Starting phenix.real_space_refine on Mon Apr 15 11:06:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v39_21030/04_2024/6v39_21030_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v39_21030/04_2024/6v39_21030.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v39_21030/04_2024/6v39_21030_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v39_21030/04_2024/6v39_21030_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v39_21030/04_2024/6v39_21030_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v39_21030/04_2024/6v39_21030.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v39_21030/04_2024/6v39_21030.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v39_21030/04_2024/6v39_21030_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v39_21030/04_2024/6v39_21030_updated.pdb" } resolution = 3.04 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= 0.007 sd= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 537 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 1 6.06 5 P 4612 5.49 5 Mg 114 5.21 5 S 140 5.16 5 Na 1 4.78 5 C 70763 2.51 5 N 26299 2.21 5 O 39967 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 ASP 3": "OD1" <-> "OD2" Residue "0 ARG 6": "NH1" <-> "NH2" Residue "0 GLU 28": "OE1" <-> "OE2" Residue "0 ARG 40": "NH1" <-> "NH2" Residue "1 ARG 3": "NH1" <-> "NH2" Residue "1 GLU 9": "OE1" <-> "OE2" Residue "1 ARG 12": "NH1" <-> "NH2" Residue "1 ARG 14": "NH1" <-> "NH2" Residue "1 ARG 33": "NH1" <-> "NH2" Residue "1 ARG 39": "NH1" <-> "NH2" Residue "2 ARG 7": "NH1" <-> "NH2" Residue "2 ARG 23": "NH1" <-> "NH2" Residue "2 ARG 39": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "2 ARG 58": "NH1" <-> "NH2" Residue "3 ARG 18": "NH1" <-> "NH2" Residue "3 ARG 24": "NH1" <-> "NH2" Residue "3 ARG 32": "NH1" <-> "NH2" Residue "3 ARG 36": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C ARG 87": "NH1" <-> "NH2" Residue "C TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "C ARG 111": "NH1" <-> "NH2" Residue "C ARG 133": "NH1" <-> "NH2" Residue "C ARG 167": "NH1" <-> "NH2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C GLU 194": "OE1" <-> "OE2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "C ARG 238": "NH1" <-> "NH2" Residue "C ARG 258": "NH1" <-> "NH2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "D ARG 8": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ASP 18": "OD1" <-> "OD2" Residue "D ARG 56": "NH1" <-> "NH2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D GLU 87": "OE1" <-> "OE2" Residue "D ARG 93": "NH1" <-> "NH2" Residue "D ARG 157": "NH1" <-> "NH2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D ASP 203": "OD1" <-> "OD2" Residue "D ARG 207": "NH1" <-> "NH2" Residue "E GLU 15": "OE1" <-> "OE2" Residue "E PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 20": "NH1" <-> "NH2" Residue "E TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 48": "NH1" <-> "NH2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "E ARG 68": "NH1" <-> "NH2" Residue "E ARG 113": "NH1" <-> "NH2" Residue "E GLU 121": "OE1" <-> "OE2" Residue "E GLU 132": "OE1" <-> "OE2" Residue "E ARG 161": "NH1" <-> "NH2" Residue "E ASP 167": "OD1" <-> "OD2" Residue "F TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 10": "OD1" <-> "OD2" Residue "F GLU 18": "OE1" <-> "OE2" Residue "F GLU 27": "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 ASP 81": "OD1" <-> "OD2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 102": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F ASP 142": "OD1" <-> "OD2" Residue "F ASP 147": "OD1" <-> "OD2" Residue "F ARG 150": "NH1" <-> "NH2" Residue "F ARG 161": "NH1" <-> "NH2" Residue "F ASP 163": "OD1" <-> "OD2" Residue "F ASP 164": "OD1" <-> "OD2" Residue "F ARG 171": "NH1" <-> "NH2" Residue "F PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G ARG 22": "NH1" <-> "NH2" Residue "G GLU 25": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G ARG 69": "NH1" <-> "NH2" Residue "G GLU 81": "OE1" <-> "OE2" Residue "G GLU 84": "OE1" <-> "OE2" Residue "G GLU 130": "OE1" <-> "OE2" Residue "G ARG 163": "NH1" <-> "NH2" Residue "G ARG 171": "NH1" <-> "NH2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 48": "OE1" <-> "OE2" Residue "H GLU 55": "OE1" <-> "OE2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "I PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 27": "NH1" <-> "NH2" Residue "I ARG 34": "NH1" <-> "NH2" Residue "I ARG 35": "NH1" <-> "NH2" Residue "I ASP 52": "OD1" <-> "OD2" Residue "I ARG 76": "NH1" <-> "NH2" Residue "I PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 103": "NH1" <-> "NH2" Residue "I GLU 129": "OE1" <-> "OE2" Residue "J ARG 18": "NH1" <-> "NH2" Residue "J ARG 31": "NH1" <-> "NH2" Residue "J ARG 49": "NH1" <-> "NH2" Residue "J ASP 56": "OD1" <-> "OD2" Residue "J ARG 71": "NH1" <-> "NH2" Residue "J ASP 73": "OD1" <-> "OD2" Residue "J ARG 104": "NH1" <-> "NH2" Residue "J GLU 105": "OE1" <-> "OE2" Residue "J GLU 109": "OE1" <-> "OE2" Residue "K ARG 16": "NH1" <-> "NH2" Residue "K GLU 17": "OE1" <-> "OE2" Residue "K ARG 19": "NH1" <-> "NH2" Residue "K ASP 90": "OD1" <-> "OD2" Residue "K ARG 104": "NH1" <-> "NH2" Residue "K ASP 106": "OD1" <-> "OD2" Residue "K ARG 109": "NH1" <-> "NH2" Residue "K ARG 111": "NH1" <-> "NH2" Residue "K ARG 120": "NH1" <-> "NH2" Residue "K GLU 146": "OE1" <-> "OE2" Residue "L ARG 16": "NH1" <-> "NH2" Residue "L PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 38": "OE1" <-> "OE2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 45": "NH1" <-> "NH2" Residue "L ARG 52": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L GLU 91": "OE1" <-> "OE2" Residue "L TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 112": "OD1" <-> "OD2" Residue "L ARG 115": "NH1" <-> "NH2" Residue "L GLU 116": "OE1" <-> "OE2" Residue "L PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 12": "NH1" <-> "NH2" Residue "M ARG 17": "NH1" <-> "NH2" Residue "M GLU 22": "OE1" <-> "OE2" Residue "M GLU 32": "OE1" <-> "OE2" Residue "M ARG 46": "NH1" <-> "NH2" Residue "M ARG 63": "NH1" <-> "NH2" Residue "M ARG 64": "NH1" <-> "NH2" Residue "M ARG 96": "NH1" <-> "NH2" Residue "M ARG 118": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 10": "NH1" <-> "NH2" Residue "N ARG 20": "NH1" <-> "NH2" Residue "N ARG 34": "NH1" <-> "NH2" Residue "N TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 68": "OE1" <-> "OE2" Residue "N ARG 80": "NH1" <-> "NH2" Residue "N ARG 93": "NH1" <-> "NH2" Residue "N ARG 110": "NH1" <-> "NH2" Residue "N GLU 111": "OE1" <-> "OE2" Residue "N GLU 115": "OE1" <-> "OE2" Residue "N PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 56": "NH1" <-> "NH2" Residue "O GLU 88": "OE1" <-> "OE2" Residue "O ARG 91": "NH1" <-> "NH2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O ARG 97": "NH1" <-> "NH2" Residue "O ARG 112": "NH1" <-> "NH2" Residue "P ARG 3": "NH1" <-> "NH2" Residue "P ARG 6": "NH1" <-> "NH2" Residue "P ARG 12": "NH1" <-> "NH2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 51": "NH1" <-> "NH2" Residue "P ARG 70": "NH1" <-> "NH2" Residue "P TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 78": "NH1" <-> "NH2" Residue "P PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 111": "OE1" <-> "OE2" Residue "Q TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 16": "OE1" <-> "OE2" Residue "Q GLU 23": "OE1" <-> "OE2" Residue "Q GLU 28": "OE1" <-> "OE2" Residue "Q ASP 37": "OD1" <-> "OD2" Residue "Q GLU 62": "OE1" <-> "OE2" Residue "Q ARG 68": "NH1" <-> "NH2" Residue "Q ASP 70": "OD1" <-> "OD2" Residue "Q ARG 73": "NH1" <-> "NH2" Residue "Q ARG 78": "NH1" <-> "NH2" Residue "Q ARG 79": "NH1" <-> "NH2" Residue "Q TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 2": "OE1" <-> "OE2" Residue "R ARG 8": "NH1" <-> "NH2" Residue "R ARG 25": "NH1" <-> "NH2" Residue "R GLU 52": "OE1" <-> "OE2" Residue "R GLU 59": "OE1" <-> "OE2" Residue "R ASP 68": "OD1" <-> "OD2" Residue "R ASP 77": "OD1" <-> "OD2" Residue "R ARG 95": "NH1" <-> "NH2" Residue "S ARG 5": "NH1" <-> "NH2" Residue "S GLU 17": "OE1" <-> "OE2" Residue "S ASP 24": "OD1" <-> "OD2" Residue "S GLU 47": "OE1" <-> "OE2" Residue "S PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 53": "OE1" <-> "OE2" Residue "S ARG 68": "NH1" <-> "NH2" Residue "S ARG 76": "NH1" <-> "NH2" Residue "S ASP 78": "OD1" <-> "OD2" Residue "T ARG 31": "NH1" <-> "NH2" Residue "T GLU 35": "OE1" <-> "OE2" Residue "T TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 99": "OE1" <-> "OE2" Residue "U PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 11": "NH1" <-> "NH2" Residue "U GLU 13": "OE1" <-> "OE2" Residue "U ARG 22": "NH1" <-> "NH2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U GLU 62": "OE1" <-> "OE2" Residue "U GLU 63": "OE1" <-> "OE2" Residue "U GLU 66": "OE1" <-> "OE2" Residue "U GLU 74": "OE1" <-> "OE2" Residue "U PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 44": "OE1" <-> "OE2" Residue "V PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 37": "NH1" <-> "NH2" Residue "W ARG 48": "NH1" <-> "NH2" Residue "X ASP 5": "OD1" <-> "OD2" Residue "X GLU 12": "OE1" <-> "OE2" Residue "X GLU 13": "OE1" <-> "OE2" Residue "X ASP 19": "OD1" <-> "OD2" Residue "X PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 27": "NH1" <-> "NH2" Residue "X ARG 29": "NH1" <-> "NH2" Residue "X ARG 52": "NH1" <-> "NH2" Residue "X GLU 59": "OE1" <-> "OE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 30": "NH1" <-> "NH2" Residue "Z ARG 7": "NH1" <-> "NH2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 16": "NH1" <-> "NH2" Residue "Z ARG 17": "NH1" <-> "NH2" Residue "Z GLU 35": "OE1" <-> "OE2" Residue "Z ARG 39": "NH1" <-> "NH2" Residue "Z ASP 45": "OD1" <-> "OD2" Residue "Z ARG 51": "NH1" <-> "NH2" Residue "b ARG 9": "NH1" <-> "NH2" Residue "b ARG 30": "NH1" <-> "NH2" Residue "b PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 37": "NH1" <-> "NH2" Residue "b ARG 76": "NH1" <-> "NH2" Residue "b ARG 83": "NH1" <-> "NH2" Residue "b ARG 88": "NH1" <-> "NH2" Residue "b ARG 110": "NH1" <-> "NH2" Residue "b ASP 118": "OD1" <-> "OD2" Residue "b PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 134": "NH1" <-> "NH2" Residue "b GLU 138": "OE1" <-> "OE2" Residue "b ARG 141": "NH1" <-> "NH2" Residue "b GLU 147": "OE1" <-> "OE2" Residue "b ARG 148": "NH1" <-> "NH2" Residue "b ASP 161": "OD1" <-> "OD2" Residue "b ASP 167": "OD1" <-> "OD2" Residue "b ASP 169": "OD1" <-> "OD2" Residue "b GLU 171": "OE1" <-> "OE2" Residue "b ASP 199": "OD1" <-> "OD2" Residue "b ASP 207": "OD1" <-> "OD2" Residue "b ARG 210": "NH1" <-> "NH2" Residue "b TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 11": "NH1" <-> "NH2" Residue "c TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 36": "OD1" <-> "OD2" Residue "c GLU 41": "OE1" <-> "OE2" Residue "c GLU 90": "OE1" <-> "OE2" Residue "c GLU 105": "OE1" <-> "OE2" Residue "c ARG 108": "NH1" <-> "NH2" Residue "c ASP 110": "OD1" <-> "OD2" Residue "c ASP 112": "OD1" <-> "OD2" Residue "c ARG 114": "NH1" <-> "NH2" Residue "c ARG 131": "NH1" <-> "NH2" Residue "c ARG 132": "NH1" <-> "NH2" Residue "c ARG 136": "NH1" <-> "NH2" Residue "c ARG 143": "NH1" <-> "NH2" Residue "c ARG 156": "NH1" <-> "NH2" Residue "c GLU 161": "OE1" <-> "OE2" Residue "c ARG 169": "NH1" <-> "NH2" Residue "c GLU 170": "OE1" <-> "OE2" Residue "c ARG 188": "NH1" <-> "NH2" Residue "c ARG 204": "NH1" <-> "NH2" Residue "d TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 14": "NH1" <-> "NH2" Residue "d GLU 15": "OE1" <-> "OE2" Residue "d PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 46": "NH1" <-> "NH2" Residue "d TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 58": "NH1" <-> "NH2" Residue "d ARG 64": "NH1" <-> "NH2" Residue "d TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 80": "OE1" <-> "OE2" Residue "d ARG 106": "NH1" <-> "NH2" Residue "d ARG 113": "NH1" <-> "NH2" Residue "d ARG 123": "NH1" <-> "NH2" Residue "d ARG 130": "NH1" <-> "NH2" Residue "d ASP 143": "OD1" <-> "OD2" Residue "d GLU 149": "OE1" <-> "OE2" Residue "d GLU 174": "OE1" <-> "OE2" Residue "d GLU 181": "OE1" <-> "OE2" Residue "d ASP 189": "OD1" <-> "OD2" Residue "d ASP 192": "OD1" <-> "OD2" Residue "e PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 49": "NH1" <-> "NH2" Residue "e ARG 53": "NH1" <-> "NH2" Residue "e ARG 92": "NH1" <-> "NH2" Residue "e ARG 111": "NH1" <-> "NH2" Residue "e GLU 115": "OE1" <-> "OE2" Residue "e PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 144": "NH1" <-> "NH2" Residue "e GLU 161": "OE1" <-> "OE2" Residue "e GLU 162": "OE1" <-> "OE2" Residue "f ASP 13": "OD1" <-> "OD2" Residue "f GLU 73": "OE1" <-> "OE2" Residue "f GLU 75": "OE1" <-> "OE2" Residue "f GLU 76": "OE1" <-> "OE2" Residue "f ARG 79": "NH1" <-> "NH2" Residue "f TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 91": "NH1" <-> "NH2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "g ARG 10": "NH1" <-> "NH2" Residue "g ASP 15": "OD1" <-> "OD2" Residue "g GLU 52": "OE1" <-> "OE2" Residue "g GLU 60": "OE1" <-> "OE2" Residue "g PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 67": "OE1" <-> "OE2" Residue "g ARG 95": "NH1" <-> "NH2" Residue "g ARG 102": "NH1" <-> "NH2" Residue "g ASP 106": "OD1" <-> "OD2" Residue "g ARG 119": "NH1" <-> "NH2" Residue "g ASP 126": "OD1" <-> "OD2" Residue "g ARG 138": "NH1" <-> "NH2" Residue "g ASP 140": "OD1" <-> "OD2" Residue "h ASP 5": "OD1" <-> "OD2" Residue "h ASP 9": "OD1" <-> "OD2" Residue "h ARG 13": "NH1" <-> "NH2" Residue "h GLU 54": "OE1" <-> "OE2" Residue "h TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 88": "NH1" <-> "NH2" Residue "h ASP 114": "OD1" <-> "OD2" Residue "h ARG 115": "NH1" <-> "NH2" Residue "h ARG 118": "NH1" <-> "NH2" Residue "i ARG 9": "NH1" <-> "NH2" Residue "i PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 40": "OE1" <-> "OE2" Residue "i GLU 54": "OE1" <-> "OE2" Residue "i ASP 105": "OD1" <-> "OD2" Residue "i GLU 108": "OE1" <-> "OE2" Residue "i ARG 122": "NH1" <-> "NH2" Residue "j ARG 5": "NH1" <-> "NH2" Residue "j ARG 7": "NH1" <-> "NH2" Residue "j ASP 14": "OD1" <-> "OD2" Residue "j ARG 16": "NH1" <-> "NH2" Residue "j GLU 27": "OE1" <-> "OE2" Residue "j ARG 45": "NH1" <-> "NH2" Residue "j GLU 47": "OE1" <-> "OE2" Residue "j TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 72": "NH1" <-> "NH2" Residue "j ASP 81": "OD1" <-> "OD2" Residue "j ASP 91": "OD1" <-> "OD2" Residue "j ASP 97": "OD1" <-> "OD2" Residue "k ARG 13": "NH1" <-> "NH2" Residue "k PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 36": "NH1" <-> "NH2" Residue "k ARG 97": "NH1" <-> "NH2" Residue "k TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 111": "OD1" <-> "OD2" Residue "l ARG 30": "NH1" <-> "NH2" Residue "l ARG 31": "NH1" <-> "NH2" Residue "l TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 50": "NH1" <-> "NH2" Residue "l ARG 54": "NH1" <-> "NH2" Residue "l GLU 76": "OE1" <-> "OE2" Residue "l TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 99": "NH1" <-> "NH2" Residue "l ASP 109": "OD1" <-> "OD2" Residue "m ARG 3": "NH1" <-> "NH2" Residue "m ASP 11": "OD1" <-> "OD2" Residue "m PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 41": "OE1" <-> "OE2" Residue "m ARG 46": "NH1" <-> "NH2" Residue "m ASP 49": "OD1" <-> "OD2" Residue "m ASP 50": "OD1" <-> "OD2" Residue "m ARG 57": "NH1" <-> "NH2" Residue "m ARG 79": "NH1" <-> "NH2" Residue "m TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 98": "NH1" <-> "NH2" Residue "m ARG 101": "NH1" <-> "NH2" Residue "m ARG 107": "NH1" <-> "NH2" Residue "n GLU 10": "OE1" <-> "OE2" Residue "n GLU 14": "OE1" <-> "OE2" Residue "n GLU 26": "OE1" <-> "OE2" Residue "n ARG 59": "NH1" <-> "NH2" Residue "n ARG 61": "NH1" <-> "NH2" Residue "n ASP 86": "OD1" <-> "OD2" Residue "o PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 19": "OE1" <-> "OE2" Residue "o ARG 58": "NH1" <-> "NH2" Residue "o ARG 64": "NH1" <-> "NH2" Residue "o GLU 76": "OE1" <-> "OE2" Residue "p ARG 46": "NH1" <-> "NH2" Residue "p PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 87": "OE1" <-> "OE2" Residue "q ASP 19": "OD1" <-> "OD2" Residue "q ARG 40": "NH1" <-> "NH2" Residue "q ARG 41": "NH1" <-> "NH2" Residue "q ASP 58": "OD1" <-> "OD2" Residue "r TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 22": "OD1" <-> "OD2" Residue "r ARG 43": "NH1" <-> "NH2" Residue "r ARG 53": "NH1" <-> "NH2" Residue "r ARG 63": "NH1" <-> "NH2" Residue "s PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 12": "OD1" <-> "OD2" Residue "s PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 20": "OE1" <-> "OE2" Residue "s ARG 28": "NH1" <-> "NH2" Residue "s GLU 64": "OE1" <-> "OE2" Residue "s ARG 81": "NH1" <-> "NH2" Residue "t ARG 12": "NH1" <-> "NH2" Residue "t ARG 18": "NH1" <-> "NH2" Residue "t ARG 29": "NH1" <-> "NH2" Residue "t ARG 34": "NH1" <-> "NH2" Residue "t ASP 43": "OD1" <-> "OD2" Residue "t TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 49": "OE1" <-> "OE2" Residue "t ASP 59": "OD1" <-> "OD2" Residue "t ARG 78": "NH1" <-> "NH2" Residue "u ARG 35": "NH1" <-> "NH2" Residue "u PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 45": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 141897 Number of models: 1 Model: "" Number of chains: 70 Chain: "0" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 427 Classifications: {'peptide': 51} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "1" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "2" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "3" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 295 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "AN" Number of atoms: 62023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2892, 62023 Classifications: {'RNA': 2892} Modifications used: {'5*END': 1, 'rna2p': 3, 'rna2p_pur': 257, 'rna2p_pyr': 144, 'rna3p': 12, 'rna3p_pur': 1391, 'rna3p_pyr': 1085} Link IDs: {'rna2p': 404, 'rna3p': 2487} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2450 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 54, 'rna3p_pyr': 48} Link IDs: {'rna2p': 13, 'rna3p': 101} Chain: "C" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2096 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 16, 'TRANS': 253} Chain: "D" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1572 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 205} Chain: "E" Number of atoms: 1419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1419 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 6, 'TRANS': 179} Chain: "F" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1381 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 6, 'TRANS': 168} Chain: "G" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1318 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 8, 'TRANS': 165} Chain: "H" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 458 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "I" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1125 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "J" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "K" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1089 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 142} Chain: "L" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1087 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 130} Chain: "M" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "N" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 857 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "O" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 919 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "P" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 934 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "Q" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 807 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "R" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 826 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain: "S" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 702 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "T" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 749 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "U" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 760 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "V" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 598 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "W" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 632 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "X" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 498 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "Y" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 463 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "Z" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 456 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "sN" Number of atoms: 32782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1528, 32782 Classifications: {'RNA': 1528} Modifications used: {'5*END': 1, 'rna2p': 1, 'rna2p_pur': 109, 'rna2p_pyr': 81, 'rna3p': 8, 'rna3p_pur': 754, 'rna3p_pyr': 575} Link IDs: {'rna2p': 190, 'rna3p': 1337} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 6 Chain: "b" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1769 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "c" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain: "d" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1631 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 200} Chain: "e" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1129 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain: "f" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 793 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "g" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1111 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "h" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 985 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "i" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 995 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "j" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 801 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "k" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 862 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "l" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 115} Chain: "m" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 903 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "n" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 792 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "o" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 705 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "p" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 649 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "q" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 630 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "r" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 438 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "s" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "t" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 658 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "u" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 182 Classifications: {'peptide': 21} Link IDs: {'PTRANS': 1, 'TRANS': 19} Chain: "v" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1636 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p': 4, 'rna3p_pur': 34, 'rna3p_pyr': 30} Link IDs: {'rna2p': 8, 'rna3p': 68} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "w" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "AN" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 70 Unusual residues: {' MG': 59, ' NA': 1} Classifications: {'peptide': 1, 'undetermined': 60} Link IDs: {None: 60} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "sN" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Unusual residues: {' MG': 55} Classifications: {'undetermined': 55} Link IDs: {None: 54} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AN" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 193 Classifications: {'water': 193} Link IDs: {None: 192} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "sN" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "s" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1382 SG CYS 3 11 183.366 131.130 135.791 1.00 71.08 S ATOM 1503 SG CYS 3 27 183.703 127.406 135.128 1.00 74.75 S Time building chain proxies: 54.37, per 1000 atoms: 0.38 Number of scatterers: 141897 At special positions: 0 Unit cell: (231.952, 245.784, 273.448, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 S 140 16.00 P 4612 15.00 Mg 114 11.99 Na 1 11.00 O 39967 8.00 N 26299 7.00 C 70763 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS l 34 " - pdb=" SG CYS l 53 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 59.59 Conformation dependent library (CDL) restraints added in 6.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 27 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 11 " pdb="ZN ZN 3 101 " - pdb=" ND1 HIS 3 33 " 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9996 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: 170 helices and 64 sheets defined 39.0% alpha, 18.6% beta 1403 base pairs and 2346 stacking pairs defined. Time for finding SS restraints: 71.22 Creating SS restraints... Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 25 removed outlier: 4.186A pdb=" N THR 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LYS 1 25 " --> pdb=" O ARG 1 21 " (cutoff:3.500A) Processing helix chain '1' and resid 26 through 38 Processing helix chain '2' and resid 7 through 14 Processing helix chain '2' and resid 31 through 36 removed outlier: 4.562A pdb=" N LYS 2 35 " --> pdb=" O ILE 2 31 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N SER 2 36 " --> pdb=" O LEU 2 32 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 31 through 36' Processing helix chain '2' and resid 37 through 44 removed outlier: 4.030A pdb=" N ARG 2 44 " --> pdb=" O ILE 2 40 " (cutoff:3.500A) Processing helix chain '2' and resid 50 through 62 removed outlier: 4.505A pdb=" N ALA 2 55 " --> pdb=" O VAL 2 51 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N SER 2 56 " --> pdb=" O SER 2 52 " (cutoff:3.500A) Proline residue: 2 62 - end of helix Processing helix chain 'C' and resid 10 through 16 removed outlier: 5.215A pdb=" N PHE C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N VAL C 16 " --> pdb=" O GLY C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.557A pdb=" N VAL C 34 " --> pdb=" O TYR C 30 " (cutoff:3.500A) removed outlier: 5.472A 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 Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 207 through 215 removed outlier: 4.024A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 3.938A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.322A 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 265 removed outlier: 5.331A pdb=" N THR C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LYS C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 260 through 265' Processing helix chain 'D' and resid 57 through 62 removed outlier: 5.485A pdb=" N THR D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 73 removed outlier: 3.688A pdb=" N ALA D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 91 removed outlier: 4.019A pdb=" N GLU D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 100 through 105 removed outlier: 3.604A pdb=" N PHE D 104 " --> pdb=" O VAL D 101 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N THR D 105 " --> pdb=" O ASP D 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 20 removed outlier: 3.547A pdb=" N ARG E 20 " --> pdb=" O VAL E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 39 removed outlier: 3.641A pdb=" N GLY E 38 " --> pdb=" O TYR E 34 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG E 39 " --> pdb=" O LEU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 52 removed outlier: 6.144A pdb=" N SER E 52 " --> pdb=" O ARG E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 115 Processing helix chain 'E' and resid 129 through 141 removed outlier: 3.669A pdb=" N LEU E 133 " --> pdb=" O LYS E 129 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU E 140 " --> pdb=" O LYS E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 164 removed outlier: 4.690A pdb=" N ASN E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU E 163 " --> pdb=" O ALA E 159 " (cutoff:3.500A) Proline residue: E 164 - end of helix Processing helix chain 'E' and resid 175 through 183 removed outlier: 5.733A pdb=" N ASP E 183 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 199 Processing helix chain 'F' and resid 5 through 21 Processing helix chain 'F' and resid 42 through 47 removed outlier: 4.698A pdb=" N ASP F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 61 removed outlier: 3.903A pdb=" N GLY F 52 " --> pdb=" O LYS F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 110 removed outlier: 4.314A pdb=" N ILE 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: 4.589A pdb=" N GLY F 174 " --> pdb=" O MET F 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 8 Proline residue: G 8 - end of helix Processing helix chain 'G' and resid 58 through 81 Processing helix chain 'G' and resid 137 through 153 removed outlier: 3.648A pdb=" N LEU G 141 " --> pdb=" O ASN G 137 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG G 152 " --> pdb=" O ILE G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 Processing helix chain 'H' and resid 40 through 49 removed outlier: 5.182A pdb=" N ALA H 49 " --> pdb=" O ALA H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 59 removed outlier: 3.507A pdb=" N GLU H 58 " --> pdb=" O LEU H 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 38 Processing helix chain 'I' and resid 67 through 72 Processing helix chain 'I' and resid 88 through 96 Processing helix chain 'I' and resid 97 through 110 Proline residue: I 110 - end of helix Processing helix chain 'I' and resid 112 through 122 removed outlier: 3.688A pdb=" N LYS I 120 " --> pdb=" O TYR I 116 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N MET I 122 " --> pdb=" O MET I 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 118 Processing helix chain 'K' and resid 58 through 64 removed outlier: 3.531A pdb=" N LEU K 63 " --> pdb=" O ILE K 59 " (cutoff:3.500A) Proline residue: K 64 - end of helix Processing helix chain 'K' and resid 70 through 77 removed outlier: 4.222A pdb=" N LEU K 74 " --> pdb=" O SER K 70 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS K 75 " --> pdb=" O GLN K 71 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR K 76 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ALA K 77 " --> pdb=" O ALA K 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 70 through 77' Processing helix chain 'K' and resid 80 through 87 removed outlier: 3.889A pdb=" N LEU K 84 " --> pdb=" O ARG K 80 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LYS K 86 " --> pdb=" O SER K 82 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL K 87 " --> pdb=" O GLU K 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 80 through 87' Processing helix chain 'K' and resid 93 through 101 removed outlier: 3.524A pdb=" N ASN K 101 " --> pdb=" O LEU K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 141 removed outlier: 3.571A pdb=" N GLY K 141 " --> pdb=" O ILE K 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 59 Processing helix chain 'L' and resid 110 through 126 removed outlier: 3.854A pdb=" N ALA L 123 " --> pdb=" O ALA L 119 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS L 124 " --> pdb=" O LEU L 120 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU L 125 " --> pdb=" O ALA L 121 " (cutoff:3.500A) Proline residue: L 126 - end of helix Processing helix chain 'M' and resid 13 through 32 Processing helix chain 'M' and resid 38 through 57 removed outlier: 4.037A pdb=" N ARG M 45 " --> pdb=" O ALA M 41 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ARG M 46 " --> pdb=" O LYS M 42 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL M 47 " --> pdb=" O GLU M 43 " (cutoff:3.500A) Proline residue: M 50 - end of helix removed outlier: 4.458A pdb=" N ASN M 57 " --> pdb=" O THR M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 71 Processing helix chain 'M' and resid 72 through 88 removed outlier: 4.597A pdb=" N GLY M 84 " --> pdb=" O PHE M 80 " (cutoff:3.500A) Proline residue: M 85 - end of helix Processing helix chain 'N' and resid 3 through 23 removed outlier: 3.508A pdb=" N LYS N 13 " --> pdb=" O LEU N 9 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER N 14 " --> pdb=" O ARG N 10 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N THR N 15 " --> pdb=" O ARG N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 61 removed outlier: 4.389A pdb=" N SER N 61 " --> pdb=" O ALA N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 66 through 85 Processing helix chain 'N' and resid 100 through 113 removed outlier: 3.921A pdb=" N GLY N 113 " --> pdb=" O ALA N 109 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 16 removed outlier: 3.864A pdb=" N SER O 14 " --> pdb=" O ALA O 10 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLN O 15 " --> pdb=" O ILE O 11 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU O 16 " --> pdb=" O GLU O 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 107 removed outlier: 4.937A pdb=" N ASP O 105 " --> pdb=" O TYR O 101 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU O 106 " --> pdb=" O TYR O 102 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N SER O 107 " --> pdb=" O LEU O 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 101 through 107' Processing helix chain 'P' and resid 7 through 22 removed outlier: 4.079A pdb=" N LYS P 22 " --> pdb=" O LEU P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 31 removed outlier: 3.819A pdb=" N ARG P 30 " --> pdb=" O GLY P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 73 removed outlier: 3.897A pdb=" N ARG P 51 " --> pdb=" O TYR P 47 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LYS P 54 " --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG P 55 " --> pdb=" O ARG P 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 75 through 87 Processing helix chain 'P' and resid 91 through 102 Processing helix chain 'P' and resid 103 through 118 Processing helix chain 'R' and resid 13 through 25 removed outlier: 3.879A pdb=" N LEU R 19 " --> pdb=" O GLN R 15 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL R 20 " --> pdb=" O LYS R 16 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU R 23 " --> pdb=" O LEU R 19 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE R 24 " --> pdb=" O VAL R 20 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG R 25 " --> pdb=" O ALA R 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 39 Processing helix chain 'R' and resid 41 through 61 removed outlier: 4.205A pdb=" N VAL R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU R 46 " --> pdb=" O LYS R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 70 removed outlier: 3.784A pdb=" N LEU R 69 " --> pdb=" O ASP R 65 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N LYS R 70 " --> pdb=" O VAL R 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 65 through 70' Processing helix chain 'S' and resid 3 through 10 removed outlier: 4.192A pdb=" N TYR S 7 " --> pdb=" O ASN S 3 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEU S 10 " --> pdb=" O ILE S 6 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 26 Processing helix chain 'S' and resid 38 through 50 Processing helix chain 'T' and resid 64 through 69 removed outlier: 3.880A pdb=" N VAL T 68 " --> pdb=" O HIS T 64 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ALA T 69 " --> pdb=" O ILE T 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 64 through 69' Processing helix chain 'U' and resid 12 through 17 removed outlier: 3.525A pdb=" N GLN U 16 " --> pdb=" O ALA U 12 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N GLY U 17 " --> pdb=" O GLU U 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 12 through 17' Processing helix chain 'U' and resid 18 through 28 removed outlier: 3.642A pdb=" N SER U 28 " --> pdb=" O LEU U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 58 removed outlier: 3.813A pdb=" N SER U 57 " --> pdb=" O LYS U 53 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ASN U 58 " --> pdb=" O ALA U 54 " (cutoff:3.500A) Processing helix chain 'W' and resid 52 through 63 Processing helix chain 'W' and resid 64 through 75 removed outlier: 4.105A pdb=" N GLY W 75 " --> pdb=" O LEU W 71 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 9 removed outlier: 4.364A pdb=" N GLU X 8 " --> pdb=" O LYS X 4 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LYS X 9 " --> pdb=" O ASP X 5 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 35 Processing helix chain 'X' and resid 39 through 63 removed outlier: 4.497A pdb=" N VAL X 43 " --> pdb=" O LYS X 39 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLN X 44 " --> pdb=" O SER X 40 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASN X 63 " --> pdb=" O GLU X 59 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 27 removed outlier: 3.574A pdb=" N LEU Y 26 " --> pdb=" O CYS Y 22 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY Y 27 " --> pdb=" O LEU Y 23 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 51 removed outlier: 3.606A pdb=" N MET Y 46 " --> pdb=" O SER Y 42 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL Y 50 " --> pdb=" O MET Y 46 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 19 removed outlier: 3.546A pdb=" N SER Z 18 " --> pdb=" O ASP Z 14 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N HIS Z 19 " --> pdb=" O MET Z 15 " (cutoff:3.500A) Processing helix chain 'b' and resid 7 through 15 Processing helix chain 'b' and resid 29 through 34 removed outlier: 4.776A pdb=" N ILE b 33 " --> pdb=" O MET b 29 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N PHE b 34 " --> pdb=" O ARG b 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 29 through 34' Processing helix chain 'b' and resid 44 through 66 removed outlier: 3.601A pdb=" N THR b 48 " --> pdb=" O ASN b 44 " (cutoff:3.500A) Proline residue: b 50 - end of helix Processing helix chain 'b' and resid 76 through 90 removed outlier: 4.796A pdb=" N ASN b 80 " --> pdb=" O ARG b 76 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILE b 81 " --> pdb=" O ALA b 77 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU b 84 " --> pdb=" O ASN b 80 " (cutoff:3.500A) Processing helix chain 'b' and resid 105 through 126 removed outlier: 4.643A pdb=" N GLN b 111 " --> pdb=" O LYS b 107 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER b 112 " --> pdb=" O THR b 108 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE b 113 " --> pdb=" O LEU b 109 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER b 123 " --> pdb=" O LEU b 119 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLN b 124 " --> pdb=" O GLN b 120 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP b 125 " --> pdb=" O THR b 121 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLY b 126 " --> pdb=" O GLN b 122 " (cutoff:3.500A) Processing helix chain 'b' and resid 127 through 132 removed outlier: 5.275A pdb=" N LEU b 131 " --> pdb=" O THR b 127 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N THR b 132 " --> pdb=" O PHE b 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 127 through 132' Processing helix chain 'b' and resid 133 through 150 removed outlier: 3.503A pdb=" N SER b 149 " --> pdb=" O LYS b 145 " (cutoff:3.500A) Processing helix chain 'b' and resid 167 through 172 removed outlier: 3.704A pdb=" N GLU b 171 " --> pdb=" O ASP b 167 " (cutoff:3.500A) Processing helix chain 'b' and resid 173 through 182 Processing helix chain 'b' and resid 208 through 226 removed outlier: 3.959A pdb=" N GLY b 226 " --> pdb=" O ALA b 222 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.671A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 28 through 48 removed outlier: 4.068A pdb=" N LYS c 48 " --> pdb=" O THR c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 78 removed outlier: 4.769A pdb=" N GLY c 78 " --> pdb=" O GLY c 74 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 96 removed outlier: 4.524A pdb=" N GLY c 96 " --> pdb=" O THR c 92 " (cutoff:3.500A) Processing helix chain 'c' and resid 112 through 127 removed outlier: 4.074A pdb=" N ARG c 127 " --> pdb=" O GLN c 123 " (cutoff:3.500A) Processing helix chain 'c' and resid 129 through 145 removed outlier: 3.803A pdb=" N GLY c 145 " --> pdb=" O THR c 141 " (cutoff:3.500A) Processing helix chain 'c' and resid 210 through 215 removed outlier: 4.026A pdb=" N VAL c 214 " --> pdb=" O GLY c 210 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.252A pdb=" N LEU d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 33 Processing helix chain 'd' and resid 51 through 68 Processing helix chain 'd' and resid 70 through 85 removed outlier: 5.030A pdb=" N LYS d 85 " --> pdb=" O ALA d 81 " (cutoff:3.500A) Processing helix chain 'd' and resid 87 through 99 removed outlier: 3.885A pdb=" N ARG d 99 " --> pdb=" O LEU d 95 " (cutoff:3.500A) Processing helix chain 'd' and resid 100 through 108 Processing helix chain 'd' and resid 112 through 123 removed outlier: 3.792A pdb=" N ARG d 123 " --> pdb=" O LEU d 119 " (cutoff:3.500A) Processing helix chain 'd' and resid 148 through 153 removed outlier: 4.491A pdb=" N GLN d 153 " --> pdb=" O GLU d 149 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 168 removed outlier: 3.775A pdb=" N LYS d 158 " --> pdb=" O GLN d 154 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU d 162 " --> pdb=" O LYS d 158 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU d 163 " --> pdb=" O ASN d 159 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLY d 168 " --> pdb=" O ALA d 164 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 194 Proline residue: d 194 - end of helix Processing helix chain 'd' and resid 198 through 208 removed outlier: 4.116A pdb=" N ILE d 202 " --> pdb=" O ASN d 198 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LYS d 208 " --> pdb=" O GLU d 204 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 3.529A pdb=" N GLU e 64 " --> pdb=" O SER e 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA e 65 " --> pdb=" O LYS e 61 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN e 69 " --> pdb=" O ALA e 65 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N MET e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 107 through 118 removed outlier: 3.759A pdb=" N VAL e 113 " --> pdb=" O ALA e 109 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 146 removed outlier: 3.607A pdb=" N ARG e 144 " --> pdb=" O PHE e 140 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP e 145 " --> pdb=" O LYS e 141 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET e 146 " --> pdb=" O GLY e 142 " (cutoff:3.500A) Processing helix chain 'e' and resid 148 through 157 Processing helix chain 'e' and resid 159 through 164 removed outlier: 3.626A pdb=" N ILE e 163 " --> pdb=" O SER e 159 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLN e 164 " --> pdb=" O VAL e 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 159 through 164' Processing helix chain 'f' and resid 11 through 16 removed outlier: 5.011A pdb=" N ASP f 16 " --> pdb=" O PRO f 12 " (cutoff:3.500A) Processing helix chain 'f' and resid 17 through 31 removed outlier: 5.073A pdb=" N GLU f 23 " --> pdb=" O VAL f 19 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG f 24 " --> pdb=" O GLY f 20 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN f 28 " --> pdb=" O ARG f 24 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE f 29 " --> pdb=" O TYR f 25 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU f 31 " --> pdb=" O SER f 27 " (cutoff:3.500A) Processing helix chain 'f' and resid 70 through 82 removed outlier: 3.819A pdb=" N PHE f 78 " --> pdb=" O LEU f 74 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ASP f 82 " --> pdb=" O PHE f 78 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 Processing helix chain 'g' and resid 35 through 55 removed outlier: 3.805A pdb=" N ALA g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN g 54 " --> pdb=" O VAL g 50 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS g 55 " --> pdb=" O GLN g 51 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.800A pdb=" N VAL g 69 " --> pdb=" O THR g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 112 removed outlier: 5.650A pdb=" N SER g 112 " --> pdb=" O ALA g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 Processing helix chain 'g' and resid 132 through 139 removed outlier: 3.798A pdb=" N LYS g 136 " --> pdb=" O GLY g 132 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N GLU g 139 " --> pdb=" O ILE g 135 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 removed outlier: 4.049A pdb=" N ASP h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 44 Processing helix chain 'h' and resid 113 through 121 Processing helix chain 'i' and resid 32 through 37 Processing helix chain 'i' and resid 39 through 54 removed outlier: 3.655A pdb=" N ARG i 43 " --> pdb=" O ARG i 39 " (cutoff:3.500A) Proline residue: i 49 - end of helix Processing helix chain 'i' and resid 69 through 90 removed outlier: 3.741A pdb=" N GLU i 90 " --> pdb=" O ILE i 86 " (cutoff:3.500A) Processing helix chain 'i' and resid 91 through 100 removed outlier: 5.185A pdb=" N VAL i 95 " --> pdb=" O THR i 91 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA i 99 " --> pdb=" O VAL i 95 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 3.698A pdb=" N ILE j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 91 removed outlier: 4.091A pdb=" N VAL j 84 " --> pdb=" O THR j 80 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASP j 85 " --> pdb=" O ASP j 81 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ASP j 91 " --> pdb=" O LEU j 87 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 4.081A pdb=" N GLN k 49 " --> pdb=" O THR k 45 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY k 50 " --> pdb=" O SER k 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 45 through 50' Processing helix chain 'k' and resid 53 through 59 removed outlier: 4.483A pdb=" N SER k 57 " --> pdb=" O GLY k 53 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR k 58 " --> pdb=" O SER k 54 " (cutoff:3.500A) Proline residue: k 59 - end of helix No H-bonds generated for 'chain 'k' and resid 53 through 59' Processing helix chain 'k' and resid 60 through 77 removed outlier: 3.620A pdb=" N VAL k 64 " --> pdb=" O PHE k 60 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP k 75 " --> pdb=" O LYS k 71 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N TYR k 76 " --> pdb=" O ALA k 72 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY k 77 " --> pdb=" O ALA k 73 " (cutoff:3.500A) Processing helix chain 'k' and resid 93 through 103 Processing helix chain 'l' and resid 3 through 10 Processing helix chain 'l' and resid 113 through 118 removed outlier: 4.917A pdb=" N TYR l 117 " --> pdb=" O SER l 113 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY l 118 " --> pdb=" O ARG l 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 113 through 118' Processing helix chain 'm' and resid 14 through 22 removed outlier: 3.740A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE m 22 " --> pdb=" O SER 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: 3.965A pdb=" N LEU m 48 " --> pdb=" O LYS m 44 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ASP 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: 3.849A pdb=" N LYS m 62 " --> pdb=" O ALA m 58 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL m 63 " --> pdb=" O GLU m 59 " (cutoff:3.500A) Proline residue: m 64 - end of helix Processing helix chain 'm' and resid 66 through 84 removed outlier: 3.807A pdb=" N ARG m 70 " --> pdb=" O GLU m 66 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY m 84 " --> pdb=" O LEU m 80 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 94 removed outlier: 3.506A pdb=" N ARG m 90 " --> pdb=" O TYR m 86 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS m 91 " --> pdb=" O ARG m 87 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG m 92 " --> pdb=" O GLY m 88 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ARG m 93 " --> pdb=" O LEU m 89 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER m 94 " --> pdb=" O ARG m 90 " (cutoff:3.500A) Processing helix chain 'm' and resid 106 through 111 Processing helix chain 'n' and resid 3 through 21 removed outlier: 3.633A pdb=" N ALA n 21 " --> pdb=" O VAL n 17 " (cutoff:3.500A) Processing helix chain 'n' and resid 22 through 33 Processing helix chain 'n' and resid 37 through 51 Processing helix chain 'n' and resid 56 through 61 removed outlier: 4.499A pdb=" N LEU n 60 " --> pdb=" O SER n 56 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ARG n 61 " --> pdb=" O PRO n 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 56 through 61' Processing helix chain 'n' and resid 80 through 91 removed outlier: 3.744A pdb=" N ASP n 86 " --> pdb=" O ASN n 82 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 16 removed outlier: 3.541A pdb=" N ARG o 8 " --> pdb=" O THR o 4 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 44 removed outlier: 3.990A pdb=" N GLY o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS o 42 " --> pdb=" O ASP o 38 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 4.028A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 Processing helix chain 'p' and resid 71 through 82 removed outlier: 3.717A pdb=" N GLY p 82 " --> pdb=" O TRP p 78 " (cutoff:3.500A) Processing helix chain 'p' and resid 86 through 101 Processing helix chain 'r' and resid 25 through 34 removed outlier: 3.715A pdb=" N LEU r 29 " --> pdb=" O ASP r 25 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TYR r 32 " --> pdb=" O THR r 28 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N THR r 34 " --> pdb=" O LYS r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 46 removed outlier: 3.611A pdb=" N THR r 45 " --> pdb=" O PRO r 41 " (cutoff:3.500A) Processing helix chain 'r' and resid 48 through 66 Processing helix chain 's' and resid 12 through 26 Processing helix chain 's' and resid 41 through 46 removed outlier: 4.032A pdb=" N VAL s 45 " --> pdb=" O LEU s 41 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLY s 46 " --> pdb=" O PRO s 42 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 41 through 46' Processing helix chain 's' and resid 70 through 76 removed outlier: 4.509A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.255A 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 42 removed outlier: 3.542A pdb=" N LYS t 8 " --> pdb=" O SER t 4 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU t 24 " --> pdb=" O HIS t 20 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY t 42 " --> pdb=" O ALA t 38 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 65 Proline residue: t 56 - end of helix removed outlier: 3.545A pdb=" N GLY t 65 " --> pdb=" O MET t 61 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 87 removed outlier: 3.627A pdb=" N LEU t 86 " --> pdb=" O GLN t 82 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA t 87 " --> pdb=" O VAL t 83 " (cutoff:3.500A) Processing helix chain 'u' and resid 38 through 54 removed outlier: 6.720A pdb=" N THR u 42 " --> pdb=" O TYR u 38 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLN u 43 " --> pdb=" O GLU u 39 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LYS u 54 " --> pdb=" O ALA u 50 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '0' and resid 16 through 20 removed outlier: 3.533A pdb=" N ILE 0 32 " --> pdb=" O PHE 0 45 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU 0 47 " --> pdb=" O MET 0 30 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N MET 0 30 " --> pdb=" O GLU 0 47 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '2' and resid 21 through 24 No H-bonds generated for sheet with id= 2 Processing sheet with id= 3, first strand: chain '3' and resid 14 through 19 Processing sheet with id= 4, first strand: chain 'C' and resid 80 through 83 removed outlier: 3.857A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N VAL C 74 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N SER C 118 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ASP C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLY C 127 " --> pdb=" O LYS C 115 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N GLN C 117 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 138 through 142 removed outlier: 4.380A pdb=" N SER C 139 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN C 163 " --> pdb=" O ARG C 175 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 90 through 96 removed outlier: 5.264A pdb=" N HIS C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 12 through 17 removed outlier: 4.240A pdb=" N VAL D 21 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL D 27 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY D 202 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 13.574A pdb=" N GLY D 201 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 11.881A pdb=" N LYS D 117 " --> pdb=" O GLY D 201 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ASP D 203 " --> pdb=" O GLN D 115 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N GLN D 115 " --> pdb=" O ASP D 203 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU D 171 " --> pdb=" O SER D 116 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N GLY D 118 " --> pdb=" O GLY D 169 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLY D 169 " --> pdb=" O GLY D 118 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY D 120 " --> pdb=" O HIS D 167 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N HIS D 167 " --> pdb=" O GLY D 120 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 33 through 36 removed outlier: 6.872A pdb=" N GLN D 50 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TYR D 46 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU D 41 " --> pdb=" O TYR D 46 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'D' and resid 182 through 185 Processing sheet with id= 10, first strand: chain 'D' and resid 25 through 30 removed outlier: 5.511A pdb=" N SER D 188 " --> pdb=" O VAL D 30 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 48 through 52 Processing sheet with id= 12, first strand: chain 'D' and resid 111 through 114 Processing sheet with id= 13, first strand: chain 'E' and resid 116 through 119 removed outlier: 3.811A pdb=" N LYS E 184 " --> pdb=" O ARG E 144 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP E 167 " --> pdb=" O ALA E 145 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR E 149 " --> pdb=" O VAL E 169 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'F' and resid 86 through 92 removed outlier: 3.988A pdb=" N CYS F 87 " --> pdb=" O MET F 38 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET F 38 " --> pdb=" O CYS F 87 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS F 33 " --> pdb=" O THR F 157 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE F 156 " --> pdb=" O TYR F 128 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TYR F 128 " --> pdb=" O ILE F 156 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'G' and resid 16 through 19 Processing sheet with id= 16, first strand: chain 'G' and resid 41 through 45 removed outlier: 4.138A pdb=" N GLU G 42 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA G 53 " --> pdb=" O GLU G 42 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'G' and resid 82 through 89 removed outlier: 3.800A pdb=" N SER G 135 " --> pdb=" O PHE G 83 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU G 133 " --> pdb=" O ARG G 85 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'G' and resid 94 through 98 Processing sheet with id= 19, first strand: chain 'H' and resid 3 through 6 removed outlier: 7.780A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'I' and resid 52 through 57 removed outlier: 5.153A pdb=" N ASP I 19 " --> pdb=" O LEU I 140 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'I' and resid 74 through 78 removed outlier: 4.429A pdb=" N GLY I 83 " --> pdb=" O THR I 78 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'J' and resid 18 through 21 removed outlier: 4.300A pdb=" N THR J 6 " --> pdb=" O CYS J 21 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ASN J 82 " --> pdb=" O MET J 7 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'L' and resid 63 through 66 removed outlier: 3.769A pdb=" N TYR L 104 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE L 34 " --> pdb=" O LEU L 103 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS L 101 " --> pdb=" O ALA L 36 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'L' and resid 31 through 37 removed outlier: 7.883A pdb=" N SER L 31 " --> pdb=" O ARG L 134 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LYS L 128 " --> pdb=" O THR L 37 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'M' and resid 33 through 37 Processing sheet with id= 26, first strand: chain 'N' and resid 50 through 53 removed outlier: 3.648A pdb=" N ALA N 50 " --> pdb=" O VAL N 40 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG N 26 " --> pdb=" O ILE N 41 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL N 29 " --> pdb=" O ASP N 92 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'O' and resid 41 through 47 removed outlier: 3.856A pdb=" N LYS O 86 " --> pdb=" O GLN O 32 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'O' and resid 52 through 55 removed outlier: 3.895A pdb=" N ALA O 52 " --> pdb=" O THR O 63 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N SER O 60 " --> pdb=" O THR O 79 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'Q' and resid 2 through 6 Processing sheet with id= 30, first strand: chain 'Q' and resid 18 through 21 removed outlier: 4.159A pdb=" N GLU Q 18 " --> pdb=" O ILE Q 98 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU Q 95 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N THR Q 60 " --> pdb=" O THR Q 99 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA Q 31 " --> pdb=" O VAL Q 63 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'Q' and resid 39 through 42 removed outlier: 5.473A pdb=" N LEU Q 39 " --> pdb=" O GLY Q 50 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY Q 50 " --> pdb=" O LEU Q 39 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'Q' and resid 68 through 78 No H-bonds generated for sheet with id= 32 Processing sheet with id= 33, first strand: chain 'R' and resid 2 through 8 removed outlier: 3.568A pdb=" N VAL R 3 " --> pdb=" O VAL R 107 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N THR R 100 " --> pdb=" O GLY R 79 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'S' and resid 28 through 32 removed outlier: 4.633A pdb=" N LYS S 65 " --> pdb=" O ARG S 76 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ASP S 78 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LYS S 63 " --> pdb=" O ASP S 78 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS S 80 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE S 61 " --> pdb=" O LYS S 80 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA S 82 " --> pdb=" O THR S 59 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR S 59 " --> pdb=" O ALA S 82 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL S 84 " --> pdb=" O VAL S 57 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL S 57 " --> pdb=" O VAL S 84 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'T' and resid 38 through 43 removed outlier: 5.405A pdb=" N ASN T 38 " --> pdb=" O ALA T 61 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'T' and resid 80 through 85 removed outlier: 6.767A pdb=" N ARG T 80 " --> pdb=" O LYS T 95 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN T 84 " --> pdb=" O THR T 91 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N THR T 91 " --> pdb=" O GLN T 84 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'U' and resid 73 through 76 removed outlier: 3.847A pdb=" N GLU U 66 " --> pdb=" O PHE U 4 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA U 93 " --> pdb=" O PRO U 31 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'U' and resid 82 through 85 removed outlier: 6.649A pdb=" N GLN U 82 " --> pdb=" O MET U 91 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR U 89 " --> pdb=" O HIS U 84 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'V' and resid 29 through 32 removed outlier: 4.845A pdb=" N GLN V 29 " --> pdb=" O VAL V 67 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL V 82 " --> pdb=" O GLY V 48 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'V' and resid 50 through 54 removed outlier: 7.251A pdb=" N ASN V 50 " --> pdb=" O THR V 62 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR V 58 " --> pdb=" O GLY V 54 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'W' and resid 12 through 19 removed outlier: 4.648A pdb=" N ASN W 23 " --> pdb=" O SER W 19 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'W' and resid 34 through 40 Processing sheet with id= 43, first strand: chain 'Y' and resid 4 through 9 removed outlier: 3.535A pdb=" N THR Y 7 " --> pdb=" O SER Y 55 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N MET Y 53 " --> pdb=" O THR Y 9 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'b' and resid 17 through 20 removed outlier: 5.823A pdb=" N HIS b 17 " --> pdb=" O ILE b 43 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N HIS b 41 " --> pdb=" O GLY b 19 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'b' and resid 68 through 73 removed outlier: 3.896A pdb=" N ILE b 166 " --> pdb=" O VAL b 72 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'c' and resid 53 through 59 removed outlier: 3.693A pdb=" N ASN c 54 " --> pdb=" O SER c 69 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA c 64 " --> pdb=" O PRO c 98 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'c' and resid 164 through 170 removed outlier: 3.545A pdb=" N GLY c 194 " --> pdb=" O THR c 191 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'd' and resid 142 through 146 removed outlier: 4.005A pdb=" N ASP d 143 " --> pdb=" O PHE d 184 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU d 181 " --> pdb=" O ASP d 176 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU d 174 " --> pdb=" O THR d 183 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS d 185 " --> pdb=" O TRP d 172 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N TRP d 172 " --> pdb=" O LYS d 185 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'e' and resid 10 through 15 removed outlier: 7.016A pdb=" N LEU e 35 " --> pdb=" O VAL e 15 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'e' and resid 83 through 87 removed outlier: 3.947A pdb=" N ALA e 98 " --> pdb=" O ASN e 121 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASN e 121 " --> pdb=" O ALA e 98 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'e' and resid 31 through 40 removed outlier: 6.816A pdb=" N ARG e 44 " --> pdb=" O ASP e 40 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'f' and resid 36 through 43 removed outlier: 4.750A pdb=" N ILE f 36 " --> pdb=" O GLU f 65 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU f 65 " --> pdb=" O ILE f 36 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ARG f 38 " --> pdb=" O ASN f 63 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASN f 63 " --> pdb=" O ARG f 38 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU f 40 " --> pdb=" O LEU f 61 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL f 10 " --> pdb=" O HIS f 58 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'f' and resid 44 through 47 removed outlier: 7.354A pdb=" N HIS f 55 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'h' and resid 23 through 29 removed outlier: 6.803A pdb=" N GLN h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N SER h 58 " --> pdb=" O SER h 29 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN h 48 " --> pdb=" O THR h 63 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'h' and resid 75 through 78 removed outlier: 4.854A pdb=" N MET h 75 " --> pdb=" O SER h 131 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA h 128 " --> pdb=" O ILE h 104 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE h 104 " --> pdb=" O ILE h 127 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'i' and resid 3 through 9 removed outlier: 3.543A pdb=" N THR i 14 " --> pdb=" O LYS i 66 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS i 25 " --> pdb=" O TYR i 59 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'j' and resid 42 through 53 removed outlier: 5.249A pdb=" N LYS j 71 " --> pdb=" O PRO j 43 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ALA j 61 " --> pdb=" O THR j 53 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ARG j 7 " --> pdb=" O ALA j 101 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'k' and resid 28 through 34 removed outlier: 3.704A pdb=" N ASN k 28 " --> pdb=" O SER k 25 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN k 80 " --> pdb=" O SER k 16 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP k 82 " --> pdb=" O GLY k 18 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS k 86 " --> pdb=" O ILE k 22 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS k 105 " --> pdb=" O LYS k 79 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N VAL k 83 " --> pdb=" O ASN k 107 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'l' and resid 29 through 34 removed outlier: 3.651A pdb=" N SER l 78 " --> pdb=" O CYS l 34 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'l' and resid 36 through 41 removed outlier: 3.710A pdb=" N ARG l 36 " --> pdb=" O ARG l 54 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE l 61 " --> pdb=" O LEU l 57 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'p' and resid 34 through 38 removed outlier: 5.417A pdb=" N LYS p 67 " --> pdb=" O ASN p 58 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'q' and resid 7 through 10 removed outlier: 6.090A pdb=" N ARG q 7 " --> pdb=" O GLU q 64 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR q 61 " --> pdb=" O VAL q 77 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'q' and resid 20 through 31 No H-bonds generated for sheet with id= 63 Processing sheet with id= 64, first strand: chain 's' and resid 30 through 33 removed outlier: 3.569A pdb=" N ILE s 31 " --> pdb=" O THR s 48 " (cutoff:3.500A) 1703 hydrogen bonds defined for protein. 5061 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3519 hydrogen bonds 5520 hydrogen bond angles 0 basepair planarities 1403 basepair parallelities 2346 stacking parallelities Total time for adding SS restraints: 241.15 Time building geometry restraints manager: 64.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 11340 1.30 - 1.43: 68739 1.43 - 1.55: 64368 1.55 - 1.68: 9229 1.68 - 1.81: 250 Bond restraints: 153926 Sorted by residual: bond pdb=" C5 5MUAN1935 " pdb=" C6 5MUAN1935 " ideal model delta sigma weight residual 1.155 1.450 -0.295 2.00e-02 2.50e+03 2.18e+02 bond pdb=" C5 5MU v 55 " pdb=" C6 5MU v 55 " ideal model delta sigma weight residual 1.155 1.450 -0.295 2.00e-02 2.50e+03 2.17e+02 bond pdb=" C4 5MU v 55 " pdb=" C5 5MU v 55 " ideal model delta sigma weight residual 1.802 1.610 0.192 2.00e-02 2.50e+03 9.26e+01 bond pdb=" C4 5MUAN1935 " pdb=" C5 5MUAN1935 " ideal model delta sigma weight residual 1.802 1.610 0.192 2.00e-02 2.50e+03 9.18e+01 bond pdb=" N1 5MU v 55 " pdb=" C2 5MU v 55 " ideal model delta sigma weight residual 1.436 1.563 -0.127 2.00e-02 2.50e+03 4.01e+01 ... (remaining 153921 not shown) Histogram of bond angle deviations from ideal: 100.12 - 109.83: 67427 109.83 - 119.55: 91082 119.55 - 129.26: 68728 129.26 - 138.98: 3438 138.98 - 148.69: 1 Bond angle restraints: 230676 Sorted by residual: angle pdb=" C1' 6MZAN2026 " pdb=" N9 6MZAN2026 " pdb=" C8 6MZAN2026 " ideal model delta sigma weight residual 126.23 148.69 -22.46 3.00e+00 1.11e-01 5.61e+01 angle pdb=" C1' 2MGsN1204 " pdb=" N9 2MGsN1204 " pdb=" C8 2MGsN1204 " ideal model delta sigma weight residual 110.07 132.39 -22.32 3.00e+00 1.11e-01 5.54e+01 angle pdb=" C1' 2MGAN2441 " pdb=" N9 2MGAN2441 " pdb=" C8 2MGAN2441 " ideal model delta sigma weight residual 110.07 131.82 -21.75 3.00e+00 1.11e-01 5.25e+01 angle pdb=" C1' 2MGsN 963 " pdb=" N9 2MGsN 963 " pdb=" C8 2MGsN 963 " ideal model delta sigma weight residual 110.07 130.97 -20.90 3.00e+00 1.11e-01 4.85e+01 angle pdb=" C1' OMGAN2247 " pdb=" N9 OMGAN2247 " pdb=" C4 OMGAN2247 " ideal model delta sigma weight residual 108.29 128.51 -20.22 3.00e+00 1.11e-01 4.54e+01 ... (remaining 230671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 86932 35.96 - 71.92: 10166 71.92 - 107.88: 1195 107.88 - 143.84: 28 143.84 - 179.80: 42 Dihedral angle restraints: 98363 sinusoidal: 82837 harmonic: 15526 Sorted by residual: dihedral pdb=" O4' UAN2880 " pdb=" C1' UAN2880 " pdb=" N1 UAN2880 " pdb=" C2 UAN2880 " ideal model delta sinusoidal sigma weight residual -160.00 18.41 -178.41 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' CAN 912 " pdb=" C1' CAN 912 " pdb=" N1 CAN 912 " pdb=" C2 CAN 912 " ideal model delta sinusoidal sigma weight residual -160.00 9.84 -169.84 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' UAN1775 " pdb=" C1' UAN1775 " pdb=" N1 UAN1775 " pdb=" C2 UAN1775 " ideal model delta sinusoidal sigma weight residual 200.00 38.52 161.48 1 1.50e+01 4.44e-03 8.31e+01 ... (remaining 98360 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 27915 0.058 - 0.116: 1469 0.116 - 0.175: 120 0.175 - 0.233: 12 0.233 - 0.291: 5 Chirality restraints: 29521 Sorted by residual: chirality pdb=" C1' C v 76 " pdb=" O4' C v 76 " pdb=" C2' C v 76 " pdb=" N1 C v 76 " both_signs ideal model delta sigma weight residual False 2.47 2.17 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C1* PSUsN 513 " pdb=" O4* PSUsN 513 " pdb=" C2* PSUsN 513 " pdb=" C5 PSUsN 513 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C1' AAN 980 " pdb=" O4' AAN 980 " pdb=" C2' AAN 980 " pdb=" N9 AAN 980 " both_signs ideal model delta sigma weight residual False 2.46 2.18 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 29518 not shown) Planarity restraints: 12109 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MGAN2065 " -0.067 2.00e-02 2.50e+03 6.23e-01 8.73e+03 pdb=" C4' 7MGAN2065 " -0.457 2.00e-02 2.50e+03 pdb=" O4' 7MGAN2065 " -0.707 2.00e-02 2.50e+03 pdb=" C3' 7MGAN2065 " 0.594 2.00e-02 2.50e+03 pdb=" O3' 7MGAN2065 " 0.657 2.00e-02 2.50e+03 pdb=" C2' 7MGAN2065 " 0.182 2.00e-02 2.50e+03 pdb=" O2' 7MGAN2065 " -0.981 2.00e-02 2.50e+03 pdb=" C1' 7MGAN2065 " -0.200 2.00e-02 2.50e+03 pdb=" N9 7MGAN2065 " 0.979 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MGAN2441 " -0.031 2.00e-02 2.50e+03 5.82e-01 7.63e+03 pdb=" C4' 2MGAN2441 " -0.440 2.00e-02 2.50e+03 pdb=" O4' 2MGAN2441 " -0.678 2.00e-02 2.50e+03 pdb=" C3' 2MGAN2441 " 0.591 2.00e-02 2.50e+03 pdb=" O3' 2MGAN2441 " 0.574 2.00e-02 2.50e+03 pdb=" C2' 2MGAN2441 " 0.215 2.00e-02 2.50e+03 pdb=" O2' 2MGAN2441 " -0.909 2.00e-02 2.50e+03 pdb=" C1' 2MGAN2441 " -0.217 2.00e-02 2.50e+03 pdb=" N9 2MGAN2441 " 0.895 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MGsN 963 " 0.028 2.00e-02 2.50e+03 5.80e-01 7.56e+03 pdb=" C4' 2MGsN 963 " -0.461 2.00e-02 2.50e+03 pdb=" O4' 2MGsN 963 " -0.867 2.00e-02 2.50e+03 pdb=" C3' 2MGsN 963 " 0.569 2.00e-02 2.50e+03 pdb=" O3' 2MGsN 963 " 0.461 2.00e-02 2.50e+03 pdb=" C2' 2MGsN 963 " 0.302 2.00e-02 2.50e+03 pdb=" O2' 2MGsN 963 " -0.754 2.00e-02 2.50e+03 pdb=" C1' 2MGsN 963 " -0.188 2.00e-02 2.50e+03 pdb=" N9 2MGsN 963 " 0.909 2.00e-02 2.50e+03 ... (remaining 12106 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.50: 806 2.50 - 3.10: 89669 3.10 - 3.70: 251138 3.70 - 4.30: 381508 4.30 - 4.90: 524359 Nonbonded interactions: 1247480 Sorted by model distance: nonbonded pdb=" N6 AAN1650 " pdb="MG MGAN3013 " model vdw 1.895 2.250 nonbonded pdb=" ND1 HIS C 53 " pdb="MG MGAN3061 " model vdw 1.895 2.250 nonbonded pdb=" N7 GsN 866 " pdb="MG MGsN1603 " model vdw 1.897 2.250 nonbonded pdb=" N7 GsN 755 " pdb="MG MGsN1601 " model vdw 1.899 2.250 nonbonded pdb=" N7 GAN2049 " pdb="MG MGAN3022 " model vdw 1.901 2.250 ... (remaining 1247475 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.620 Construct map_model_manager: 0.150 Extract box with map and model: 29.680 Check model and map are aligned: 1.500 Set scattering table: 0.990 Process input model: 547.660 Find NCS groups from input model: 2.840 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 594.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 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 : 0.002 0.295 153926 Z= 0.138 Angle : 0.490 22.463 230676 Z= 0.262 Chirality : 0.028 0.291 29521 Planarity : 0.016 0.623 12109 Dihedral : 22.888 179.798 88364 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.52 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.10), residues: 5361 helix: -0.13 (0.11), residues: 1762 sheet: 0.24 (0.16), residues: 1016 loop : -1.42 (0.10), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP d 172 HIS 0.003 0.001 HIS j 56 PHE 0.016 0.001 PHE H 47 TYR 0.015 0.001 TYR f 25 ARG 0.004 0.000 ARG U 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1307 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1307 time to evaluate : 5.751 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 211 LYS cc_start: 0.7279 (mttt) cc_final: 0.6323 (tptm) REVERT: E 110 GLU cc_start: 0.8177 (tp30) cc_final: 0.7808 (tp30) REVERT: E 134 LEU cc_start: 0.8975 (tp) cc_final: 0.8526 (tp) REVERT: F 152 MET cc_start: 0.6074 (mtp) cc_final: 0.5439 (mtp) REVERT: G 85 ARG cc_start: 0.7394 (tpm170) cc_final: 0.7104 (tpm170) REVERT: J 53 LYS cc_start: 0.8172 (tttm) cc_final: 0.7922 (tttm) REVERT: M 69 ARG cc_start: 0.7914 (mtt180) cc_final: 0.7484 (mtt180) REVERT: N 66 ASN cc_start: 0.6433 (t0) cc_final: 0.6185 (t0) REVERT: O 109 LYS cc_start: 0.7853 (ttpp) cc_final: 0.7561 (ttpp) REVERT: S 3 ASN cc_start: 0.7328 (m110) cc_final: 0.6822 (m-40) REVERT: X 25 GLN cc_start: 0.8772 (tt0) cc_final: 0.8436 (tt0) REVERT: Y 39 ASP cc_start: 0.8371 (t70) cc_final: 0.8092 (t0) REVERT: c 187 MET cc_start: 0.7521 (tpt) cc_final: 0.7093 (tpt) REVERT: d 133 ASN cc_start: 0.8448 (p0) cc_final: 0.8223 (p0) REVERT: e 30 PHE cc_start: 0.8412 (m-80) cc_final: 0.8192 (m-10) REVERT: f 89 ILE cc_start: 0.8912 (mt) cc_final: 0.8556 (mp) REVERT: g 12 ILE cc_start: 0.8868 (mt) cc_final: 0.8444 (mm) REVERT: h 88 ARG cc_start: 0.8981 (mmt-90) cc_final: 0.8643 (mpt180) REVERT: i 59 TYR cc_start: 0.8863 (m-80) cc_final: 0.8653 (m-80) REVERT: m 32 ASN cc_start: 0.7611 (m-40) cc_final: 0.7368 (m110) REVERT: n 39 GLU cc_start: 0.8405 (tm-30) cc_final: 0.7723 (tm-30) REVERT: r 68 ILE cc_start: 0.8725 (pt) cc_final: 0.8450 (tp) REVERT: s 16 PHE cc_start: 0.8140 (t80) cc_final: 0.7827 (t80) REVERT: s 39 MET cc_start: 0.7847 (tpp) cc_final: 0.7370 (tpt) outliers start: 0 outliers final: 0 residues processed: 1307 average time/residue: 1.3548 time to fit residues: 2945.7682 Evaluate side-chains 1038 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1038 time to evaluate : 5.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 986 random chunks: chunk 832 optimal weight: 10.0000 chunk 747 optimal weight: 10.0000 chunk 414 optimal weight: 5.9990 chunk 255 optimal weight: 6.9990 chunk 504 optimal weight: 3.9990 chunk 399 optimal weight: 9.9990 chunk 772 optimal weight: 6.9990 chunk 299 optimal weight: 5.9990 chunk 469 optimal weight: 3.9990 chunk 575 optimal weight: 0.8980 chunk 895 optimal weight: 10.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 19 ASN 2 50 HIS C 4 GLN C 23 HIS C 48 HIS C 58 HIS C 60 GLN C 90 HIS C 117 GLN C 163 GLN C 200 ASN C 230 HIS D 47 GLN D 50 GLN D 65 GLN D 108 GLN D 137 HIS E 29 GLN E 45 HIS E 96 ASN ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN ** F 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN G 106 ASN I 40 HIS I 135 GLN K 40 GLN K 56 GLN N 99 HIS O 9 GLN O 13 ASN O 55 ASN O 78 GLN P 11 HIS P 87 GLN Q 46 ASN Q 87 GLN R 37 ASN R 57 ASN R 60 HIS T 43 HIS T 47 ASN U 16 GLN U 58 ASN U 79 GLN U 84 HIS W 76 GLN Y 18 ASN Z 41 HIS b 5 ASN b 13 GLN b 57 ASN b 67 ASN b 96 HIS b 111 GLN b 122 GLN b 155 ASN b 170 HIS b 197 ASN c 3 GLN c 6 HIS ** c 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 50 GLN d 73 GLN ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 138 GLN d 154 GLN e 121 ASN e 131 ASN ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 94 HIS i 4 ASN i 73 GLN i 79 HIS ** j 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 50 ASN j 56 HIS ** j 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 27 ASN k 28 ASN l 5 ASN ** l 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 72 HIS l 77 HIS l 96 HIS l 111 ASN m 12 ASN m 14 HIS m 52 GLN n 8 ASN o 42 HIS p 44 ASN q 31 GLN q 32 HIS r 36 ASN r 54 GLN s 52 HIS s 83 HIS t 6 GLN t 13 GLN t 75 HIS Total number of N/Q/H flips: 94 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 153926 Z= 0.415 Angle : 0.736 16.516 230676 Z= 0.379 Chirality : 0.042 0.396 29521 Planarity : 0.007 0.146 12109 Dihedral : 23.337 179.911 77741 Min Nonbonded Distance : 1.609 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.45 % Favored : 96.49 % Rotamer: Outliers : 2.73 % Allowed : 14.56 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.11), residues: 5361 helix: 0.88 (0.12), residues: 1791 sheet: 0.25 (0.16), residues: 1009 loop : -1.16 (0.11), residues: 2561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP s 34 HIS 0.012 0.002 HIS C 61 PHE 0.029 0.002 PHE s 16 TYR 0.022 0.002 TYR c 184 ARG 0.011 0.001 ARG F 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1137 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1016 time to evaluate : 5.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 41 ARG cc_start: 0.8945 (ttm110) cc_final: 0.8665 (ttm110) REVERT: 2 58 ARG cc_start: 0.8683 (ttm-80) cc_final: 0.8483 (ttm110) REVERT: C 25 HIS cc_start: 0.7990 (t70) cc_final: 0.7672 (t-170) REVERT: D 211 LYS cc_start: 0.7397 (mttt) cc_final: 0.6419 (tptm) REVERT: E 110 GLU cc_start: 0.8286 (tp30) cc_final: 0.7824 (tp30) REVERT: G 19 GLN cc_start: 0.5746 (tt0) cc_final: 0.5261 (pt0) REVERT: G 85 ARG cc_start: 0.7713 (tpm170) cc_final: 0.7374 (tpm170) REVERT: I 108 MET cc_start: 0.8930 (mtt) cc_final: 0.8690 (mtt) REVERT: K 1 MET cc_start: 0.0078 (mtp) cc_final: -0.0164 (mtp) REVERT: K 71 GLN cc_start: 0.8889 (mm110) cc_final: 0.8674 (tp40) REVERT: L 128 LYS cc_start: 0.8046 (tptp) cc_final: 0.7808 (tttm) REVERT: O 88 GLU cc_start: 0.7090 (tm-30) cc_final: 0.6778 (tm-30) REVERT: O 91 ARG cc_start: 0.6282 (ttp80) cc_final: 0.6014 (ttp80) REVERT: X 15 LYS cc_start: 0.7090 (tptt) cc_final: 0.6586 (tptt) REVERT: X 25 GLN cc_start: 0.8833 (tt0) cc_final: 0.8413 (tt0) REVERT: d 133 ASN cc_start: 0.8594 (p0) cc_final: 0.8328 (p0) REVERT: e 110 MET cc_start: 0.8046 (mtm) cc_final: 0.7622 (mtm) REVERT: f 89 ILE cc_start: 0.8999 (mt) cc_final: 0.8657 (mp) REVERT: g 120 LEU cc_start: 0.9379 (tp) cc_final: 0.9149 (tp) REVERT: h 43 GLU cc_start: 0.8189 (tp30) cc_final: 0.7959 (tp30) REVERT: o 64 ARG cc_start: 0.8458 (tpp-160) cc_final: 0.8238 (tpm170) REVERT: q 52 ASN cc_start: 0.8694 (m-40) cc_final: 0.8451 (m-40) REVERT: q 78 GLU cc_start: 0.8249 (pp20) cc_final: 0.7952 (pm20) REVERT: s 7 LYS cc_start: 0.8971 (mttt) cc_final: 0.8684 (mttt) REVERT: t 18 ARG cc_start: 0.8687 (ttm-80) cc_final: 0.8391 (ttt180) outliers start: 121 outliers final: 88 residues processed: 1064 average time/residue: 1.2993 time to fit residues: 2356.6282 Evaluate side-chains 1057 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 969 time to evaluate : 5.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 20 THR Chi-restraints excluded: chain 2 residue 30 HIS Chi-restraints excluded: chain 3 residue 17 ILE Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain E residue 60 ARG Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 104 ASN Chi-restraints excluded: chain J residue 58 MET Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 79 GLU Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 55 ASN Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain T residue 70 ILE Chi-restraints excluded: chain U residue 68 LYS Chi-restraints excluded: chain U residue 88 ASN Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain Y residue 3 THR Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Z residue 53 LEU Chi-restraints excluded: chain b residue 122 GLN Chi-restraints excluded: chain b residue 189 VAL Chi-restraints excluded: chain b residue 201 VAL Chi-restraints excluded: chain c residue 76 VAL Chi-restraints excluded: chain c residue 84 ILE Chi-restraints excluded: chain c residue 97 VAL Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain e residue 79 THR Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 60 ILE Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain g residue 19 SER Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 124 LEU Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 75 MET Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain i residue 30 ASN Chi-restraints excluded: chain i residue 57 GLU Chi-restraints excluded: chain i residue 89 ASP Chi-restraints excluded: chain l residue 49 MET Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain m residue 48 LEU Chi-restraints excluded: chain m residue 60 VAL Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain n residue 27 LEU Chi-restraints excluded: chain n residue 34 VAL Chi-restraints excluded: chain o residue 19 GLU Chi-restraints excluded: chain o residue 21 ASP Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain p residue 30 LYS Chi-restraints excluded: chain q residue 8 THR Chi-restraints excluded: chain q residue 42 SER Chi-restraints excluded: chain q residue 58 ASP Chi-restraints excluded: chain q residue 62 ILE Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 43 ASP Chi-restraints excluded: chain s residue 47 LEU Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain t residue 39 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 986 random chunks: chunk 497 optimal weight: 7.9990 chunk 277 optimal weight: 4.9990 chunk 745 optimal weight: 20.0000 chunk 609 optimal weight: 8.9990 chunk 246 optimal weight: 7.9990 chunk 897 optimal weight: 9.9990 chunk 969 optimal weight: 0.6980 chunk 798 optimal weight: 20.0000 chunk 889 optimal weight: 9.9990 chunk 305 optimal weight: 5.9990 chunk 719 optimal weight: 6.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 ASN F 58 GLN G 106 ASN ** H 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 9 GLN P 71 GLN R 61 ASN W 22 ASN Y 18 ASN Y 38 GLN b 122 GLN ** c 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 121 ASN e 164 GLN ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 GLN i 4 ASN j 3 ASN j 50 ASN j 56 HIS j 58 ASN j 78 GLN l 5 ASN ** l 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 ASN p 64 GLN q 31 GLN r 54 GLN s 69 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.092 153926 Z= 0.518 Angle : 0.816 17.626 230676 Z= 0.416 Chirality : 0.046 0.460 29521 Planarity : 0.008 0.145 12109 Dihedral : 23.584 178.503 77741 Min Nonbonded Distance : 1.629 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.38 % Favored : 95.56 % Rotamer: Outliers : 4.71 % Allowed : 17.54 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.50 (0.11), residues: 5361 helix: 0.80 (0.12), residues: 1808 sheet: -0.14 (0.16), residues: 1039 loop : -1.24 (0.11), residues: 2514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP c 201 HIS 0.018 0.002 HIS P 101 PHE 0.021 0.003 PHE e 140 TYR 0.020 0.002 TYR c 184 ARG 0.014 0.001 ARG T 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1206 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 997 time to evaluate : 5.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 41 ARG cc_start: 0.8948 (ttm110) cc_final: 0.8725 (ttm110) REVERT: 2 58 ARG cc_start: 0.8789 (ttm-80) cc_final: 0.8581 (ttm110) REVERT: C 267 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7649 (mp) REVERT: E 110 GLU cc_start: 0.8300 (tp30) cc_final: 0.7813 (tp30) REVERT: E 144 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7833 (mtt180) REVERT: F 38 MET cc_start: 0.6779 (OUTLIER) cc_final: 0.6550 (mmt) REVERT: F 112 ARG cc_start: 0.5664 (tpm170) cc_final: 0.5380 (tpm170) REVERT: G 19 GLN cc_start: 0.6133 (tt0) cc_final: 0.5767 (pt0) REVERT: G 36 ASN cc_start: 0.8227 (t0) cc_final: 0.7943 (t0) REVERT: G 85 ARG cc_start: 0.7781 (tpm170) cc_final: 0.7368 (tpm170) REVERT: I 95 HIS cc_start: 0.7785 (OUTLIER) cc_final: 0.6233 (p-80) REVERT: I 108 MET cc_start: 0.8990 (mtt) cc_final: 0.8771 (mtt) REVERT: K 2 THR cc_start: 0.6230 (OUTLIER) cc_final: 0.5914 (m) REVERT: K 71 GLN cc_start: 0.8946 (mm110) cc_final: 0.8695 (tp40) REVERT: N 8 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.8113 (ttt90) REVERT: Q 1 MET cc_start: 0.7293 (tpp) cc_final: 0.7079 (tpp) REVERT: Q 77 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7684 (tmm) REVERT: S 3 ASN cc_start: 0.7405 (m110) cc_final: 0.6989 (m-40) REVERT: V 53 MET cc_start: 0.7955 (ttt) cc_final: 0.7476 (ttt) REVERT: V 70 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7856 (pm20) REVERT: V 72 LYS cc_start: 0.8708 (mtpp) cc_final: 0.8163 (mtpp) REVERT: V 77 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7908 (ptt180) REVERT: X 6 LEU cc_start: 0.8998 (mp) cc_final: 0.8725 (mp) REVERT: X 15 LYS cc_start: 0.7226 (tptt) cc_final: 0.6730 (tptt) REVERT: X 25 GLN cc_start: 0.8899 (tt0) cc_final: 0.8498 (tt0) REVERT: d 133 ASN cc_start: 0.8697 (p0) cc_final: 0.8389 (p0) REVERT: e 12 GLU cc_start: 0.8425 (pp20) cc_final: 0.8140 (pp20) REVERT: e 85 ASN cc_start: 0.9041 (OUTLIER) cc_final: 0.8830 (t0) REVERT: e 121 ASN cc_start: 0.8812 (m-40) cc_final: 0.8440 (m-40) REVERT: f 91 ARG cc_start: 0.8156 (ttt-90) cc_final: 0.7890 (ttt180) REVERT: h 43 GLU cc_start: 0.8178 (tp30) cc_final: 0.7915 (tp30) REVERT: i 125 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.6849 (t80) REVERT: j 85 ASP cc_start: 0.7747 (OUTLIER) cc_final: 0.7411 (p0) REVERT: m 32 ASN cc_start: 0.7751 (m-40) cc_final: 0.7460 (m110) REVERT: m 73 ILE cc_start: 0.9026 (pt) cc_final: 0.8768 (mp) REVERT: n 39 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8145 (tm-30) REVERT: n 43 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7614 (mt-10) REVERT: n 47 LYS cc_start: 0.8668 (mtmt) cc_final: 0.8369 (mtpt) REVERT: o 64 ARG cc_start: 0.8468 (tpp-160) cc_final: 0.8251 (tpm170) REVERT: q 70 LYS cc_start: 0.9174 (tttt) cc_final: 0.8917 (tttt) REVERT: q 78 GLU cc_start: 0.8291 (pp20) cc_final: 0.8000 (pm20) REVERT: r 32 TYR cc_start: 0.8381 (m-80) cc_final: 0.8025 (m-80) REVERT: s 83 HIS cc_start: 0.8577 (OUTLIER) cc_final: 0.8345 (m90) REVERT: u 36 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6539 (tm-30) outliers start: 209 outliers final: 139 residues processed: 1108 average time/residue: 1.3072 time to fit residues: 2487.5591 Evaluate side-chains 1118 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 965 time to evaluate : 5.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 53 ASP Chi-restraints excluded: chain 3 residue 4 GLN Chi-restraints excluded: chain 3 residue 17 ILE Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain E residue 60 ARG Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 115 ASP Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 144 ARG Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 38 MET Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 95 HIS Chi-restraints excluded: chain I residue 96 LYS Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain K residue 2 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain N residue 8 ARG Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 79 GLU Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain P residue 104 VAL Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 60 THR Chi-restraints excluded: chain Q residue 77 MET Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain S residue 16 SER Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 70 ILE Chi-restraints excluded: chain U residue 68 LYS Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain V residue 77 ARG Chi-restraints excluded: chain V residue 84 THR Chi-restraints excluded: chain W residue 2 SER Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 44 LYS Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain Y residue 3 THR Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 53 LEU Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 122 GLN Chi-restraints excluded: chain b residue 173 ILE Chi-restraints excluded: chain b residue 189 VAL Chi-restraints excluded: chain b residue 201 VAL Chi-restraints excluded: chain c residue 43 LEU Chi-restraints excluded: chain c residue 76 VAL Chi-restraints excluded: chain c residue 84 ILE Chi-restraints excluded: chain c residue 97 VAL Chi-restraints excluded: chain c residue 101 VAL Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain d residue 155 LEU Chi-restraints excluded: chain e residue 18 ASP Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain e residue 79 THR Chi-restraints excluded: chain e residue 85 ASN Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 151 LYS Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain e residue 164 GLN Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 60 ILE Chi-restraints excluded: chain f residue 66 CYS Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain g residue 19 SER Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 124 LEU Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 59 THR Chi-restraints excluded: chain h residue 75 MET Chi-restraints excluded: chain h residue 113 THR Chi-restraints excluded: chain i residue 30 ASN Chi-restraints excluded: chain i residue 57 GLU Chi-restraints excluded: chain i residue 89 ASP Chi-restraints excluded: chain i residue 125 PHE Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain k residue 82 ASP Chi-restraints excluded: chain l residue 82 ILE Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 102 LEU Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 37 VAL Chi-restraints excluded: chain m residue 48 LEU Chi-restraints excluded: chain m residue 54 ASP Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain n residue 34 VAL Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain n residue 92 ASP Chi-restraints excluded: chain o residue 19 GLU Chi-restraints excluded: chain o residue 21 ASP Chi-restraints excluded: chain o residue 33 THR Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain p residue 30 LYS Chi-restraints excluded: chain q residue 8 THR Chi-restraints excluded: chain q residue 58 ASP Chi-restraints excluded: chain q residue 62 ILE Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 43 ASP Chi-restraints excluded: chain s residue 47 LEU Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain s residue 83 HIS Chi-restraints excluded: chain t residue 39 ILE Chi-restraints excluded: chain t residue 58 ILE Chi-restraints excluded: chain u residue 36 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 986 random chunks: chunk 886 optimal weight: 2.9990 chunk 674 optimal weight: 7.9990 chunk 465 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 428 optimal weight: 3.9990 chunk 602 optimal weight: 7.9990 chunk 900 optimal weight: 8.9990 chunk 953 optimal weight: 6.9990 chunk 470 optimal weight: 0.7980 chunk 853 optimal weight: 1.9990 chunk 256 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 24 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 9 GLN O 55 ASN P 71 GLN Q 6 GLN b 122 GLN ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 55 HIS j 3 ASN j 50 ASN k 80 ASN o 20 ASN p 64 GLN q 31 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 153926 Z= 0.231 Angle : 0.616 16.535 230676 Z= 0.327 Chirality : 0.036 0.461 29521 Planarity : 0.006 0.128 12109 Dihedral : 23.388 179.537 77741 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.64 % Favored : 96.31 % Rotamer: Outliers : 3.56 % Allowed : 20.42 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.11), residues: 5361 helix: 1.32 (0.12), residues: 1811 sheet: -0.04 (0.16), residues: 1019 loop : -1.04 (0.12), residues: 2531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 201 HIS 0.008 0.001 HIS P 101 PHE 0.016 0.001 PHE S 69 TYR 0.020 0.001 TYR E 157 ARG 0.005 0.000 ARG G 163 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1165 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1007 time to evaluate : 5.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 41 ARG cc_start: 0.8926 (ttm110) cc_final: 0.8681 (ttm110) REVERT: 2 48 MET cc_start: 0.7701 (mmt) cc_final: 0.7313 (mmt) REVERT: C 25 HIS cc_start: 0.7792 (t70) cc_final: 0.7495 (t-170) REVERT: C 267 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.7570 (mp) REVERT: E 29 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8422 (tt0) REVERT: E 110 GLU cc_start: 0.8247 (tp30) cc_final: 0.7772 (tp30) REVERT: G 19 GLN cc_start: 0.6123 (tt0) cc_final: 0.5678 (pt0) REVERT: G 85 ARG cc_start: 0.7545 (tpm170) cc_final: 0.7025 (tpm170) REVERT: I 95 HIS cc_start: 0.7587 (OUTLIER) cc_final: 0.6189 (p-80) REVERT: I 108 MET cc_start: 0.8753 (mtt) cc_final: 0.8411 (mtt) REVERT: S 3 ASN cc_start: 0.7310 (m110) cc_final: 0.6921 (m-40) REVERT: V 53 MET cc_start: 0.7938 (ttt) cc_final: 0.7519 (ttt) REVERT: V 72 LYS cc_start: 0.8651 (mtpp) cc_final: 0.8100 (mtpp) REVERT: V 77 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7842 (ptt180) REVERT: X 15 LYS cc_start: 0.7108 (tptt) cc_final: 0.6578 (tptt) REVERT: X 25 GLN cc_start: 0.8858 (tt0) cc_final: 0.8407 (tt0) REVERT: b 43 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7280 (mp) REVERT: b 82 ILE cc_start: 0.7343 (tp) cc_final: 0.7105 (mt) REVERT: d 133 ASN cc_start: 0.8659 (p0) cc_final: 0.8358 (p0) REVERT: e 12 GLU cc_start: 0.8397 (pp20) cc_final: 0.8096 (pp20) REVERT: f 89 ILE cc_start: 0.8908 (mt) cc_final: 0.8576 (mp) REVERT: h 43 GLU cc_start: 0.8085 (tp30) cc_final: 0.7847 (tp30) REVERT: n 39 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7828 (tm-30) REVERT: n 43 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7396 (mt-10) REVERT: r 32 TYR cc_start: 0.8250 (m-80) cc_final: 0.7895 (m-80) REVERT: t 18 ARG cc_start: 0.8612 (ttm-80) cc_final: 0.8292 (ttt180) REVERT: u 36 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6147 (tm-30) outliers start: 158 outliers final: 103 residues processed: 1090 average time/residue: 1.3393 time to fit residues: 2506.9430 Evaluate side-chains 1090 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 981 time to evaluate : 6.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 30 HIS Chi-restraints excluded: chain 3 residue 8 LYS Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain E residue 29 GLN Chi-restraints excluded: chain E residue 60 ARG Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain I residue 95 HIS Chi-restraints excluded: chain I residue 96 LYS Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 58 MET Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain N residue 37 TYR Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 37 ASP Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain T residue 70 ILE Chi-restraints excluded: chain U residue 68 LYS Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain V residue 77 ARG Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 44 LYS Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 53 LEU Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 122 GLN Chi-restraints excluded: chain b residue 189 VAL Chi-restraints excluded: chain b residue 201 VAL Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 84 ILE Chi-restraints excluded: chain c residue 97 VAL Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain d residue 29 ASP Chi-restraints excluded: chain d residue 144 VAL Chi-restraints excluded: chain e residue 18 ASP Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain e residue 79 THR Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 60 ILE Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 59 THR Chi-restraints excluded: chain h residue 75 MET Chi-restraints excluded: chain h residue 102 ILE Chi-restraints excluded: chain i residue 57 GLU Chi-restraints excluded: chain i residue 89 ASP Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 48 LEU Chi-restraints excluded: chain m residue 59 GLU Chi-restraints excluded: chain m residue 60 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain o residue 19 GLU Chi-restraints excluded: chain o residue 21 ASP Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain p residue 30 LYS Chi-restraints excluded: chain q residue 8 THR Chi-restraints excluded: chain q residue 42 SER Chi-restraints excluded: chain q residue 58 ASP Chi-restraints excluded: chain q residue 62 ILE Chi-restraints excluded: chain r residue 68 ILE Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 43 ASP Chi-restraints excluded: chain s residue 47 LEU Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain t residue 39 ILE Chi-restraints excluded: chain u residue 36 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 986 random chunks: chunk 793 optimal weight: 8.9990 chunk 541 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 709 optimal weight: 10.0000 chunk 393 optimal weight: 10.0000 chunk 813 optimal weight: 9.9990 chunk 658 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 486 optimal weight: 5.9990 chunk 855 optimal weight: 0.0670 chunk 240 optimal weight: 5.9990 overall best weight: 3.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN I 63 GLN J 29 HIS O 9 GLN P 71 GLN S 8 GLN Y 18 ASN b 122 GLN ** c 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 120 HIS ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 3 ASN j 50 ASN p 64 GLN q 31 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.127 153926 Z= 0.339 Angle : 0.675 16.980 230676 Z= 0.354 Chirality : 0.039 0.459 29521 Planarity : 0.006 0.134 12109 Dihedral : 23.409 179.320 77741 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.35 % Favored : 95.60 % Rotamer: Outliers : 4.51 % Allowed : 21.28 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.11 (0.11), residues: 5361 helix: 1.30 (0.12), residues: 1806 sheet: -0.08 (0.17), residues: 997 loop : -1.06 (0.11), residues: 2558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 201 HIS 0.011 0.001 HIS P 101 PHE 0.018 0.002 PHE e 140 TYR 0.020 0.002 TYR c 184 ARG 0.009 0.001 ARG S 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1187 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 987 time to evaluate : 5.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 30 HIS cc_start: 0.7466 (OUTLIER) cc_final: 0.7218 (t-170) REVERT: C 267 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7605 (mp) REVERT: E 29 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8493 (tt0) REVERT: E 110 GLU cc_start: 0.8277 (tp30) cc_final: 0.7767 (tp30) REVERT: G 19 GLN cc_start: 0.6229 (tt0) cc_final: 0.5724 (pt0) REVERT: G 85 ARG cc_start: 0.7565 (tpm170) cc_final: 0.7022 (tpm170) REVERT: G 90 VAL cc_start: 0.7833 (OUTLIER) cc_final: 0.7399 (m) REVERT: I 95 HIS cc_start: 0.7641 (OUTLIER) cc_final: 0.6184 (p-80) REVERT: K 71 GLN cc_start: 0.8942 (mm110) cc_final: 0.8695 (tp40) REVERT: Q 77 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7657 (tmm) REVERT: S 3 ASN cc_start: 0.7356 (m110) cc_final: 0.6951 (m-40) REVERT: V 53 MET cc_start: 0.7958 (ttt) cc_final: 0.7678 (ttt) REVERT: V 72 LYS cc_start: 0.8692 (mtpp) cc_final: 0.8151 (mtpp) REVERT: V 77 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7901 (ptt180) REVERT: X 15 LYS cc_start: 0.7150 (tptt) cc_final: 0.6678 (tptt) REVERT: X 25 GLN cc_start: 0.8899 (tt0) cc_final: 0.8466 (tt0) REVERT: b 43 ILE cc_start: 0.7750 (OUTLIER) cc_final: 0.7320 (mp) REVERT: d 133 ASN cc_start: 0.8702 (p0) cc_final: 0.8357 (p0) REVERT: e 12 GLU cc_start: 0.8435 (pp20) cc_final: 0.8129 (pp20) REVERT: e 68 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7609 (ttt180) REVERT: e 110 MET cc_start: 0.7719 (mtm) cc_final: 0.7397 (mtm) REVERT: h 43 GLU cc_start: 0.8120 (tp30) cc_final: 0.7774 (mm-30) REVERT: i 125 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.6705 (t80) REVERT: m 32 ASN cc_start: 0.7693 (m-40) cc_final: 0.7492 (m110) REVERT: n 39 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7874 (tm-30) REVERT: n 43 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7419 (mt-10) REVERT: q 70 LYS cc_start: 0.9145 (tttt) cc_final: 0.8906 (tttt) REVERT: r 32 TYR cc_start: 0.8319 (m-80) cc_final: 0.8038 (m-80) REVERT: u 36 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6278 (tm-30) outliers start: 200 outliers final: 149 residues processed: 1093 average time/residue: 1.2661 time to fit residues: 2386.3120 Evaluate side-chains 1137 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 977 time to evaluate : 5.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 4 THR Chi-restraints excluded: chain 2 residue 30 HIS Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain E residue 29 GLN Chi-restraints excluded: chain E residue 60 ARG Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 178 SER Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 104 ASN Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain I residue 95 HIS Chi-restraints excluded: chain I residue 96 LYS Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 58 MET Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 110 ASN Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 37 TYR Chi-restraints excluded: chain N residue 79 GLU Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain N residue 110 ARG Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 55 ASN Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 37 ASP Chi-restraints excluded: chain Q residue 77 MET Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain S residue 16 SER Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 25 LEU Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 67 ASN Chi-restraints excluded: chain T residue 70 ILE Chi-restraints excluded: chain U residue 68 LYS Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain V residue 77 ARG Chi-restraints excluded: chain W residue 2 SER Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 44 LYS Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain Y residue 3 THR Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 53 LEU Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 122 GLN Chi-restraints excluded: chain b residue 173 ILE Chi-restraints excluded: chain b residue 189 VAL Chi-restraints excluded: chain b residue 201 VAL Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 84 ILE Chi-restraints excluded: chain c residue 97 VAL Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 29 ASP Chi-restraints excluded: chain d residue 144 VAL Chi-restraints excluded: chain d residue 166 GLN Chi-restraints excluded: chain e residue 18 ASP Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 37 VAL Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 68 ARG Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain e residue 79 THR Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 150 GLU Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 60 ILE Chi-restraints excluded: chain f residue 66 CYS Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 59 THR Chi-restraints excluded: chain h residue 75 MET Chi-restraints excluded: chain h residue 131 SER Chi-restraints excluded: chain i residue 57 GLU Chi-restraints excluded: chain i residue 89 ASP Chi-restraints excluded: chain i residue 125 PHE Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain l residue 117 TYR Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 48 LEU Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain n residue 34 VAL Chi-restraints excluded: chain n residue 92 ASP Chi-restraints excluded: chain o residue 19 GLU Chi-restraints excluded: chain o residue 21 ASP Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain p residue 30 LYS Chi-restraints excluded: chain q residue 8 THR Chi-restraints excluded: chain q residue 42 SER Chi-restraints excluded: chain q residue 58 ASP Chi-restraints excluded: chain r residue 68 ILE Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 43 ASP Chi-restraints excluded: chain s residue 47 LEU Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain t residue 39 ILE Chi-restraints excluded: chain u residue 36 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 986 random chunks: chunk 320 optimal weight: 0.9980 chunk 858 optimal weight: 7.9990 chunk 188 optimal weight: 9.9990 chunk 559 optimal weight: 0.4980 chunk 235 optimal weight: 20.0000 chunk 953 optimal weight: 2.9990 chunk 791 optimal weight: 4.9990 chunk 441 optimal weight: 0.6980 chunk 79 optimal weight: 5.9990 chunk 315 optimal weight: 5.9990 chunk 500 optimal weight: 3.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 63 GLN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN J 29 HIS O 9 GLN P 71 GLN Q 82 HIS S 8 GLN S 29 GLN Y 18 ASN c 176 HIS ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 3 ASN j 50 ASN p 64 GLN q 31 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 153926 Z= 0.203 Angle : 0.595 16.649 230676 Z= 0.318 Chirality : 0.035 0.448 29521 Planarity : 0.005 0.127 12109 Dihedral : 23.340 179.584 77741 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.73 % Favored : 96.21 % Rotamer: Outliers : 4.17 % Allowed : 22.05 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.11), residues: 5361 helix: 1.53 (0.12), residues: 1800 sheet: 0.02 (0.16), residues: 1034 loop : -0.95 (0.12), residues: 2527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP c 201 HIS 0.007 0.001 HIS P 101 PHE 0.014 0.001 PHE e 140 TYR 0.018 0.001 TYR c 184 ARG 0.011 0.000 ARG i 43 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1180 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 995 time to evaluate : 7.847 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: 0 4 LYS cc_start: 0.8632 (mttt) cc_final: 0.8384 (mttt) REVERT: 2 30 HIS cc_start: 0.7334 (OUTLIER) cc_final: 0.7047 (t-170) REVERT: C 267 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7553 (mp) REVERT: E 110 GLU cc_start: 0.8233 (tp30) cc_final: 0.7764 (tp30) REVERT: F 38 MET cc_start: 0.6285 (mmp) cc_final: 0.5887 (mmp) REVERT: G 19 GLN cc_start: 0.6219 (tt0) cc_final: 0.5717 (pt0) REVERT: G 85 ARG cc_start: 0.7494 (tpm170) cc_final: 0.6880 (tpm170) REVERT: G 90 VAL cc_start: 0.7660 (t) cc_final: 0.7343 (m) REVERT: I 95 HIS cc_start: 0.7446 (OUTLIER) cc_final: 0.6127 (p-80) REVERT: I 108 MET cc_start: 0.8714 (mtt) cc_final: 0.8314 (mtt) REVERT: K 71 GLN cc_start: 0.8911 (mm110) cc_final: 0.8685 (tp40) REVERT: S 3 ASN cc_start: 0.7328 (m110) cc_final: 0.6933 (m-40) REVERT: V 53 MET cc_start: 0.7910 (ttt) cc_final: 0.7575 (ttt) REVERT: V 72 LYS cc_start: 0.8666 (mtpp) cc_final: 0.8120 (mtpp) REVERT: V 77 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7800 (ptt180) REVERT: X 15 LYS cc_start: 0.7153 (tptt) cc_final: 0.6631 (tptt) REVERT: X 25 GLN cc_start: 0.8866 (tt0) cc_final: 0.8432 (tt0) REVERT: b 43 ILE cc_start: 0.7663 (OUTLIER) cc_final: 0.7296 (mt) REVERT: d 133 ASN cc_start: 0.8662 (p0) cc_final: 0.8337 (p0) REVERT: e 12 GLU cc_start: 0.8395 (pp20) cc_final: 0.8098 (pp20) REVERT: e 110 MET cc_start: 0.7688 (mtm) cc_final: 0.7399 (mtm) REVERT: e 120 HIS cc_start: 0.7286 (OUTLIER) cc_final: 0.6675 (p90) REVERT: f 89 ILE cc_start: 0.8895 (mt) cc_final: 0.8565 (mp) REVERT: h 43 GLU cc_start: 0.8105 (tp30) cc_final: 0.7854 (tp30) REVERT: i 125 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.6739 (t80) REVERT: j 84 VAL cc_start: 0.7595 (OUTLIER) cc_final: 0.7296 (t) REVERT: j 85 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.7275 (p0) REVERT: q 20 LYS cc_start: 0.8938 (mtpt) cc_final: 0.8596 (mtmt) REVERT: q 70 LYS cc_start: 0.9141 (tttt) cc_final: 0.8866 (tttt) REVERT: r 32 TYR cc_start: 0.8218 (m-80) cc_final: 0.7966 (m-80) REVERT: t 18 ARG cc_start: 0.8565 (ttm-80) cc_final: 0.8255 (ttt180) REVERT: u 36 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6871 (tt0) outliers start: 185 outliers final: 140 residues processed: 1094 average time/residue: 1.3093 time to fit residues: 2470.3923 Evaluate side-chains 1129 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 979 time to evaluate : 5.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 4 THR Chi-restraints excluded: chain 2 residue 30 HIS Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain E residue 60 ARG Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 104 ASN Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 95 HIS Chi-restraints excluded: chain I residue 96 LYS Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 58 MET Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 110 ASN Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain N residue 37 TYR Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain N residue 110 ARG Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain O residue 55 ASN Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 37 ASP Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain S residue 16 SER Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 67 ASN Chi-restraints excluded: chain T residue 70 ILE Chi-restraints excluded: chain U residue 68 LYS Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain V residue 77 ARG Chi-restraints excluded: chain W residue 2 SER Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 44 LYS Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain X residue 32 LYS Chi-restraints excluded: chain Y residue 4 ILE Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 189 VAL Chi-restraints excluded: chain b residue 201 VAL Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 84 ILE Chi-restraints excluded: chain c residue 97 VAL Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 29 ASP Chi-restraints excluded: chain d residue 144 VAL Chi-restraints excluded: chain d residue 166 GLN Chi-restraints excluded: chain e residue 18 ASP Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain e residue 79 THR Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 150 GLU Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 66 CYS Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 54 ASN Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 59 THR Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain h residue 102 ILE Chi-restraints excluded: chain h residue 131 SER Chi-restraints excluded: chain i residue 57 GLU Chi-restraints excluded: chain i residue 89 ASP Chi-restraints excluded: chain i residue 125 PHE Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 102 LEU Chi-restraints excluded: chain l residue 123 LYS Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 48 LEU Chi-restraints excluded: chain m residue 54 ASP Chi-restraints excluded: chain m residue 59 GLU Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain n residue 34 VAL Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain n residue 92 ASP Chi-restraints excluded: chain o residue 19 GLU Chi-restraints excluded: chain o residue 21 ASP Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain p residue 30 LYS Chi-restraints excluded: chain p residue 73 ASP Chi-restraints excluded: chain q residue 8 THR Chi-restraints excluded: chain q residue 42 SER Chi-restraints excluded: chain q residue 58 ASP Chi-restraints excluded: chain r residue 68 ILE Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 43 ASP Chi-restraints excluded: chain s residue 47 LEU Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain t residue 39 ILE Chi-restraints excluded: chain u residue 36 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 986 random chunks: chunk 919 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 543 optimal weight: 0.9980 chunk 696 optimal weight: 6.9990 chunk 539 optimal weight: 8.9990 chunk 803 optimal weight: 7.9990 chunk 532 optimal weight: 0.0370 chunk 950 optimal weight: 2.9990 chunk 594 optimal weight: 2.9990 chunk 579 optimal weight: 0.6980 chunk 438 optimal weight: 4.9990 overall best weight: 1.1460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN I 63 GLN J 29 HIS O 9 GLN P 71 GLN S 8 GLN Y 18 ASN d 102 ASN ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 3 ASN j 50 ASN ** k 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 32 ASN o 20 ASN p 64 GLN q 31 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 153926 Z= 0.147 Angle : 0.556 16.618 230676 Z= 0.298 Chirality : 0.032 0.428 29521 Planarity : 0.005 0.123 12109 Dihedral : 23.269 179.284 77741 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.47 % Favored : 96.47 % Rotamer: Outliers : 3.79 % Allowed : 22.97 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.12), residues: 5361 helix: 1.71 (0.12), residues: 1806 sheet: 0.17 (0.17), residues: 1016 loop : -0.79 (0.12), residues: 2539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP c 201 HIS 0.008 0.001 HIS f 11 PHE 0.016 0.001 PHE S 69 TYR 0.018 0.001 TYR o 78 ARG 0.006 0.000 ARG S 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1162 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 994 time to evaluate : 5.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 4 LYS cc_start: 0.8607 (mttt) cc_final: 0.8376 (mttt) REVERT: 0 6 ARG cc_start: 0.7518 (ttm170) cc_final: 0.7224 (ttp80) REVERT: 2 30 HIS cc_start: 0.7192 (OUTLIER) cc_final: 0.6876 (t-170) REVERT: C 25 HIS cc_start: 0.7803 (t70) cc_final: 0.7485 (t-170) REVERT: C 125 ARG cc_start: 0.7805 (mmp80) cc_final: 0.7592 (mmt-90) REVERT: C 267 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7519 (mp) REVERT: E 110 GLU cc_start: 0.8198 (tp30) cc_final: 0.7747 (tp30) REVERT: G 19 GLN cc_start: 0.6305 (tt0) cc_final: 0.5732 (pt0) REVERT: G 85 ARG cc_start: 0.7500 (tpm170) cc_final: 0.6822 (tpm170) REVERT: I 95 HIS cc_start: 0.7370 (OUTLIER) cc_final: 0.6151 (p-80) REVERT: I 108 MET cc_start: 0.8639 (mtt) cc_final: 0.8168 (mtt) REVERT: K 71 GLN cc_start: 0.8911 (mm110) cc_final: 0.8710 (tp40) REVERT: O 97 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.6988 (mmt-90) REVERT: S 3 ASN cc_start: 0.7302 (m110) cc_final: 0.6942 (m-40) REVERT: V 53 MET cc_start: 0.7893 (ttt) cc_final: 0.7558 (ttt) REVERT: V 72 LYS cc_start: 0.8651 (mtpp) cc_final: 0.8093 (mtpp) REVERT: V 77 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7683 (ptt180) REVERT: X 15 LYS cc_start: 0.7117 (tptt) cc_final: 0.6636 (tptt) REVERT: X 25 GLN cc_start: 0.8858 (tt0) cc_final: 0.8405 (tt0) REVERT: Y 44 ARG cc_start: 0.8433 (mmt180) cc_final: 0.8104 (mmt180) REVERT: d 133 ASN cc_start: 0.8629 (p0) cc_final: 0.8298 (p0) REVERT: e 12 GLU cc_start: 0.8361 (pp20) cc_final: 0.8047 (pp20) REVERT: e 68 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7565 (ttt180) REVERT: e 110 MET cc_start: 0.7709 (mtm) cc_final: 0.7472 (mtm) REVERT: e 120 HIS cc_start: 0.7265 (OUTLIER) cc_final: 0.6579 (p90) REVERT: f 91 ARG cc_start: 0.7864 (tpt-90) cc_final: 0.7517 (tpt-90) REVERT: h 43 GLU cc_start: 0.8073 (tp30) cc_final: 0.7816 (tp30) REVERT: j 85 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.7371 (p0) REVERT: q 20 LYS cc_start: 0.8879 (mtpt) cc_final: 0.8534 (mtmt) REVERT: q 70 LYS cc_start: 0.9139 (tttt) cc_final: 0.8876 (tttt) REVERT: r 32 TYR cc_start: 0.8070 (m-80) cc_final: 0.7812 (m-80) REVERT: r 52 GLN cc_start: 0.8452 (tp40) cc_final: 0.8204 (tt0) REVERT: t 18 ARG cc_start: 0.8457 (ttm-80) cc_final: 0.8156 (ttt180) REVERT: u 36 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.5758 (tm-30) outliers start: 168 outliers final: 120 residues processed: 1087 average time/residue: 1.2154 time to fit residues: 2261.6403 Evaluate side-chains 1096 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 967 time to evaluate : 5.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 30 HIS Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 104 ASN Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 95 HIS Chi-restraints excluded: chain I residue 96 LYS Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 58 MET Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 110 ASN Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain N residue 37 TYR Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 55 ASN Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain O residue 97 ARG Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 70 ILE Chi-restraints excluded: chain U residue 68 LYS Chi-restraints excluded: chain U residue 72 LYS Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain V residue 77 ARG Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain Y residue 3 THR Chi-restraints excluded: chain Y residue 4 ILE Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 173 ILE Chi-restraints excluded: chain b residue 189 VAL Chi-restraints excluded: chain b residue 201 VAL Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 84 ILE Chi-restraints excluded: chain c residue 97 VAL Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain d residue 29 ASP Chi-restraints excluded: chain d residue 144 VAL Chi-restraints excluded: chain d residue 166 GLN Chi-restraints excluded: chain e residue 18 ASP Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 68 ARG Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain e residue 79 THR Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 150 GLU Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 54 ASN Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 59 THR Chi-restraints excluded: chain h residue 75 MET Chi-restraints excluded: chain h residue 131 SER Chi-restraints excluded: chain i residue 89 ASP Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 102 LEU Chi-restraints excluded: chain l residue 117 TYR Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 48 LEU Chi-restraints excluded: chain m residue 54 ASP Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 89 LEU Chi-restraints excluded: chain n residue 34 VAL Chi-restraints excluded: chain o residue 19 GLU Chi-restraints excluded: chain o residue 21 ASP Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain p residue 73 ASP Chi-restraints excluded: chain q residue 8 THR Chi-restraints excluded: chain q residue 42 SER Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 58 ASP Chi-restraints excluded: chain r residue 68 ILE Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 43 ASP Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 47 LEU Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain u residue 36 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 986 random chunks: chunk 587 optimal weight: 1.9990 chunk 379 optimal weight: 5.9990 chunk 567 optimal weight: 0.0870 chunk 286 optimal weight: 5.9990 chunk 186 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 chunk 604 optimal weight: 8.9990 chunk 647 optimal weight: 20.0000 chunk 469 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 746 optimal weight: 10.0000 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN H 7 GLN I 63 GLN J 29 HIS O 9 GLN S 8 GLN b 122 GLN ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 55 HIS ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 3 ASN j 50 ASN p 64 GLN q 31 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 153926 Z= 0.383 Angle : 0.698 17.079 230676 Z= 0.362 Chirality : 0.040 0.442 29521 Planarity : 0.006 0.135 12109 Dihedral : 23.350 179.787 77741 Min Nonbonded Distance : 1.680 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.38 % Favored : 95.56 % Rotamer: Outliers : 5.07 % Allowed : 22.09 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.07 (0.11), residues: 5361 helix: 1.45 (0.12), residues: 1801 sheet: -0.01 (0.17), residues: 1013 loop : -0.95 (0.12), residues: 2547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP c 201 HIS 0.011 0.001 HIS P 101 PHE 0.018 0.002 PHE S 69 TYR 0.029 0.002 TYR s 80 ARG 0.013 0.001 ARG C 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1190 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 965 time to evaluate : 5.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 30 HIS cc_start: 0.7372 (OUTLIER) cc_final: 0.7113 (t-170) REVERT: C 267 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7604 (mp) REVERT: E 110 GLU cc_start: 0.8285 (tp30) cc_final: 0.7793 (tp30) REVERT: E 150 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7626 (p0) REVERT: G 19 GLN cc_start: 0.6283 (tt0) cc_final: 0.5834 (pt0) REVERT: G 85 ARG cc_start: 0.7590 (tpm170) cc_final: 0.6834 (tpm170) REVERT: I 95 HIS cc_start: 0.7592 (OUTLIER) cc_final: 0.6143 (p-80) REVERT: K 71 GLN cc_start: 0.8945 (mm110) cc_final: 0.8687 (tp40) REVERT: L 80 GLU cc_start: 0.6148 (OUTLIER) cc_final: 0.4795 (tt0) REVERT: O 88 GLU cc_start: 0.7100 (tm-30) cc_final: 0.6670 (tm-30) REVERT: O 97 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7154 (mmt-90) REVERT: Q 77 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7610 (tmm) REVERT: S 3 ASN cc_start: 0.7362 (m110) cc_final: 0.6950 (m-40) REVERT: S 68 ARG cc_start: 0.7134 (ttm-80) cc_final: 0.6721 (ttm-80) REVERT: S 73 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7836 (tp) REVERT: V 53 MET cc_start: 0.7934 (ttt) cc_final: 0.7643 (ttt) REVERT: V 72 LYS cc_start: 0.8709 (mtpp) cc_final: 0.8152 (mtpp) REVERT: V 77 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7902 (ptt180) REVERT: X 15 LYS cc_start: 0.7259 (tptt) cc_final: 0.6766 (tptt) REVERT: X 25 GLN cc_start: 0.8913 (tt0) cc_final: 0.8484 (tt0) REVERT: b 43 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.7303 (mt) REVERT: d 133 ASN cc_start: 0.8644 (p0) cc_final: 0.8313 (p0) REVERT: e 12 GLU cc_start: 0.8452 (pp20) cc_final: 0.8111 (pp20) REVERT: e 68 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7666 (ttt180) REVERT: e 110 MET cc_start: 0.7849 (mtm) cc_final: 0.7408 (mtm) REVERT: e 120 HIS cc_start: 0.7352 (OUTLIER) cc_final: 0.6618 (p90) REVERT: f 55 HIS cc_start: 0.7955 (OUTLIER) cc_final: 0.7163 (m90) REVERT: h 43 GLU cc_start: 0.8109 (tp30) cc_final: 0.7838 (tp30) REVERT: i 125 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.6635 (t80) REVERT: j 85 ASP cc_start: 0.7767 (OUTLIER) cc_final: 0.7380 (p0) REVERT: n 39 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7721 (tm-30) REVERT: n 43 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7536 (mt-10) REVERT: n 47 LYS cc_start: 0.8655 (mtmt) cc_final: 0.8384 (mtmt) REVERT: q 20 LYS cc_start: 0.8975 (mtpt) cc_final: 0.8576 (mtmt) REVERT: q 70 LYS cc_start: 0.9163 (tttt) cc_final: 0.8912 (tttt) REVERT: r 32 TYR cc_start: 0.8342 (m-80) cc_final: 0.8015 (m-80) REVERT: u 36 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6221 (tt0) outliers start: 225 outliers final: 170 residues processed: 1087 average time/residue: 1.3231 time to fit residues: 2485.0834 Evaluate side-chains 1143 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 957 time to evaluate : 5.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 20 THR Chi-restraints excluded: chain 1 residue 4 THR Chi-restraints excluded: chain 2 residue 30 HIS Chi-restraints excluded: chain 3 residue 4 GLN Chi-restraints excluded: chain 3 residue 17 ILE Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 104 ASN Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 95 HIS Chi-restraints excluded: chain I residue 96 LYS Chi-restraints excluded: chain I residue 98 GLU Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 58 MET Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain K residue 53 GLU Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 110 ASN Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 37 TYR Chi-restraints excluded: chain N residue 56 ASP Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 55 ASN Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain O residue 97 ARG Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 77 MET Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 16 SER Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 70 ILE Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain U residue 68 LYS Chi-restraints excluded: chain U residue 72 LYS Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain V residue 77 ARG Chi-restraints excluded: chain W residue 2 SER Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain X residue 32 LYS Chi-restraints excluded: chain Y residue 3 THR Chi-restraints excluded: chain Y residue 4 ILE Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 53 LEU Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 122 GLN Chi-restraints excluded: chain b residue 173 ILE Chi-restraints excluded: chain b residue 189 VAL Chi-restraints excluded: chain b residue 201 VAL Chi-restraints excluded: chain c residue 77 ILE Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 84 ILE Chi-restraints excluded: chain c residue 97 VAL Chi-restraints excluded: chain c residue 101 VAL Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 29 ASP Chi-restraints excluded: chain d residue 144 VAL Chi-restraints excluded: chain d residue 166 GLN Chi-restraints excluded: chain e residue 18 ASP Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 37 VAL Chi-restraints excluded: chain e residue 68 ARG Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain e residue 79 THR Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 150 GLU Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain g residue 89 MET Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 59 THR Chi-restraints excluded: chain h residue 75 MET Chi-restraints excluded: chain h residue 131 SER Chi-restraints excluded: chain i residue 57 GLU Chi-restraints excluded: chain i residue 89 ASP Chi-restraints excluded: chain i residue 125 PHE Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 47 GLU Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain k residue 106 ILE Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 82 ILE Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 102 LEU Chi-restraints excluded: chain l residue 117 TYR Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 48 LEU Chi-restraints excluded: chain m residue 54 ASP Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain n residue 34 VAL Chi-restraints excluded: chain n residue 92 ASP Chi-restraints excluded: chain o residue 19 GLU Chi-restraints excluded: chain o residue 21 ASP Chi-restraints excluded: chain o residue 33 THR Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain p residue 30 LYS Chi-restraints excluded: chain p residue 73 ASP Chi-restraints excluded: chain q residue 8 THR Chi-restraints excluded: chain q residue 18 MET Chi-restraints excluded: chain q residue 39 ILE Chi-restraints excluded: chain q residue 42 SER Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 58 ASP Chi-restraints excluded: chain r residue 68 ILE Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 43 ASP Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 47 LEU Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain t residue 39 ILE Chi-restraints excluded: chain u residue 36 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 986 random chunks: chunk 864 optimal weight: 0.9980 chunk 910 optimal weight: 9.9990 chunk 830 optimal weight: 6.9990 chunk 885 optimal weight: 9.9990 chunk 533 optimal weight: 1.9990 chunk 385 optimal weight: 4.9990 chunk 695 optimal weight: 6.9990 chunk 271 optimal weight: 4.9990 chunk 800 optimal weight: 10.0000 chunk 837 optimal weight: 8.9990 chunk 882 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN J 29 HIS O 9 GLN P 71 GLN P 87 GLN S 8 GLN Y 18 ASN ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 55 HIS ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 3 ASN j 50 ASN m 32 ASN p 64 GLN q 31 GLN t 3 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 153926 Z= 0.300 Angle : 0.649 16.723 230676 Z= 0.341 Chirality : 0.038 0.445 29521 Planarity : 0.006 0.131 12109 Dihedral : 23.357 179.613 77741 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.16 % Favored : 95.78 % Rotamer: Outliers : 4.51 % Allowed : 22.86 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.11), residues: 5361 helix: 1.48 (0.12), residues: 1800 sheet: -0.06 (0.17), residues: 1026 loop : -0.98 (0.12), residues: 2535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP c 201 HIS 0.009 0.001 HIS P 101 PHE 0.023 0.002 PHE e 140 TYR 0.031 0.002 TYR s 80 ARG 0.012 0.001 ARG C 175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1172 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 972 time to evaluate : 5.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 4 LYS cc_start: 0.8651 (mttt) cc_final: 0.8374 (mttt) REVERT: 2 30 HIS cc_start: 0.7391 (OUTLIER) cc_final: 0.7104 (t-170) REVERT: C 25 HIS cc_start: 0.7882 (t70) cc_final: 0.7626 (t-170) REVERT: C 267 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7589 (mp) REVERT: E 110 GLU cc_start: 0.8265 (tp30) cc_final: 0.7783 (tp30) REVERT: E 150 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7616 (p0) REVERT: G 19 GLN cc_start: 0.6240 (tt0) cc_final: 0.5855 (pt0) REVERT: G 85 ARG cc_start: 0.7586 (tpm170) cc_final: 0.6773 (tpm170) REVERT: I 95 HIS cc_start: 0.7574 (OUTLIER) cc_final: 0.6182 (p-80) REVERT: J 113 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7518 (ptpp) REVERT: K 2 THR cc_start: 0.6003 (OUTLIER) cc_final: 0.5452 (m) REVERT: K 71 GLN cc_start: 0.8938 (mm110) cc_final: 0.8680 (tp40) REVERT: M 98 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8380 (mt) REVERT: O 88 GLU cc_start: 0.7081 (tm-30) cc_final: 0.6686 (tm-30) REVERT: O 97 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7034 (mmt-90) REVERT: Q 77 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7614 (tmm) REVERT: S 3 ASN cc_start: 0.7347 (m110) cc_final: 0.6930 (m-40) REVERT: V 53 MET cc_start: 0.7936 (ttt) cc_final: 0.7653 (ttt) REVERT: V 72 LYS cc_start: 0.8656 (mtpp) cc_final: 0.8134 (mtpp) REVERT: V 77 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7886 (ptt180) REVERT: X 15 LYS cc_start: 0.7221 (tptt) cc_final: 0.6740 (tptt) REVERT: X 25 GLN cc_start: 0.8897 (tt0) cc_final: 0.8475 (tt0) REVERT: b 43 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.7301 (mt) REVERT: d 133 ASN cc_start: 0.8659 (p0) cc_final: 0.8357 (p0) REVERT: e 12 GLU cc_start: 0.8435 (pp20) cc_final: 0.8108 (pp20) REVERT: e 68 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7678 (ttt180) REVERT: e 110 MET cc_start: 0.7858 (mtm) cc_final: 0.7436 (mtm) REVERT: e 120 HIS cc_start: 0.7385 (OUTLIER) cc_final: 0.6621 (p90) REVERT: f 55 HIS cc_start: 0.7854 (OUTLIER) cc_final: 0.7397 (m90) REVERT: h 43 GLU cc_start: 0.8099 (tp30) cc_final: 0.7836 (tp30) REVERT: i 125 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.6693 (t80) REVERT: j 85 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7371 (p0) REVERT: n 39 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7781 (tm-30) REVERT: n 43 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7581 (mt-10) REVERT: q 20 LYS cc_start: 0.8918 (mtpt) cc_final: 0.8488 (mtmt) REVERT: q 70 LYS cc_start: 0.9165 (tttt) cc_final: 0.8917 (tttt) REVERT: r 32 TYR cc_start: 0.8377 (m-80) cc_final: 0.8008 (m-80) REVERT: r 70 TYR cc_start: 0.7451 (m-80) cc_final: 0.7080 (m-80) REVERT: u 36 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6211 (tt0) outliers start: 200 outliers final: 164 residues processed: 1083 average time/residue: 1.2525 time to fit residues: 2322.5039 Evaluate side-chains 1147 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 966 time to evaluate : 5.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 26 MET Chi-restraints excluded: chain 2 residue 30 HIS Chi-restraints excluded: chain 2 residue 53 ASP Chi-restraints excluded: chain 3 residue 4 GLN Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 157 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 95 HIS Chi-restraints excluded: chain I residue 96 LYS Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 58 MET Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 113 LYS Chi-restraints excluded: chain K residue 2 THR Chi-restraints excluded: chain K residue 53 GLU Chi-restraints excluded: chain K residue 84 LEU Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 110 ASN Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 37 TYR Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 56 ASP Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 55 ASN Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain O residue 97 ARG Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 77 MET Chi-restraints excluded: chain R residue 96 ILE Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 16 SER Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain S residue 79 VAL Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 70 ILE Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain V residue 77 ARG Chi-restraints excluded: chain W residue 2 SER Chi-restraints excluded: chain W residue 13 VAL Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain X residue 32 LYS Chi-restraints excluded: chain Y residue 3 THR Chi-restraints excluded: chain Y residue 4 ILE Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 53 LEU Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 173 ILE Chi-restraints excluded: chain b residue 189 VAL Chi-restraints excluded: chain b residue 201 VAL Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 84 ILE Chi-restraints excluded: chain c residue 97 VAL Chi-restraints excluded: chain c residue 101 VAL Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 29 ASP Chi-restraints excluded: chain d residue 144 VAL Chi-restraints excluded: chain d residue 166 GLN Chi-restraints excluded: chain e residue 18 ASP Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 37 VAL Chi-restraints excluded: chain e residue 68 ARG Chi-restraints excluded: chain e residue 72 THR Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain e residue 79 THR Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 59 THR Chi-restraints excluded: chain h residue 75 MET Chi-restraints excluded: chain h residue 76 VAL Chi-restraints excluded: chain h residue 131 SER Chi-restraints excluded: chain i residue 57 GLU Chi-restraints excluded: chain i residue 89 ASP Chi-restraints excluded: chain i residue 125 PHE Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 82 ILE Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 102 LEU Chi-restraints excluded: chain l residue 117 TYR Chi-restraints excluded: chain l residue 123 LYS Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 48 LEU Chi-restraints excluded: chain m residue 54 ASP Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain n residue 27 LEU Chi-restraints excluded: chain n residue 34 VAL Chi-restraints excluded: chain n residue 92 ASP Chi-restraints excluded: chain o residue 19 GLU Chi-restraints excluded: chain o residue 21 ASP Chi-restraints excluded: chain o residue 33 THR Chi-restraints excluded: chain o residue 39 LEU Chi-restraints excluded: chain p residue 30 LYS Chi-restraints excluded: chain p residue 73 ASP Chi-restraints excluded: chain q residue 8 THR Chi-restraints excluded: chain q residue 18 MET Chi-restraints excluded: chain q residue 42 SER Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 58 ASP Chi-restraints excluded: chain r residue 68 ILE Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 43 ASP Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 47 LEU Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain t residue 39 ILE Chi-restraints excluded: chain u residue 36 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 986 random chunks: chunk 581 optimal weight: 0.2980 chunk 936 optimal weight: 4.9990 chunk 571 optimal weight: 0.0270 chunk 444 optimal weight: 0.7980 chunk 651 optimal weight: 20.0000 chunk 982 optimal weight: 6.9990 chunk 904 optimal weight: 6.9990 chunk 782 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 604 optimal weight: 8.9990 chunk 479 optimal weight: 0.9980 overall best weight: 1.4240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN J 29 HIS O 9 GLN P 71 GLN S 8 GLN V 29 GLN Y 18 ASN b 96 HIS ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 55 HIS ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 35 GLN j 3 ASN j 50 ASN m 32 ASN p 64 GLN q 31 GLN t 3 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 153926 Z= 0.167 Angle : 0.597 16.552 230676 Z= 0.320 Chirality : 0.034 0.440 29521 Planarity : 0.005 0.125 12109 Dihedral : 23.372 179.743 77741 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.79 % Favored : 96.14 % Rotamer: Outliers : 3.61 % Allowed : 23.94 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.11), residues: 5361 helix: 1.61 (0.12), residues: 1800 sheet: 0.09 (0.17), residues: 1013 loop : -0.91 (0.12), residues: 2548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 201 HIS 0.047 0.001 HIS f 55 PHE 0.022 0.001 PHE S 69 TYR 0.031 0.001 TYR s 80 ARG 0.015 0.000 ARG C 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10722 Ramachandran restraints generated. 5361 Oldfield, 0 Emsley, 5361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1126 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 966 time to evaluate : 5.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 4 LYS cc_start: 0.8645 (mttt) cc_final: 0.8363 (mttt) REVERT: 0 6 ARG cc_start: 0.7459 (ttm170) cc_final: 0.7072 (ttp80) REVERT: 2 30 HIS cc_start: 0.7285 (OUTLIER) cc_final: 0.6982 (t-170) REVERT: C 25 HIS cc_start: 0.7859 (t70) cc_final: 0.7612 (t-170) REVERT: C 125 ARG cc_start: 0.7819 (mmp80) cc_final: 0.7596 (mmt-90) REVERT: C 267 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7546 (mp) REVERT: E 110 GLU cc_start: 0.8234 (tp30) cc_final: 0.7765 (tp30) REVERT: E 150 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7575 (p0) REVERT: G 19 GLN cc_start: 0.6240 (tt0) cc_final: 0.5858 (pt0) REVERT: G 85 ARG cc_start: 0.7544 (tpm170) cc_final: 0.6744 (tpm170) REVERT: I 95 HIS cc_start: 0.7476 (OUTLIER) cc_final: 0.6104 (p-80) REVERT: I 108 MET cc_start: 0.8533 (mtt) cc_final: 0.8026 (mtt) REVERT: K 2 THR cc_start: 0.5711 (OUTLIER) cc_final: 0.5071 (m) REVERT: K 71 GLN cc_start: 0.8917 (mm110) cc_final: 0.8677 (tp40) REVERT: L 80 GLU cc_start: 0.6085 (OUTLIER) cc_final: 0.4814 (tt0) REVERT: M 98 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8304 (mt) REVERT: O 88 GLU cc_start: 0.7053 (tm-30) cc_final: 0.6620 (tm-30) REVERT: O 97 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7022 (mmt-90) REVERT: S 3 ASN cc_start: 0.7328 (m110) cc_final: 0.6916 (m-40) REVERT: V 53 MET cc_start: 0.7947 (ttt) cc_final: 0.7586 (ttt) REVERT: V 72 LYS cc_start: 0.8633 (mtpp) cc_final: 0.8106 (mtpp) REVERT: V 77 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7806 (ptt180) REVERT: X 15 LYS cc_start: 0.7182 (tptt) cc_final: 0.6703 (tptt) REVERT: X 25 GLN cc_start: 0.8878 (tt0) cc_final: 0.8442 (tt0) REVERT: b 43 ILE cc_start: 0.7595 (OUTLIER) cc_final: 0.7275 (mt) REVERT: d 107 MET cc_start: 0.7424 (mmt) cc_final: 0.7222 (mtt) REVERT: d 133 ASN cc_start: 0.8631 (p0) cc_final: 0.8330 (p0) REVERT: d 172 TRP cc_start: 0.6592 (p90) cc_final: 0.6387 (p90) REVERT: e 12 GLU cc_start: 0.8393 (pp20) cc_final: 0.8094 (pp20) REVERT: e 68 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7644 (ttt180) REVERT: e 110 MET cc_start: 0.7784 (mtm) cc_final: 0.7405 (mtm) REVERT: e 120 HIS cc_start: 0.7325 (OUTLIER) cc_final: 0.6485 (p90) REVERT: g 79 ARG cc_start: 0.6599 (mmt180) cc_final: 0.6170 (ttt-90) REVERT: h 43 GLU cc_start: 0.8099 (tp30) cc_final: 0.7843 (tp30) REVERT: i 125 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.6736 (t80) REVERT: j 85 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.7322 (p0) REVERT: q 20 LYS cc_start: 0.8903 (mtpt) cc_final: 0.8495 (mtmt) REVERT: q 70 LYS cc_start: 0.9139 (tttt) cc_final: 0.8865 (tttt) REVERT: r 32 TYR cc_start: 0.8346 (m-80) cc_final: 0.7981 (m-80) REVERT: r 70 TYR cc_start: 0.7434 (m-80) cc_final: 0.7069 (m-80) REVERT: u 36 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6266 (tt0) outliers start: 160 outliers final: 134 residues processed: 1054 average time/residue: 1.2721 time to fit residues: 2297.5592 Evaluate side-chains 1110 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 961 time to evaluate : 5.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 26 MET Chi-restraints excluded: chain 1 residue 4 THR Chi-restraints excluded: chain 2 residue 30 HIS Chi-restraints excluded: chain 2 residue 53 ASP Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 15 ILE Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 150 ASP Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 87 CYS Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 104 ASN Chi-restraints excluded: chain G residue 122 THR Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 95 HIS Chi-restraints excluded: chain I residue 96 LYS Chi-restraints excluded: chain I residue 98 GLU Chi-restraints excluded: chain J residue 53 LYS Chi-restraints excluded: chain J residue 58 MET Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain K residue 2 THR Chi-restraints excluded: chain K residue 91 ILE Chi-restraints excluded: chain L residue 55 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 110 ASN Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 133 THR Chi-restraints excluded: chain L residue 136 VAL Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 98 LEU Chi-restraints excluded: chain N residue 37 TYR Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain O residue 19 ASP Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 55 ASN Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain O residue 97 ARG Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 70 ILE Chi-restraints excluded: chain T residue 75 THR Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain V residue 77 ARG Chi-restraints excluded: chain W residue 2 SER Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain Y residue 4 ILE Chi-restraints excluded: chain Y residue 13 SER Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 173 ILE Chi-restraints excluded: chain b residue 189 VAL Chi-restraints excluded: chain b residue 201 VAL Chi-restraints excluded: chain c residue 47 LEU Chi-restraints excluded: chain c residue 83 ASP Chi-restraints excluded: chain c residue 84 ILE Chi-restraints excluded: chain c residue 97 VAL Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain d residue 29 ASP Chi-restraints excluded: chain d residue 144 VAL Chi-restraints excluded: chain d residue 166 GLN Chi-restraints excluded: chain e residue 18 ASP Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 37 VAL Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 68 ARG Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain e residue 79 THR Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 150 GLU Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 54 ASN Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 59 THR Chi-restraints excluded: chain h residue 75 MET Chi-restraints excluded: chain h residue 131 SER Chi-restraints excluded: chain i residue 35 GLN Chi-restraints excluded: chain i residue 57 GLU Chi-restraints excluded: chain i residue 89 ASP Chi-restraints excluded: chain i residue 125 PHE Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain l residue 33 VAL Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 102 LEU Chi-restraints excluded: chain l residue 117 TYR Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 48 LEU Chi-restraints excluded: chain m residue 54 ASP Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain n residue 27 LEU Chi-restraints excluded: chain o residue 19 GLU Chi-restraints excluded: chain o residue 21 ASP Chi-restraints excluded: chain p residue 30 LYS Chi-restraints excluded: chain p residue 73 ASP Chi-restraints excluded: chain q residue 8 THR Chi-restraints excluded: chain q residue 18 MET Chi-restraints excluded: chain q residue 42 SER Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 58 ASP Chi-restraints excluded: chain r residue 68 ILE Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 43 ASP Chi-restraints excluded: chain s residue 47 LEU Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain u residue 36 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 986 random chunks: chunk 621 optimal weight: 10.0000 chunk 833 optimal weight: 8.9990 chunk 239 optimal weight: 6.9990 chunk 721 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 217 optimal weight: 5.9990 chunk 783 optimal weight: 0.7980 chunk 327 optimal weight: 1.9990 chunk 804 optimal weight: 0.0870 chunk 99 optimal weight: 5.9990 chunk 144 optimal weight: 6.9990 overall best weight: 2.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 29 HIS O 9 GLN P 71 GLN S 8 GLN U 7 ASN Y 18 ASN ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 3 ASN j 50 ASN m 32 ASN p 64 GLN q 31 GLN t 3 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.128266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.087099 restraints weight = 254809.045| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.15 r_work: 0.2862 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 153926 Z= 0.302 Angle : 0.649 16.773 230676 Z= 0.341 Chirality : 0.037 0.445 29521 Planarity : 0.006 0.131 12109 Dihedral : 23.348 179.953 77741 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.40 % Favored : 95.54 % Rotamer: Outliers : 4.04 % Allowed : 23.69 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.11), residues: 5361 helix: 1.51 (0.12), residues: 1808 sheet: -0.01 (0.17), residues: 1016 loop : -0.96 (0.12), residues: 2537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP c 201 HIS 0.010 0.001 HIS P 101 PHE 0.023 0.002 PHE e 140 TYR 0.023 0.002 TYR s 80 ARG 0.015 0.001 ARG C 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 38187.49 seconds wall clock time: 664 minutes 37.91 seconds (39877.91 seconds total)