (pt0) REVERT: s 73 GLU cc_start: 0.7247 (tt0) cc_final: 0.7019 (tt0) REVERT: t 54 MET cc_start: 0.8473 (ttp) cc_final: 0.7855 (ttp) REVERT: u 33 ARG cc_start: 0.6495 (ttm110) cc_final: 0.5789 (mtt180) outliers start: 336 outliers final: 292 residues processed: 1470 average time/residue: 1.3461 time to fit residues: 3427.0139 Evaluate side-chains 1561 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 306 poor density : 1255 time to evaluate : 6.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 27 GLU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 66 ASN Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 11 GLN Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 45 GLU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 65 ILE Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 82 ILE Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 56 MET Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 46 ASP Chi-restraints excluded: chain 1 residue 11 LEU Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 48 ILE Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 3 residue 32 ILE Chi-restraints excluded: chain 3 residue 33 LEU Chi-restraints excluded: chain 4 residue 14 CYS Chi-restraints excluded: chain 4 residue 17 VAL Chi-restraints excluded: chain 5 residue 5 ILE Chi-restraints excluded: chain 5 residue 9 TYR Chi-restraints excluded: chain 5 residue 32 LEU Chi-restraints excluded: chain 5 residue 37 CYS Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 28 LYS Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 123 ASP Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 147 SER Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 191 SER Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 44 THR Chi-restraints excluded: chain c residue 63 SER Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 185 ASN Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 34 ILE Chi-restraints excluded: chain d residue 35 GLU Chi-restraints excluded: chain d residue 40 GLN Chi-restraints excluded: chain d residue 123 ILE Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 131 ASN Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain d residue 145 ILE Chi-restraints excluded: chain d residue 171 LEU Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain e residue 69 ARG Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 90 THR Chi-restraints excluded: chain e residue 100 SER Chi-restraints excluded: chain e residue 122 ASN Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain e residue 145 GLU Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 46 GLN Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 104 ILE Chi-restraints excluded: chain h residue 10 MET Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 31 LYS Chi-restraints excluded: chain h residue 67 GLN Chi-restraints excluded: chain h residue 74 SER Chi-restraints excluded: chain h residue 79 SER Chi-restraints excluded: chain h residue 90 ASP Chi-restraints excluded: chain h residue 104 VAL Chi-restraints excluded: chain h residue 105 SER Chi-restraints excluded: chain i residue 18 ARG Chi-restraints excluded: chain i residue 22 LYS Chi-restraints excluded: chain i residue 30 ILE Chi-restraints excluded: chain i residue 58 VAL Chi-restraints excluded: chain i residue 84 THR Chi-restraints excluded: chain i residue 90 TYR Chi-restraints excluded: chain i residue 91 ASP Chi-restraints excluded: chain i residue 112 GLU Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 123 ARG Chi-restraints excluded: chain j residue 7 ARG Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain j residue 83 THR Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 72 ASP Chi-restraints excluded: chain k residue 93 ARG Chi-restraints excluded: chain k residue 95 SER Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 109 ASN Chi-restraints excluded: chain l residue 4 VAL Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain l residue 102 LEU Chi-restraints excluded: chain l residue 115 SER Chi-restraints excluded: chain m residue 7 ILE Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 19 LEU Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 45 ILE Chi-restraints excluded: chain m residue 65 VAL Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain n residue 37 SER Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain o residue 61 SER Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain p residue 57 ILE Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain p residue 75 ILE Chi-restraints excluded: chain q residue 13 VAL Chi-restraints excluded: chain q residue 14 SER Chi-restraints excluded: chain q residue 17 MET Chi-restraints excluded: chain q residue 18 GLU Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain r residue 44 ILE Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 11 ILE Chi-restraints excluded: chain s residue 44 MET Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 55 ARG Chi-restraints excluded: chain s residue 67 VAL Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 27 MET Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain u residue 42 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 890 optimal weight: 3.9990 chunk 938 optimal weight: 6.9990 chunk 855 optimal weight: 10.0000 chunk 912 optimal weight: 9.9990 chunk 937 optimal weight: 5.9990 chunk 549 optimal weight: 8.9990 chunk 397 optimal weight: 30.0000 chunk 716 optimal weight: 6.9990 chunk 280 optimal weight: 10.0000 chunk 824 optimal weight: 0.0060 chunk 863 optimal weight: 9.9990 overall best weight: 4.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 117 GLN ** C 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** O 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 66 ASN Q 37 GLN Q 71 GLN ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 12 GLN ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 45 GLN ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 93 ASN ** b 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 185 ASN d 131 ASN i 37 GLN l 5 ASN l 112 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 158944 Z= 0.361 Angle : 0.685 28.084 238049 Z= 0.349 Chirality : 0.042 2.106 30459 Planarity : 0.005 0.068 12565 Dihedral : 23.655 179.660 80245 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.96 % Favored : 91.86 % Rotamer: Outliers : 7.00 % Allowed : 23.93 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.16 % 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: -1.20 (0.11), residues: 5592 helix: 0.58 (0.12), residues: 1896 sheet: -0.69 (0.16), residues: 1043 loop : -1.88 (0.11), residues: 2653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 213 HIS 0.009 0.001 HIS r 74 PHE 0.020 0.002 PHE i 39 TYR 0.022 0.002 TYR d 76 ARG 0.016 0.001 ARG f 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11184 Ramachandran restraints generated. 5592 Oldfield, 0 Emsley, 5592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11184 Ramachandran restraints generated. 5592 Oldfield, 0 Emsley, 5592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1587 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 326 poor density : 1261 time to evaluate : 6.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 167 ASN cc_start: 0.8614 (t0) cc_final: 0.8276 (t0) REVERT: E 94 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8028 (pm20) REVERT: E 163 ASN cc_start: 0.8526 (t0) cc_final: 0.8058 (t0) REVERT: G 166 ASP cc_start: 0.6082 (OUTLIER) cc_final: 0.5416 (m-30) REVERT: H 1 MET cc_start: 0.4282 (tmm) cc_final: 0.2733 (mpp) REVERT: H 12 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.7144 (pp) REVERT: J 1 MET cc_start: 0.4230 (ptt) cc_final: 0.3901 (ptt) REVERT: K 105 ARG cc_start: 0.7649 (tpp-160) cc_final: 0.7335 (tpp-160) REVERT: L 1 MET cc_start: 0.6581 (pmm) cc_final: 0.5991 (pmm) REVERT: L 14 LYS cc_start: 0.7574 (mtpp) cc_final: 0.7263 (ttpt) REVERT: L 27 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8927 (pp) REVERT: L 55 MET cc_start: 0.7904 (tpp) cc_final: 0.7703 (tpt) REVERT: P 102 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6158 (mp0) REVERT: R 11 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.8724 (mp10) REVERT: R 13 ARG cc_start: 0.8511 (ttp80) cc_final: 0.7934 (ttt90) REVERT: R 16 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7403 (mm-30) REVERT: S 52 GLU cc_start: 0.7472 (tp30) cc_final: 0.7178 (tp30) REVERT: T 1 MET cc_start: 0.2706 (ptp) cc_final: 0.2218 (mtm) REVERT: T 28 ASN cc_start: 0.8210 (t0) cc_final: 0.7952 (t0) REVERT: U 96 PHE cc_start: 0.8202 (m-10) cc_final: 0.7905 (m-10) REVERT: V 9 ARG cc_start: 0.8610 (mtp180) cc_final: 0.8225 (mtm180) REVERT: Y 9 LYS cc_start: 0.8481 (mtpt) cc_final: 0.8142 (tttm) REVERT: Y 60 LYS cc_start: 0.6805 (ttmt) cc_final: 0.6499 (tttt) REVERT: b 28 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7410 (ttmt) REVERT: b 186 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8175 (mp) REVERT: b 221 VAL cc_start: 0.7927 (m) cc_final: 0.7708 (t) REVERT: c 45 LYS cc_start: 0.7901 (ptpp) cc_final: 0.7497 (mtmm) REVERT: c 100 GLN cc_start: 0.7868 (tm-30) cc_final: 0.7457 (tm-30) REVERT: d 47 ARG cc_start: 0.6097 (tpp-160) cc_final: 0.4985 (ttp-170) REVERT: d 88 GLU cc_start: 0.5904 (tt0) cc_final: 0.5650 (tt0) REVERT: d 113 GLU cc_start: 0.7795 (tt0) cc_final: 0.7318 (tt0) REVERT: d 202 GLU cc_start: 0.6928 (mt-10) cc_final: 0.6557 (tt0) REVERT: e 156 LYS cc_start: 0.8329 (mtmt) cc_final: 0.7983 (ptpt) REVERT: f 98 GLU cc_start: 0.7064 (pm20) cc_final: 0.6818 (pm20) REVERT: g 59 LEU cc_start: 0.7836 (tt) cc_final: 0.7623 (tp) REVERT: h 3 MET cc_start: 0.8377 (tpp) cc_final: 0.8098 (mmm) REVERT: h 50 LYS cc_start: 0.7691 (mmmt) cc_final: 0.7408 (mmtt) REVERT: h 67 GLN cc_start: 0.6157 (OUTLIER) cc_final: 0.5826 (pm20) REVERT: i 119 ARG cc_start: 0.7710 (mmm-85) cc_final: 0.7509 (mmm-85) REVERT: i 123 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8037 (tmt-80) REVERT: j 7 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7739 (mtm180) REVERT: k 72 ASP cc_start: 0.7309 (OUTLIER) cc_final: 0.6616 (m-30) REVERT: k 93 ARG cc_start: 0.6527 (OUTLIER) cc_final: 0.5474 (ptp-170) REVERT: o 57 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7968 (mm) REVERT: p 1 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7259 (ptm) REVERT: s 56 GLN cc_start: 0.7770 (pt0) cc_final: 0.7521 (pt0) REVERT: s 73 GLU cc_start: 0.7235 (tt0) cc_final: 0.6982 (tt0) REVERT: t 54 MET cc_start: 0.8463 (ttp) cc_final: 0.7836 (ttp) outliers start: 326 outliers final: 292 residues processed: 1457 average time/residue: 1.2812 time to fit residues: 3223.0628 Evaluate side-chains 1555 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 1248 time to evaluate : 8.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 27 GLU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 66 ASN Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain R residue 11 GLN Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 45 GLU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 65 ILE Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 82 ILE Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 14 THR Chi-restraints excluded: chain X residue 56 MET Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 46 ASP Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 48 ILE Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 3 residue 32 ILE Chi-restraints excluded: chain 3 residue 33 LEU Chi-restraints excluded: chain 3 residue 61 CYS Chi-restraints excluded: chain 4 residue 14 CYS Chi-restraints excluded: chain 4 residue 17 VAL Chi-restraints excluded: chain 5 residue 5 ILE Chi-restraints excluded: chain 5 residue 9 TYR Chi-restraints excluded: chain 5 residue 32 LEU Chi-restraints excluded: chain 5 residue 37 CYS Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 8 ASP Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 28 LYS Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 123 ASP Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 147 SER Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 191 SER Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 63 SER Chi-restraints excluded: chain c residue 119 SER Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 185 ASN Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 34 ILE Chi-restraints excluded: chain d residue 35 GLU Chi-restraints excluded: chain d residue 40 GLN Chi-restraints excluded: chain d residue 123 ILE Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 131 ASN Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain d residue 145 ILE Chi-restraints excluded: chain d residue 171 LEU Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain e residue 69 ARG Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 90 THR Chi-restraints excluded: chain e residue 100 SER Chi-restraints excluded: chain e residue 122 ASN Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain e residue 145 GLU Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 29 ILE Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 46 GLN Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 104 ILE Chi-restraints excluded: chain h residue 10 MET Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 31 LYS Chi-restraints excluded: chain h residue 36 ILE Chi-restraints excluded: chain h residue 67 GLN Chi-restraints excluded: chain h residue 74 SER Chi-restraints excluded: chain h residue 79 SER Chi-restraints excluded: chain h residue 90 ASP Chi-restraints excluded: chain h residue 104 VAL Chi-restraints excluded: chain h residue 105 SER Chi-restraints excluded: chain i residue 18 ARG Chi-restraints excluded: chain i residue 22 LYS Chi-restraints excluded: chain i residue 30 ILE Chi-restraints excluded: chain i residue 58 VAL Chi-restraints excluded: chain i residue 84 THR Chi-restraints excluded: chain i residue 90 TYR Chi-restraints excluded: chain i residue 91 ASP Chi-restraints excluded: chain i residue 112 GLU Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 123 ARG Chi-restraints excluded: chain j residue 7 ARG Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain j residue 83 THR Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 72 ASP Chi-restraints excluded: chain k residue 93 ARG Chi-restraints excluded: chain k residue 95 SER Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 109 ASN Chi-restraints excluded: chain l residue 4 VAL Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain l residue 102 LEU Chi-restraints excluded: chain l residue 115 SER Chi-restraints excluded: chain m residue 7 ILE Chi-restraints excluded: chain m residue 12 HIS Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 19 LEU Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 45 ILE Chi-restraints excluded: chain m residue 65 VAL Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain n residue 37 SER Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain o residue 61 SER Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain p residue 75 ILE Chi-restraints excluded: chain q residue 13 VAL Chi-restraints excluded: chain q residue 14 SER Chi-restraints excluded: chain q residue 17 MET Chi-restraints excluded: chain q residue 18 GLU Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 11 ILE Chi-restraints excluded: chain s residue 44 MET Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 55 ARG Chi-restraints excluded: chain s residue 67 VAL Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 27 MET Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain u residue 42 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 909 optimal weight: 5.9990 chunk 599 optimal weight: 0.5980 chunk 964 optimal weight: 5.9990 chunk 588 optimal weight: 2.9990 chunk 457 optimal weight: 5.9990 chunk 670 optimal weight: 20.0000 chunk 1012 optimal weight: 10.0000 chunk 931 optimal weight: 0.7980 chunk 806 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 622 optimal weight: 10.0000 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 117 GLN ** C 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN F 27 GLN ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 66 ASN Q 37 GLN Q 71 GLN ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 12 GLN ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 45 GLN ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 93 ASN ** b 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 121 HIS i 37 GLN l 5 ASN l 112 GLN o 35 GLN t 13 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 158944 Z= 0.264 Angle : 0.631 27.886 238049 Z= 0.324 Chirality : 0.039 2.114 30459 Planarity : 0.005 0.062 12565 Dihedral : 23.651 179.863 80245 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.32 % Favored : 92.50 % Rotamer: Outliers : 6.27 % Allowed : 24.79 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.16 % 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: -1.10 (0.11), residues: 5592 helix: 0.71 (0.12), residues: 1889 sheet: -0.71 (0.16), residues: 1039 loop : -1.83 (0.11), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 248 HIS 0.011 0.001 HIS J 80 PHE 0.016 0.002 PHE i 39 TYR 0.020 0.002 TYR d 76 ARG 0.016 0.000 ARG f 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11184 Ramachandran restraints generated. 5592 Oldfield, 0 Emsley, 5592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11184 Ramachandran restraints generated. 5592 Oldfield, 0 Emsley, 5592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1550 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 1258 time to evaluate : 6.399 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: D 167 ASN cc_start: 0.8592 (t0) cc_final: 0.8236 (t0) REVERT: E 94 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8009 (pm20) REVERT: E 163 ASN cc_start: 0.8546 (t0) cc_final: 0.8074 (t0) REVERT: G 166 ASP cc_start: 0.5950 (OUTLIER) cc_final: 0.5348 (m-30) REVERT: H 1 MET cc_start: 0.4199 (tmm) cc_final: 0.2802 (mpp) REVERT: H 12 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6995 (pp) REVERT: J 1 MET cc_start: 0.4121 (ptt) cc_final: 0.3838 (ptt) REVERT: K 105 ARG cc_start: 0.7659 (tpp-160) cc_final: 0.7326 (tpp-160) REVERT: L 1 MET cc_start: 0.6507 (pmm) cc_final: 0.5970 (pmm) REVERT: L 14 LYS cc_start: 0.7576 (mtpp) cc_final: 0.7263 (ttpt) REVERT: L 27 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8958 (pp) REVERT: P 102 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6149 (mp0) REVERT: R 11 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.8474 (mp10) REVERT: R 13 ARG cc_start: 0.8511 (ttp80) cc_final: 0.7946 (ttt90) REVERT: R 16 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7581 (mm-30) REVERT: S 52 GLU cc_start: 0.7584 (tp30) cc_final: 0.7281 (tp30) REVERT: T 1 MET cc_start: 0.2668 (ptp) cc_final: 0.2178 (mtm) REVERT: T 28 ASN cc_start: 0.8200 (t0) cc_final: 0.7952 (t0) REVERT: U 96 PHE cc_start: 0.8179 (m-10) cc_final: 0.7877 (m-10) REVERT: U 101 GLU cc_start: 0.6640 (mp0) cc_final: 0.6268 (mp0) REVERT: V 9 ARG cc_start: 0.8580 (mtp180) cc_final: 0.8173 (mtm180) REVERT: Y 9 LYS cc_start: 0.8421 (mtpt) cc_final: 0.8149 (tttm) REVERT: Y 28 LEU cc_start: 0.8558 (mm) cc_final: 0.8328 (tp) REVERT: Y 60 LYS cc_start: 0.6782 (ttmt) cc_final: 0.6466 (tttt) REVERT: b 186 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8224 (mp) REVERT: b 221 VAL cc_start: 0.7934 (m) cc_final: 0.7727 (t) REVERT: c 45 LYS cc_start: 0.7855 (ptpp) cc_final: 0.7468 (mtmm) REVERT: c 100 GLN cc_start: 0.7832 (tm-30) cc_final: 0.7452 (tm-30) REVERT: d 47 ARG cc_start: 0.6103 (tpp-160) cc_final: 0.4975 (ttp-170) REVERT: d 113 GLU cc_start: 0.7743 (tt0) cc_final: 0.7297 (tt0) REVERT: d 202 GLU cc_start: 0.6957 (mt-10) cc_final: 0.6567 (tt0) REVERT: e 156 LYS cc_start: 0.8304 (mtmt) cc_final: 0.7967 (ptpt) REVERT: f 98 GLU cc_start: 0.7006 (pm20) cc_final: 0.6748 (pm20) REVERT: h 3 MET cc_start: 0.8279 (tpp) cc_final: 0.8031 (mmm) REVERT: h 67 GLN cc_start: 0.6057 (OUTLIER) cc_final: 0.5734 (pm20) REVERT: i 123 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7991 (tmt-80) REVERT: j 7 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7704 (mtm180) REVERT: k 72 ASP cc_start: 0.7222 (OUTLIER) cc_final: 0.6637 (m-30) REVERT: k 93 ARG cc_start: 0.6440 (OUTLIER) cc_final: 0.5311 (ptp-170) REVERT: m 42 ASP cc_start: 0.7228 (t0) cc_final: 0.6988 (t0) REVERT: o 57 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7990 (mm) REVERT: p 1 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7234 (ptm) REVERT: r 25 ASP cc_start: 0.7696 (p0) cc_final: 0.7487 (p0) REVERT: s 56 GLN cc_start: 0.7778 (pt0) cc_final: 0.7537 (pt0) REVERT: s 73 GLU cc_start: 0.7291 (tt0) cc_final: 0.7019 (tt0) REVERT: t 54 MET cc_start: 0.8437 (ttp) cc_final: 0.7796 (ttp) outliers start: 292 outliers final: 272 residues processed: 1427 average time/residue: 1.2967 time to fit residues: 3185.1587 Evaluate side-chains 1533 residues out of total 4653 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 1247 time to evaluate : 6.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 94 VAL Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 46 ARG Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 17 VAL Chi-restraints excluded: chain P residue 27 GLU Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 66 ASN Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 81 VAL Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 110 ILE Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 117 LEU Chi-restraints excluded: chain R residue 11 GLN Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 31 GLU Chi-restraints excluded: chain R residue 45 GLU Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 66 HIS Chi-restraints excluded: chain R residue 98 ILE Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 12 ILE Chi-restraints excluded: chain U residue 65 ILE Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 17 SER Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain W residue 31 VAL Chi-restraints excluded: chain W residue 43 THR Chi-restraints excluded: chain W residue 64 ASP Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 82 ILE Chi-restraints excluded: chain X residue 2 SER Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 56 MET Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 57 VAL Chi-restraints excluded: chain 0 residue 9 THR Chi-restraints excluded: chain 0 residue 46 ASP Chi-restraints excluded: chain 1 residue 12 VAL Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 48 ILE Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 3 residue 28 ASN Chi-restraints excluded: chain 3 residue 32 ILE Chi-restraints excluded: chain 3 residue 33 LEU Chi-restraints excluded: chain 3 residue 61 CYS Chi-restraints excluded: chain 4 residue 14 CYS Chi-restraints excluded: chain 4 residue 17 VAL Chi-restraints excluded: chain 5 residue 5 ILE Chi-restraints excluded: chain 5 residue 9 TYR Chi-restraints excluded: chain 5 residue 37 CYS Chi-restraints excluded: chain b residue 4 VAL Chi-restraints excluded: chain b residue 8 ASP Chi-restraints excluded: chain b residue 38 VAL Chi-restraints excluded: chain b residue 123 ASP Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 147 SER Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 191 SER Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 63 SER Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 34 ILE Chi-restraints excluded: chain d residue 35 GLU Chi-restraints excluded: chain d residue 40 GLN Chi-restraints excluded: chain d residue 123 ILE Chi-restraints excluded: chain d residue 125 VAL Chi-restraints excluded: chain d residue 143 VAL Chi-restraints excluded: chain d residue 144 SER Chi-restraints excluded: chain d residue 145 ILE Chi-restraints excluded: chain d residue 171 LEU Chi-restraints excluded: chain e residue 32 SER Chi-restraints excluded: chain e residue 69 ARG Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 90 THR Chi-restraints excluded: chain e residue 100 SER Chi-restraints excluded: chain e residue 122 ASN Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain e residue 145 GLU Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 29 ILE Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain g residue 104 ILE Chi-restraints excluded: chain h residue 10 MET Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 31 LYS Chi-restraints excluded: chain h residue 36 ILE Chi-restraints excluded: chain h residue 67 GLN Chi-restraints excluded: chain h residue 74 SER Chi-restraints excluded: chain h residue 79 SER Chi-restraints excluded: chain h residue 90 ASP Chi-restraints excluded: chain h residue 104 VAL Chi-restraints excluded: chain h residue 105 SER Chi-restraints excluded: chain i residue 18 ARG Chi-restraints excluded: chain i residue 22 LYS Chi-restraints excluded: chain i residue 30 ILE Chi-restraints excluded: chain i residue 84 THR Chi-restraints excluded: chain i residue 90 TYR Chi-restraints excluded: chain i residue 91 ASP Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 123 ARG Chi-restraints excluded: chain j residue 7 ARG Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 40 ILE Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain j residue 83 THR Chi-restraints excluded: chain j residue 92 LEU Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 50 SER Chi-restraints excluded: chain k residue 55 SER Chi-restraints excluded: chain k residue 72 ASP Chi-restraints excluded: chain k residue 93 ARG Chi-restraints excluded: chain k residue 95 SER Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 109 ASN Chi-restraints excluded: chain l residue 4 VAL Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 64 THR Chi-restraints excluded: chain l residue 102 LEU Chi-restraints excluded: chain l residue 115 SER Chi-restraints excluded: chain m residue 7 ILE Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 45 ILE Chi-restraints excluded: chain m residue 65 VAL Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain m residue 108 THR Chi-restraints excluded: chain n residue 37 SER Chi-restraints excluded: chain n residue 56 SER Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 57 LEU Chi-restraints excluded: chain o residue 61 SER Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain p residue 75 ILE Chi-restraints excluded: chain q residue 13 VAL Chi-restraints excluded: chain q residue 17 MET Chi-restraints excluded: chain q residue 18 GLU Chi-restraints excluded: chain q residue 33 ILE Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 11 ILE Chi-restraints excluded: chain s residue 44 MET Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 55 ARG Chi-restraints excluded: chain s residue 67 VAL Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 27 MET Chi-restraints excluded: chain t residue 30 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1016 random chunks: chunk 494 optimal weight: 1.9990 chunk 640 optimal weight: 20.0000 chunk 858 optimal weight: 4.9990 chunk 246 optimal weight: 10.0000 chunk 743 optimal weight: 10.0000 chunk 119 optimal weight: 8.9990 chunk 223 optimal weight: 8.9990 chunk 807 optimal weight: 0.4980 chunk 337 optimal weight: 0.9990 chunk 828 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 117 GLN ** C 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 66 ASN Q 37 GLN Q 71 GLN ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 12 GLN 1 45 GLN ** 4 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 131 ASN i 37 GLN l 5 ASN l 112 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.138864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.107863 restraints weight = 252219.103| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.03 r_work: 0.3114 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 158944 Z= 0.252 Angle : 0.618 27.846 238049 Z= 0.317 Chirality : 0.039 2.111 30459 Planarity : 0.005 0.064 12565 Dihedral : 23.627 179.788 80245 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.57 % Favored : 92.27 % Rotamer: Outliers : 6.42 % Allowed : 24.60 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.16 % 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: -1.04 (0.11), residues: 5592 helix: 0.79 (0.12), residues: 1891 sheet: -0.72 (0.16), residues: 1039 loop : -1.80 (0.11), residues: 2662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 248 HIS 0.007 0.001 HIS r 74 PHE 0.015 0.001 PHE Y 26 TYR 0.022 0.002 TYR c 42 ARG 0.015 0.000 ARG f 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 47011.12 seconds wall clock time: 816 minutes 43.61 seconds (49003.61 seconds total)