Starting phenix.real_space_refine on Wed Mar 20 11:23:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3a_21031/03_2024/6v3a_21031_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3a_21031/03_2024/6v3a_21031.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3a_21031/03_2024/6v3a_21031_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3a_21031/03_2024/6v3a_21031_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3a_21031/03_2024/6v3a_21031_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3a_21031/03_2024/6v3a_21031.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3a_21031/03_2024/6v3a_21031.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3a_21031/03_2024/6v3a_21031_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3a_21031/03_2024/6v3a_21031_updated.pdb" } resolution = 2.82 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= 0.117 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 93 5.21 5 S 139 5.16 5 Na 1 4.78 5 C 70757 2.51 5 N 26298 2.21 5 O 40212 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 ARG 40": "NH1" <-> "NH2" Residue "1 ARG 3": "NH1" <-> "NH2" 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 ASP 53": "OD1" <-> "OD2" 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 ASP 22": "OD1" <-> "OD2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C ARG 87": "NH1" <-> "NH2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "C ARG 111": "NH1" <-> "NH2" Residue "C ASP 121": "OD1" <-> "OD2" Residue "C ARG 133": "NH1" <-> "NH2" Residue "C ARG 167": "NH1" <-> "NH2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C GLU 199": "OE1" <-> "OE2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "C GLU 236": "OE1" <-> "OE2" 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 ARG 93": "NH1" <-> "NH2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D ARG 157": "NH1" <-> "NH2" Residue "D ASP 170": "OD1" <-> "OD2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D ASP 184": "OD1" <-> "OD2" Residue "D ASP 203": "OD1" <-> "OD2" Residue "D ARG 207": "NH1" <-> "NH2" Residue "E GLU 15": "OE1" <-> "OE2" Residue "E ARG 20": "NH1" <-> "NH2" Residue "E GLU 24": "OE1" <-> "OE2" 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 ASP 115": "OD1" <-> "OD2" Residue "E GLU 121": "OE1" <-> "OE2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E GLU 132": "OE1" <-> "OE2" Residue "E ASP 150": "OD1" <-> "OD2" Residue "E ARG 161": "NH1" <-> "NH2" Residue "E PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 198": "OE1" <-> "OE2" Residue "F ASP 10": "OD1" <-> "OD2" Residue "F GLU 18": "OE1" <-> "OE2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F ARG 80": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ASP 94": "OD1" <-> "OD2" Residue "F ASP 101": "OD1" <-> "OD2" 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 PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 150": "NH1" <-> "NH2" Residue "F ARG 161": "NH1" <-> "NH2" 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 ARG 69": "NH1" <-> "NH2" Residue "G ARG 163": "NH1" <-> "NH2" Residue "G GLU 167": "OE1" <-> "OE2" Residue "G ARG 171": "NH1" <-> "NH2" Residue "G GLU 173": "OE1" <-> "OE2" Residue "H ASP 2": "OD1" <-> "OD2" Residue "H PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 10": "OE1" <-> "OE2" Residue "I ARG 27": "NH1" <-> "NH2" Residue "I ARG 34": "NH1" <-> "NH2" Residue "I ARG 35": "NH1" <-> "NH2" Residue "I GLU 60": "OE1" <-> "OE2" Residue "I ASP 71": "OD1" <-> "OD2" Residue "I TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 76": "NH1" <-> "NH2" Residue "I PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 90": "OE1" <-> "OE2" Residue "I ARG 103": "NH1" <-> "NH2" Residue "J ASP 9": "OD1" <-> "OD2" 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 ARG 104": "NH1" <-> "NH2" Residue "K ARG 16": "NH1" <-> "NH2" Residue "K GLU 17": "OE1" <-> "OE2" Residue "K ARG 19": "NH1" <-> "NH2" Residue "K GLU 95": "OE1" <-> "OE2" Residue "K ARG 104": "NH1" <-> "NH2" 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 ARG 41": "NH1" <-> "NH2" Residue "L ARG 45": "NH1" <-> "NH2" Residue "L ARG 52": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 115": "NH1" <-> "NH2" 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 ARG 46": "NH1" <-> "NH2" Residue "M ARG 63": "NH1" <-> "NH2" Residue "M ARG 64": "NH1" <-> "NH2" Residue "M ARG 96": "NH1" <-> "NH2" Residue "M GLU 114": "OE1" <-> "OE2" 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 ARG 80": "NH1" <-> "NH2" Residue "N ARG 93": "NH1" <-> "NH2" Residue "N ASP 107": "OD1" <-> "OD2" Residue "N ARG 110": "NH1" <-> "NH2" Residue "N GLU 115": "OE1" <-> "OE2" Residue "N PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 37": "OE1" <-> "OE2" Residue "O ARG 56": "NH1" <-> "NH2" Residue "O ARG 91": "NH1" <-> "NH2" Residue "O ASP 94": "OD1" <-> "OD2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O ARG 97": "NH1" <-> "NH2" Residue "O ARG 112": "NH1" <-> "NH2" Residue "O GLU 115": "OE1" <-> "OE2" 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 ASP 49": "OD1" <-> "OD2" 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 "Q GLU 16": "OE1" <-> "OE2" Residue "Q GLU 23": "OE1" <-> "OE2" Residue "Q ASP 36": "OD1" <-> "OD2" 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 "R ARG 8": "NH1" <-> "NH2" Residue "R ARG 25": "NH1" <-> "NH2" Residue "R ASP 67": "OD1" <-> "OD2" Residue "R ARG 95": "NH1" <-> "NH2" Residue "S ARG 5": "NH1" <-> "NH2" Residue "S ASP 24": "OD1" <-> "OD2" 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 TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 30": "OD1" <-> "OD2" Residue "T ARG 31": "NH1" <-> "NH2" Residue "T GLU 60": "OE1" <-> "OE2" Residue "T ASP 79": "OD1" <-> "OD2" Residue "U PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 11": "NH1" <-> "NH2" Residue "U ARG 22": "NH1" <-> "NH2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 44": "OE1" <-> "OE2" Residue "V PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 83": "OE1" <-> "OE2" Residue "W ARG 37": "NH1" <-> "NH2" Residue "W ARG 48": "NH1" <-> "NH2" Residue "W ASP 70": "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 "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 ASP 30": "OD1" <-> "OD2" Residue "Z ARG 39": "NH1" <-> "NH2" Residue "Z ARG 51": "NH1" <-> "NH2" Residue "b ARG 9": "NH1" <-> "NH2" Residue "b ARG 30": "NH1" <-> "NH2" Residue "b ARG 37": "NH1" <-> "NH2" Residue "b PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 76": "NH1" <-> "NH2" Residue "b ARG 83": "NH1" <-> "NH2" Residue "b GLU 84": "OE1" <-> "OE2" Residue "b ARG 88": "NH1" <-> "NH2" Residue "b TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 110": "NH1" <-> "NH2" Residue "b ARG 134": "NH1" <-> "NH2" Residue "b ARG 141": "NH1" <-> "NH2" Residue "b ARG 148": "NH1" <-> "NH2" Residue "b ASP 169": "OD1" <-> "OD2" Residue "b TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 206": "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 ASP 107": "OD1" <-> "OD2" Residue "c ARG 108": "NH1" <-> "NH2" Residue "c ASP 110": "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 GLU 152": "OE1" <-> "OE2" Residue "c ARG 156": "NH1" <-> "NH2" Residue "c GLU 161": "OE1" <-> "OE2" Residue "c GLU 166": "OE1" <-> "OE2" Residue "c ARG 169": "NH1" <-> "NH2" 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 ASP 18": "OD1" <-> "OD2" Residue "d ASP 29": "OD1" <-> "OD2" 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 PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 162": "OE1" <-> "OE2" Residue "d ASP 189": "OD1" <-> "OD2" Residue "e ASP 40": "OD1" <-> "OD2" Residue "e PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 49": "NH1" <-> "NH2" Residue "e ARG 53": "NH1" <-> "NH2" Residue "e ASP 74": "OD1" <-> "OD2" 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 150": "OE1" <-> "OE2" Residue "f GLU 65": "OE1" <-> "OE2" Residue "f ARG 79": "NH1" <-> "NH2" Residue "f ARG 91": "NH1" <-> "NH2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "g ARG 10": "NH1" <-> "NH2" Residue "g PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 67": "OE1" <-> "OE2" Residue "g TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 90": "OE1" <-> "OE2" Residue "g ARG 95": "NH1" <-> "NH2" Residue "g ARG 102": "NH1" <-> "NH2" Residue "g ARG 119": "NH1" <-> "NH2" Residue "g GLU 129": "OE1" <-> "OE2" Residue "g ARG 138": "NH1" <-> "NH2" Residue "g ASP 140": "OD1" <-> "OD2" Residue "h ARG 13": "NH1" <-> "NH2" Residue "h GLU 55": "OE1" <-> "OE2" Residue "h ARG 88": "NH1" <-> "NH2" Residue "h ASP 91": "OD1" <-> "OD2" Residue "h ARG 115": "NH1" <-> "NH2" Residue "h ARG 118": "NH1" <-> "NH2" Residue "h GLU 125": "OE1" <-> "OE2" 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 54": "OE1" <-> "OE2" Residue "i ARG 122": "NH1" <-> "NH2" Residue "i PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 5": "NH1" <-> "NH2" Residue "j ARG 7": "NH1" <-> "NH2" Residue "j ARG 16": "NH1" <-> "NH2" Residue "j GLU 24": "OE1" <-> "OE2" Residue "j GLU 27": "OE1" <-> "OE2" Residue "j ARG 45": "NH1" <-> "NH2" Residue "j ASP 60": "OD1" <-> "OD2" Residue "j TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 72": "NH1" <-> "NH2" Residue "j ASP 85": "OD1" <-> "OD2" Residue "j ASP 97": "OD1" <-> "OD2" Residue "k ARG 13": "NH1" <-> "NH2" Residue "k GLU 17": "OE1" <-> "OE2" Residue "k PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 36": "NH1" <-> "NH2" Residue "k GLU 93": "OE1" <-> "OE2" Residue "k ARG 97": "NH1" <-> "NH2" Residue "k TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 99": "NH1" <-> "NH2" Residue "l ASP 103": "OD1" <-> "OD2" Residue "l TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 3": "NH1" <-> "NH2" Residue "m ASP 11": "OD1" <-> "OD2" Residue "m PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 46": "NH1" <-> "NH2" Residue "m ASP 50": "OD1" <-> "OD2" Residue "m ARG 57": "NH1" <-> "NH2" Residue "m ARG 79": "NH1" <-> "NH2" 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 39": "OE1" <-> "OE2" Residue "n GLU 43": "OE1" <-> "OE2" Residue "n ARG 59": "NH1" <-> "NH2" Residue "n ARG 61": "NH1" <-> "NH2" Residue "o ASP 7": "OD1" <-> "OD2" Residue "o PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 58": "NH1" <-> "NH2" Residue "o ARG 64": "NH1" <-> "NH2" 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 "q ARG 40": "NH1" <-> "NH2" Residue "q ARG 41": "NH1" <-> "NH2" Residue "q ASP 49": "OD1" <-> "OD2" Residue "r TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 43": "NH1" <-> "NH2" Residue "r ARG 53": "NH1" <-> "NH2" Residue "r ARG 63": "NH1" <-> "NH2" Residue "s ARG 28": "NH1" <-> "NH2" 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 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-5265/modules/chem_data/mon_lib" Total number of atoms: 142113 Number of models: 1 Model: "" Number of chains: 74 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': 259, 'rna2p_pyr': 146, 'rna3p': 12, 'rna3p_pur': 1389, 'rna3p_pyr': 1083} Link IDs: {'rna2p': 408, 'rna3p': 2483} 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': 107, 'rna2p_pyr': 82, 'rna3p': 8, 'rna3p_pur': 756, 'rna3p_pyr': 574} Link IDs: {'rna2p': 189, 'rna3p': 1338} 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': 5, 'rna3p': 4, 'rna3p_pur': 34, 'rna3p_pyr': 29} Link IDs: {'rna2p': 9, 'rna3p': 67} 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 50 Unusual residues: {' MG': 49, ' NA': 1} Classifications: {'undetermined': 50} Link IDs: {None: 49} Chain: "sN" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Unusual residues: {' MG': 44} Classifications: {'undetermined': 44} Link IDs: {None: 43} Chain: "AN" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 319 Classifications: {'water': 319} Link IDs: {None: 318} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "sN" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 163 Classifications: {'water': 163} Link IDs: {None: 162} Chain: "i" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "j" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "t" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1382 SG CYS 3 11 44.201 120.047 135.650 1.00 32.31 S ATOM 1503 SG CYS 3 27 44.034 124.091 134.676 1.00 27.88 S Time building chain proxies: 55.84, per 1000 atoms: 0.39 Number of scatterers: 142113 At special positions: 0 Unit cell: (224.504, 250.04, 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 139 16.00 P 4612 15.00 Mg 93 11.99 Na 1 11.00 O 40212 8.00 N 26298 7.00 C 70757 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 55.69 Conformation dependent library (CDL) restraints added in 6.4 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 " 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: 9994 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 39.1% alpha, 18.8% beta 1411 base pairs and 2363 stacking pairs defined. Time for finding SS restraints: 73.14 Creating SS restraints... Processing helix chain '0' and resid 22 through 27 Proline residue: 0 27 - end of helix Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 25 removed outlier: 4.013A pdb=" N THR 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) removed outlier: 5.230A 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 15 removed outlier: 3.715A pdb=" N ARG 2 13 " --> pdb=" O GLY 2 9 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LYS 2 15 " --> pdb=" O ALA 2 11 " (cutoff:3.500A) Processing helix chain '2' and resid 31 through 36 removed outlier: 4.688A pdb=" N LYS 2 35 " --> pdb=" O ILE 2 31 " (cutoff:3.500A) removed outlier: 5.101A 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: 4.120A pdb=" N ARG 2 44 " --> pdb=" O ILE 2 40 " (cutoff:3.500A) Processing helix chain '2' and resid 50 through 62 removed outlier: 4.544A pdb=" N ALA 2 55 " --> pdb=" O VAL 2 51 " (cutoff:3.500A) removed outlier: 5.025A 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 15 removed outlier: 3.545A pdb=" N ARG C 14 " --> pdb=" O SER C 10 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N PHE C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 10 through 15' Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.697A pdb=" N VAL C 34 " --> pdb=" O TYR C 30 " (cutoff:3.500A) removed outlier: 5.453A 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: 3.946A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 3.940A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.454A 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 263 through 268 removed outlier: 4.069A pdb=" N ILE C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ILE C 268 " --> pdb=" O THR C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 263 through 268' Processing helix chain 'D' and resid 57 through 62 removed outlier: 5.543A pdb=" N THR D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 73 removed outlier: 3.783A pdb=" N ALA D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 91 removed outlier: 3.567A pdb=" N LEU D 90 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 86 through 91' Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'E' and resid 15 through 20 removed outlier: 3.536A pdb=" N GLY E 19 " --> pdb=" O GLU E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 39 removed outlier: 3.681A pdb=" N GLY E 38 " --> pdb=" O TYR E 34 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG E 39 " --> pdb=" O LEU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 52 removed outlier: 6.219A 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: 3.734A pdb=" N LEU E 133 " --> pdb=" O LYS E 129 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU E 140 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN E 141 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 164 removed outlier: 4.572A pdb=" N ASN E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 4.405A 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 182 removed outlier: 3.834A pdb=" N PHE E 182 " --> pdb=" O SER E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 199 Processing helix chain 'F' and resid 5 through 21 removed outlier: 3.571A pdb=" N ASN F 9 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASP F 10 " --> pdb=" O ALA F 6 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU F 11 " --> pdb=" O ARG F 7 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS F 15 " --> pdb=" O GLU F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 removed outlier: 4.582A pdb=" N ASP F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 62 removed outlier: 3.686A pdb=" N GLY F 52 " --> pdb=" O LYS F 48 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLY F 62 " --> pdb=" O GLN F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 111 removed outlier: 4.452A 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: 3.669A pdb=" N GLY F 166 " --> pdb=" O THR F 162 " (cutoff:3.500A) removed outlier: 4.167A 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: 3.902A pdb=" N ARG G 152 " --> pdb=" O ILE G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 34 removed outlier: 4.971A pdb=" N ILE H 31 " --> pdb=" O ARG H 27 " (cutoff:3.500A) Proline residue: H 32 - end of helix Processing helix chain 'H' and resid 40 through 48 removed outlier: 3.543A pdb=" N GLU H 48 " --> pdb=" O THR H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 59 removed outlier: 4.594A pdb=" N GLU H 58 " --> pdb=" O LEU H 54 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA H 59 " --> pdb=" O GLU H 55 " (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: 3.761A pdb=" N LYS I 120 " --> pdb=" O TYR I 116 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) removed outlier: 4.481A 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 39 through 44 removed outlier: 3.640A pdb=" N ARG K 43 " --> pdb=" O GLY K 39 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LYS K 44 " --> pdb=" O GLN K 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 39 through 44' Processing helix chain 'K' and resid 58 through 64 removed outlier: 3.508A 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: 3.963A pdb=" N LEU K 74 " --> pdb=" O SER K 70 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS K 75 " --> pdb=" O GLN K 71 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR K 76 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 5.807A 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 88 removed outlier: 4.101A pdb=" N LEU K 84 " --> pdb=" O ARG K 80 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N SER K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LYS K 86 " --> pdb=" O SER K 82 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL K 87 " --> pdb=" O GLU K 83 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N GLU K 88 " --> pdb=" O LEU K 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 80 through 88' Processing helix chain 'K' and resid 93 through 101 removed outlier: 3.575A pdb=" N ASN K 101 " --> pdb=" O LEU K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 141 removed outlier: 3.582A 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: 3.682A pdb=" N ALA L 123 " --> pdb=" O ALA L 119 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS L 124 " --> pdb=" O LEU L 120 " (cutoff:3.500A) removed outlier: 3.538A 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 56 removed outlier: 3.918A pdb=" N ARG M 45 " --> pdb=" O ALA M 41 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ARG M 46 " --> pdb=" O LYS M 42 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL M 47 " --> pdb=" O GLU M 43 " (cutoff:3.500A) Proline residue: M 50 - end of helix Processing helix chain 'M' and resid 59 through 71 Processing helix chain 'M' and resid 72 through 88 removed outlier: 4.782A 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: 4.492A pdb=" N SER N 14 " --> pdb=" O ARG N 10 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N THR N 15 " --> pdb=" O ARG N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 63 removed outlier: 4.249A pdb=" N SER N 61 " --> pdb=" O ALA N 57 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY N 62 " --> pdb=" O SER N 58 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N THR N 63 " --> pdb=" O LEU N 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 66 through 85 Processing helix chain 'N' and resid 100 through 113 removed outlier: 3.886A pdb=" N GLY N 113 " --> pdb=" O ALA N 109 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 17 removed outlier: 3.932A pdb=" N SER O 14 " --> pdb=" O ALA O 10 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLN O 15 " --> pdb=" O ILE O 11 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU O 16 " --> pdb=" O GLU O 12 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LYS O 17 " --> pdb=" O ASN O 13 " (cutoff:3.500A) Processing helix chain 'O' and resid 107 through 112 removed outlier: 3.535A pdb=" N ALA O 111 " --> pdb=" O SER O 107 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ARG O 112 " --> pdb=" O GLY O 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 107 through 112' Processing helix chain 'O' and resid 100 through 105 removed outlier: 3.509A pdb=" N LEU O 103 " --> pdb=" O LEU O 100 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG O 104 " --> pdb=" O TYR O 101 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP O 105 " --> pdb=" O TYR O 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 100 through 105' Processing helix chain 'P' and resid 7 through 22 removed outlier: 4.138A pdb=" N LYS P 22 " --> pdb=" O LEU P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 31 removed outlier: 3.789A pdb=" N ARG P 30 " --> pdb=" O GLY P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 73 removed outlier: 3.872A pdb=" N ARG P 51 " --> pdb=" O TYR P 47 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N LYS P 54 " --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 4.070A 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: 3.882A pdb=" N LEU R 19 " --> pdb=" O GLN R 15 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL R 20 " --> pdb=" O LYS R 16 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU R 23 " --> pdb=" O LEU R 19 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE R 24 " --> pdb=" O VAL R 20 " (cutoff:3.500A) removed outlier: 3.515A 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: 4.491A pdb=" N VAL R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU R 46 " --> pdb=" O LYS R 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 3 through 10 removed outlier: 4.403A pdb=" N TYR S 7 " --> pdb=" O ASN S 3 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN S 8 " --> pdb=" O GLU S 4 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU S 10 " --> pdb=" O ILE S 6 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 25 Processing helix chain 'S' and resid 38 through 50 Processing helix chain 'T' and resid 64 through 69 removed outlier: 3.873A pdb=" N VAL T 68 " --> pdb=" O HIS T 64 " (cutoff:3.500A) removed outlier: 5.414A 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: 5.161A pdb=" N GLY U 17 " --> pdb=" O GLU U 13 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 28 removed outlier: 3.731A pdb=" N SER U 28 " --> pdb=" O LEU U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 58 removed outlier: 3.980A pdb=" N SER U 57 " --> pdb=" O LYS U 53 " (cutoff:3.500A) removed outlier: 5.425A 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: 4.484A pdb=" N GLN W 74 " --> pdb=" O ASP W 70 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLY W 75 " --> pdb=" O LEU W 71 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 9 removed outlier: 4.401A pdb=" N GLU X 8 " --> pdb=" O LYS X 4 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LYS X 9 " --> pdb=" O ASP X 5 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 35 Processing helix chain 'X' and resid 39 through 63 removed outlier: 4.469A pdb=" N VAL X 43 " --> pdb=" O LYS X 39 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLN X 44 " --> pdb=" O SER X 40 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN X 63 " --> pdb=" O GLU X 59 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 27 removed outlier: 3.509A pdb=" N LEU Y 26 " --> pdb=" O CYS Y 22 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY Y 27 " --> pdb=" O LEU Y 23 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 51 removed outlier: 3.538A pdb=" N MET Y 46 " --> pdb=" O SER Y 42 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL Y 50 " --> pdb=" O MET Y 46 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 19 removed outlier: 5.054A pdb=" N HIS Z 19 " --> pdb=" O MET Z 15 " (cutoff:3.500A) Processing helix chain 'b' and resid 7 through 15 removed outlier: 3.629A pdb=" N LEU b 11 " --> pdb=" O SER b 7 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 34 removed outlier: 4.971A pdb=" N ILE b 33 " --> pdb=" O MET b 29 " (cutoff:3.500A) removed outlier: 5.848A 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: 3.702A 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 79 through 90 removed outlier: 3.738A pdb=" N ARG b 83 " --> pdb=" O SER b 79 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU b 84 " --> pdb=" O ASN b 80 " (cutoff:3.500A) Processing helix chain 'b' and resid 107 through 126 removed outlier: 4.400A pdb=" N GLN b 111 " --> pdb=" O LYS b 107 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N SER b 112 " --> pdb=" O THR b 108 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE b 113 " --> pdb=" O LEU b 109 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER b 123 " --> pdb=" O LEU b 119 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLN b 124 " --> pdb=" O GLN b 120 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP b 125 " --> pdb=" O THR b 121 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLY b 126 " --> pdb=" O GLN b 122 " (cutoff:3.500A) Processing helix chain 'b' and resid 127 through 132 removed outlier: 5.864A pdb=" N LEU b 131 " --> pdb=" O THR b 127 " (cutoff:3.500A) removed outlier: 5.615A 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: 4.154A pdb=" N SER b 149 " --> pdb=" O LYS b 145 " (cutoff:3.500A) Processing helix chain 'b' and resid 167 through 172 removed outlier: 3.555A pdb=" N ALA b 172 " --> pdb=" O VAL b 168 " (cutoff:3.500A) Processing helix chain 'b' and resid 173 through 182 Processing helix chain 'b' and resid 208 through 227 removed outlier: 3.596A pdb=" N LEU b 224 " --> pdb=" O ALA b 220 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLY b 226 " --> pdb=" O ALA b 222 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LYS b 227 " --> pdb=" O ILE b 223 " (cutoff:3.500A) Processing helix chain 'b' and resid 101 through 106 removed outlier: 4.400A pdb=" N TRP b 106 " --> pdb=" O GLY b 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 101 through 106' Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.863A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 25 through 48 removed outlier: 5.157A pdb=" N ALA c 30 " --> pdb=" O PRO c 26 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N GLU c 31 " --> pdb=" O LYS c 27 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LYS c 48 " --> pdb=" O THR c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 78 removed outlier: 4.377A pdb=" N GLY c 78 " --> pdb=" O GLY c 74 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 96 removed outlier: 3.700A pdb=" N GLU c 85 " --> pdb=" O GLY c 81 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY c 96 " --> pdb=" O THR c 92 " (cutoff:3.500A) Processing helix chain 'c' and resid 112 through 127 removed outlier: 4.021A pdb=" N ARG c 127 " --> pdb=" O GLN c 123 " (cutoff:3.500A) Processing helix chain 'c' and resid 129 through 145 removed outlier: 3.776A pdb=" N GLY c 145 " --> pdb=" O THR c 141 " (cutoff:3.500A) Processing helix chain 'c' and resid 210 through 215 removed outlier: 4.199A pdb=" N VAL c 214 " --> pdb=" O GLY c 210 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.285A 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: 5.231A pdb=" N LYS d 85 " --> pdb=" O ALA d 81 " (cutoff:3.500A) Processing helix chain 'd' and resid 87 through 99 removed outlier: 3.728A pdb=" N ASN d 91 " --> pdb=" O ALA d 87 " (cutoff:3.500A) removed outlier: 4.076A 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: 3.986A pdb=" N ARG d 123 " --> pdb=" O LEU d 119 " (cutoff:3.500A) Processing helix chain 'd' and resid 148 through 154 removed outlier: 4.476A pdb=" N GLN d 153 " --> pdb=" O GLU d 149 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLN d 154 " --> pdb=" O GLY d 150 " (cutoff:3.500A) Processing helix chain 'd' and resid 155 through 168 removed outlier: 4.334A pdb=" N GLU d 162 " --> pdb=" O LYS d 158 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU d 163 " --> pdb=" O ASN d 159 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG d 167 " --> pdb=" O LEU d 163 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N GLY d 168 " --> pdb=" O ALA d 164 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 194 removed outlier: 3.700A pdb=" N LEU d 193 " --> pdb=" O ASP d 189 " (cutoff:3.500A) Proline residue: d 194 - end of helix No H-bonds generated for 'chain 'd' and resid 189 through 194' Processing helix chain 'd' and resid 198 through 208 removed outlier: 4.516A pdb=" N ILE d 202 " --> pdb=" O ASN d 198 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N LYS d 208 " --> pdb=" O GLU d 204 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 3.775A pdb=" N GLU e 64 " --> pdb=" O SER e 60 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA e 65 " --> pdb=" O LYS e 61 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN e 69 " --> pdb=" O ALA e 65 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N MET e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 107 through 118 removed outlier: 3.743A pdb=" N VAL e 113 " --> pdb=" O ALA e 109 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 146 removed outlier: 3.559A pdb=" N ARG e 144 " --> pdb=" O PHE e 140 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP e 145 " --> pdb=" O LYS e 141 " (cutoff:3.500A) removed outlier: 3.761A 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: 3.760A pdb=" N ILE e 163 " --> pdb=" O SER e 159 " (cutoff:3.500A) removed outlier: 4.204A 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: 4.788A pdb=" N ASP f 16 " --> pdb=" O PRO f 12 " (cutoff:3.500A) Processing helix chain 'f' and resid 17 through 31 removed outlier: 5.214A pdb=" N GLU f 23 " --> pdb=" O VAL f 19 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG f 24 " --> pdb=" O GLY f 20 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLN f 28 " --> pdb=" O ARG f 24 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE f 29 " --> pdb=" O TYR f 25 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLU f 31 " --> pdb=" O SER f 27 " (cutoff:3.500A) Processing helix chain 'f' and resid 70 through 82 removed outlier: 4.040A pdb=" N PHE f 78 " --> pdb=" O LEU f 74 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR f 80 " --> pdb=" O GLU f 76 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN f 81 " --> pdb=" O LEU f 77 " (cutoff:3.500A) removed outlier: 5.425A 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: 3.665A pdb=" N ALA g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS g 53 " --> pdb=" O ARG g 49 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN g 54 " --> pdb=" O VAL g 50 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 4.042A pdb=" N VAL g 69 " --> pdb=" O THR g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 112 removed outlier: 3.673A pdb=" N ARG g 111 " --> pdb=" O ALA g 107 " (cutoff:3.500A) removed outlier: 5.724A 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: 3.888A pdb=" N LYS g 136 " --> pdb=" O GLY g 132 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N GLU g 139 " --> pdb=" O ILE g 135 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 removed outlier: 3.826A 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 38 removed outlier: 4.627A pdb=" N GLY i 38 " --> pdb=" O GLU i 34 " (cutoff:3.500A) Processing helix chain 'i' and resid 39 through 54 removed outlier: 3.619A 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: 3.575A pdb=" N GLU i 90 " --> pdb=" O ILE i 86 " (cutoff:3.500A) Processing helix chain 'i' and resid 91 through 100 removed outlier: 4.824A pdb=" N VAL i 95 " --> pdb=" O THR i 91 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN i 98 " --> pdb=" O PRO i 94 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA i 99 " --> pdb=" O VAL i 95 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 3.737A pdb=" N ILE j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 3.738A pdb=" N VAL j 84 " --> pdb=" O THR j 80 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP j 85 " --> pdb=" O ASP j 81 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 4.074A pdb=" N GLN k 49 " --> pdb=" O THR k 45 " (cutoff:3.500A) removed outlier: 3.632A 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: 4.170A pdb=" N SER k 57 " --> pdb=" O GLY k 53 " (cutoff:3.500A) removed outlier: 3.584A 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: 3.921A pdb=" N VAL k 64 " --> pdb=" O PHE k 60 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASP k 75 " --> pdb=" O LYS k 71 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TYR k 76 " --> pdb=" O ALA k 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 93 through 103 removed outlier: 3.806A pdb=" N GLY k 103 " --> pdb=" O LEU k 99 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 Processing helix chain 'l' and resid 113 through 118 removed outlier: 4.769A pdb=" N TYR l 117 " --> pdb=" O SER l 113 " (cutoff:3.500A) removed outlier: 3.892A 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: 3.942A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.775A 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: 3.614A pdb=" N LEU m 48 " --> pdb=" O LYS m 44 " (cutoff:3.500A) removed outlier: 5.411A 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: 3.676A pdb=" N ALA m 55 " --> pdb=" O ALA m 51 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS m 62 " --> pdb=" O ALA m 58 " (cutoff:3.500A) removed outlier: 4.336A 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: 3.759A pdb=" N GLY m 84 " --> pdb=" O LEU m 80 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 94 removed outlier: 4.812A pdb=" N ARG m 93 " --> pdb=" O LEU m 89 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N SER m 94 " --> pdb=" O ARG m 90 " (cutoff:3.500A) Processing helix chain 'n' and resid 3 through 21 removed outlier: 3.554A pdb=" N TYR n 20 " --> pdb=" O THR n 16 " (cutoff:3.500A) Processing helix chain 'n' and resid 22 through 33 Processing helix chain 'n' and resid 37 through 52 Proline residue: n 52 - end of helix Processing helix chain 'n' and resid 56 through 61 removed outlier: 4.500A pdb=" N LEU n 60 " --> pdb=" O SER n 56 " (cutoff:3.500A) removed outlier: 5.757A 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: 3.888A pdb=" N ASP n 86 " --> pdb=" O ASN n 82 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 16 Processing helix chain 'o' and resid 24 through 44 removed outlier: 4.057A pdb=" N GLY o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS o 42 " --> pdb=" O ASP o 38 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 4.209A 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: 3.537A pdb=" N GLN p 81 " --> pdb=" O HIS p 77 " (cutoff:3.500A) removed outlier: 3.652A 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: 3.752A pdb=" N TYR r 32 " --> pdb=" O THR r 28 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N THR r 34 " --> pdb=" O LYS r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 46 removed outlier: 3.622A 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 70 through 76 removed outlier: 4.458A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.187A 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: 3.554A pdb=" N LYS t 8 " --> pdb=" O SER t 4 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU t 24 " --> pdb=" O HIS t 20 " (cutoff:3.500A) removed outlier: 3.880A 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: 3.688A pdb=" N GLY t 65 " --> pdb=" O MET t 61 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 87 removed outlier: 3.798A pdb=" N LEU t 86 " --> pdb=" O GLN t 82 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA t 87 " --> pdb=" O VAL t 83 " (cutoff:3.500A) Processing helix chain 'u' and resid 39 through 54 removed outlier: 4.179A pdb=" N GLN u 43 " --> pdb=" O GLU u 39 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS u 54 " --> pdb=" O ALA u 50 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '0' and resid 15 through 20 removed outlier: 6.292A pdb=" N TYR 0 15 " --> pdb=" O SER 0 9 " (cutoff:3.500A) removed outlier: 5.788A 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: 4.109A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ALA C 76 " --> pdb=" O LYS C 115 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS C 115 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL C 78 " --> pdb=" O GLY C 113 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLY C 127 " --> pdb=" O LYS C 115 " (cutoff:3.500A) removed outlier: 4.933A 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: 4.210A pdb=" N SER C 139 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N SER C 170 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 4.282A 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: 5.335A pdb=" N HIS C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 4.750A 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: 4.396A pdb=" N VAL D 21 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL D 27 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY D 202 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ASP D 203 " --> pdb=" O GLN D 115 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLN D 115 " --> pdb=" O ASP D 203 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLU D 171 " --> pdb=" O SER D 116 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N GLY D 118 " --> pdb=" O GLY D 169 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLY D 169 " --> pdb=" O GLY D 118 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 37 through 40 removed outlier: 6.889A pdb=" N GLN D 50 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY D 97 " --> pdb=" O ILE D 35 " (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: 5.527A pdb=" N SER D 188 " --> pdb=" O VAL D 30 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 47 through 52 removed outlier: 5.035A pdb=" N GLN D 47 " --> pdb=" O VAL D 85 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'E' and resid 43 through 46 No H-bonds generated for sheet with id= 12 Processing sheet with id= 13, first strand: chain 'E' and resid 116 through 119 removed outlier: 3.652A pdb=" N LYS E 184 " --> pdb=" O ARG E 144 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'F' and resid 33 through 40 removed outlier: 3.653A pdb=" N MET F 38 " --> pdb=" O CYS F 87 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N CYS F 87 " --> pdb=" O MET F 38 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL F 40 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE F 85 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N TRP F 83 " --> pdb=" O ALA F 70 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N THR F 68 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N CYS F 87 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL F 66 " --> pdb=" O CYS F 87 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'F' and resid 127 through 133 removed outlier: 4.624A pdb=" N TYR F 128 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE F 156 " --> pdb=" O TYR F 128 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'G' and resid 16 through 19 Processing sheet with id= 17, first strand: chain 'G' and resid 82 through 89 removed outlier: 6.263A pdb=" N LEU G 133 " --> pdb=" O ARG G 85 " (cutoff:3.500A) removed outlier: 6.032A 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 'I' and resid 52 through 57 removed outlier: 5.133A pdb=" N ASP I 19 " --> pdb=" O LEU I 140 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'I' and resid 74 through 78 removed outlier: 4.161A pdb=" N GLY I 83 " --> pdb=" O THR I 78 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'J' and resid 18 through 21 removed outlier: 4.153A pdb=" N THR J 6 " --> pdb=" O CYS J 21 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ASN J 82 " --> pdb=" O MET J 7 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ASP J 81 " --> pdb=" O LYS J 66 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS J 66 " --> pdb=" O ASP J 81 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG J 64 " --> pdb=" O ALA J 83 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'J' and resid 68 through 71 removed outlier: 3.906A pdb=" N SER J 75 " --> pdb=" O ARG J 71 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'L' and resid 38 through 41 No H-bonds generated for sheet with id= 23 Processing sheet with id= 24, first strand: chain 'L' and resid 63 through 66 removed outlier: 3.719A pdb=" N TYR L 104 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE L 32 " --> pdb=" O ILE L 106 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N SER L 31 " --> pdb=" O ARG L 134 " (cutoff:3.500A) removed outlier: 6.375A 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 Processing sheet with id= 27, first strand: chain 'O' and resid 52 through 56 removed outlier: 3.783A pdb=" N ALA O 52 " --> pdb=" O THR O 63 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ARG O 56 " --> pdb=" O ASN O 59 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASN O 59 " --> pdb=" O ARG O 56 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N THR O 63 " --> pdb=" O ILE O 51 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ASP O 27 " --> pdb=" O VAL O 50 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR O 28 " --> pdb=" O LYS O 90 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS O 86 " --> pdb=" O GLN O 32 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'O' and resid 60 through 67 removed outlier: 7.688A 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: 4.240A pdb=" N GLU Q 18 " --> pdb=" O ILE Q 98 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLU Q 95 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR Q 60 " --> pdb=" O THR Q 99 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA Q 31 " --> pdb=" O VAL Q 63 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'Q' and resid 57 through 60 removed outlier: 3.507A pdb=" N SER Q 102 " --> pdb=" O LYS Q 58 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'Q' and resid 71 through 78 removed outlier: 4.271A pdb=" N TYR Q 83 " --> pdb=" O ARG Q 78 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'R' and resid 2 through 8 removed outlier: 6.874A pdb=" N LYS R 106 " --> pdb=" O SER R 72 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS R 70 " --> pdb=" O GLY R 108 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'R' and resid 73 through 79 removed outlier: 5.024A pdb=" N THR R 100 " --> pdb=" O GLY R 79 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'S' and resid 28 through 33 removed outlier: 4.354A pdb=" N LYS S 80 " --> pdb=" O VAL S 33 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY S 74 " --> pdb=" O LYS S 67 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LYS S 65 " --> pdb=" O ARG S 76 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ASP S 78 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LYS S 63 " --> pdb=" O ASP S 78 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LYS S 80 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE S 61 " --> pdb=" O LYS S 80 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA S 82 " --> pdb=" O THR S 59 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR S 59 " --> pdb=" O ALA S 82 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL S 84 " --> pdb=" O VAL S 57 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL S 57 " --> pdb=" O VAL S 84 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'U' and resid 73 through 76 removed outlier: 3.665A pdb=" N GLU U 66 " --> pdb=" O PHE U 4 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA U 93 " --> pdb=" O PRO U 31 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'U' and resid 82 through 85 removed outlier: 6.576A pdb=" N GLN U 82 " --> pdb=" O MET U 91 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N THR U 89 " --> pdb=" O HIS U 84 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'V' and resid 29 through 32 removed outlier: 4.605A pdb=" N GLN V 29 " --> pdb=" O VAL V 67 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL V 82 " --> pdb=" O GLY V 48 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'V' and resid 50 through 54 removed outlier: 7.062A pdb=" N ASN V 50 " --> pdb=" O THR V 62 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR V 58 " --> pdb=" O GLY V 54 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'W' and resid 12 through 19 removed outlier: 4.528A pdb=" N ASN W 23 " --> pdb=" O SER W 19 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'W' and resid 34 through 41 Processing sheet with id= 42, first strand: chain 'Y' and resid 33 through 38 removed outlier: 4.659A pdb=" N HIS Y 33 " --> pdb=" O GLN Y 8 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N MET Y 53 " --> pdb=" O THR Y 9 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'Z' and resid 28 through 31 removed outlier: 3.526A pdb=" N GLU Z 35 " --> pdb=" O ASP Z 30 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'b' and resid 17 through 20 removed outlier: 6.202A pdb=" N HIS b 17 " --> pdb=" O ILE b 43 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY b 19 " --> pdb=" O HIS b 41 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N HIS b 41 " --> pdb=" O GLY b 19 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'b' and resid 69 through 73 removed outlier: 3.588A 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: 3.804A pdb=" N ASN c 54 " --> pdb=" O SER c 69 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'c' and resid 164 through 169 Processing sheet with id= 48, first strand: chain 'd' and resid 142 through 146 removed outlier: 3.588A pdb=" N ASP d 143 " --> pdb=" O PHE d 184 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU d 174 " --> pdb=" O THR d 183 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'e' and resid 10 through 15 removed outlier: 6.877A 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: 3.817A pdb=" N ALA e 98 " --> pdb=" O ASN e 121 " (cutoff:3.500A) removed outlier: 6.273A 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: 6.740A 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 42 removed outlier: 4.700A pdb=" N ILE f 36 " --> pdb=" O GLU f 65 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU f 65 " --> pdb=" O ILE f 36 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG f 38 " --> pdb=" O ASN f 63 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN f 63 " --> pdb=" O ARG f 38 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE f 60 " --> pdb=" O LEU f 8 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU f 8 " --> pdb=" O ILE f 60 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'g' and resid 73 through 79 removed outlier: 3.874A pdb=" N VAL g 87 " --> pdb=" O LYS g 76 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG g 78 " --> pdb=" O TYR g 85 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR g 85 " --> pdb=" O ARG g 78 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'h' and resid 23 through 29 removed outlier: 6.783A pdb=" N GLN h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N SER h 58 " --> pdb=" O SER h 29 " (cutoff:3.500A) removed outlier: 3.836A 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: 5.100A pdb=" N MET h 75 " --> pdb=" O SER h 131 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA h 128 " --> pdb=" O ILE h 104 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE h 104 " --> pdb=" O ILE h 127 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU h 125 " --> pdb=" O SER h 106 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'i' and resid 4 through 9 removed outlier: 3.562A pdb=" N THR i 14 " --> pdb=" O LYS i 66 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'j' and resid 35 through 40 removed outlier: 3.682A pdb=" N GLN j 35 " --> pdb=" O VAL j 77 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASP j 75 " --> pdb=" O CYS j 37 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU j 73 " --> pdb=" O PRO j 39 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ARG j 7 " --> pdb=" O ALA j 101 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'k' and resid 41 through 44 removed outlier: 4.092A pdb=" N ASN k 28 " --> pdb=" O SER k 25 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY k 18 " --> pdb=" O ASN k 80 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASP k 82 " --> pdb=" O GLY k 18 " (cutoff:3.500A) removed outlier: 7.784A 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 32 removed outlier: 5.158A pdb=" N LEU l 81 " --> pdb=" O VAL l 98 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'l' and resid 51 through 57 removed outlier: 4.877A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N PHE l 61 " --> pdb=" O LEU l 57 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'p' and resid 22 through 28 removed outlier: 5.299A 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 12 removed outlier: 6.231A pdb=" N ARG q 7 " --> pdb=" O GLU q 64 " (cutoff:3.500A) removed outlier: 6.909A 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 34 1698 hydrogen bonds defined for protein. 5034 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3542 hydrogen bonds 5554 hydrogen bond angles 0 basepair planarities 1411 basepair parallelities 2363 stacking parallelities Total time for adding SS restraints: 274.22 Time building geometry restraints manager: 60.47 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: 11405 1.30 - 1.43: 70126 1.43 - 1.56: 62909 1.56 - 1.69: 9229 1.69 - 1.82: 248 Bond restraints: 153917 Sorted by residual: bond pdb=" C5 5MUAN1935 " pdb=" C6 5MUAN1935 " ideal model delta sigma weight residual 1.155 1.452 -0.297 2.00e-02 2.50e+03 2.20e+02 bond pdb=" C5 5MU v 55 " pdb=" C6 5MU v 55 " ideal model delta sigma weight residual 1.155 1.451 -0.296 2.00e-02 2.50e+03 2.19e+02 bond pdb=" C4 5MUAN1935 " pdb=" C5 5MUAN1935 " ideal model delta sigma weight residual 1.802 1.609 0.193 2.00e-02 2.50e+03 9.34e+01 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 9.22e+01 bond pdb=" N1 5MU v 55 " pdb=" C2 5MU v 55 " ideal model delta sigma weight residual 1.436 1.564 -0.128 2.00e-02 2.50e+03 4.07e+01 ... (remaining 153912 not shown) Histogram of bond angle deviations from ideal: 98.39 - 108.43: 55135 108.43 - 118.47: 93342 118.47 - 128.51: 76347 128.51 - 138.55: 5840 138.55 - 148.59: 3 Bond angle restraints: 230667 Sorted by residual: angle pdb=" C1' 6MZAN2026 " pdb=" N9 6MZAN2026 " pdb=" C8 6MZAN2026 " ideal model delta sigma weight residual 126.23 148.59 -22.36 3.00e+00 1.11e-01 5.56e+01 angle pdb=" C1' 2MGsN 963 " pdb=" N9 2MGsN 963 " pdb=" C8 2MGsN 963 " ideal model delta sigma weight residual 110.07 132.37 -22.30 3.00e+00 1.11e-01 5.52e+01 angle pdb=" C1' 2MGsN1204 " pdb=" N9 2MGsN1204 " pdb=" C8 2MGsN1204 " ideal model delta sigma weight residual 110.07 132.08 -22.01 3.00e+00 1.11e-01 5.38e+01 angle pdb=" C1' 2MGAN2441 " pdb=" N9 2MGAN2441 " pdb=" C8 2MGAN2441 " ideal model delta sigma weight residual 110.07 132.05 -21.98 3.00e+00 1.11e-01 5.37e+01 angle pdb=" C1' OMGAN2247 " pdb=" N9 OMGAN2247 " pdb=" C4 OMGAN2247 " ideal model delta sigma weight residual 108.29 130.10 -21.81 3.00e+00 1.11e-01 5.28e+01 ... (remaining 230662 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 87088 35.99 - 71.99: 10053 71.99 - 107.98: 1146 107.98 - 143.97: 28 143.97 - 179.97: 45 Dihedral angle restraints: 98360 sinusoidal: 82836 harmonic: 15524 Sorted by residual: 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 12.57 -172.57 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' CAN 715 " pdb=" C1' CAN 715 " pdb=" N1 CAN 715 " pdb=" C2 CAN 715 " ideal model delta sinusoidal sigma weight residual -160.00 3.06 -163.06 1 1.50e+01 4.44e-03 8.35e+01 dihedral pdb=" O4' CAN2436 " pdb=" C1' CAN2436 " pdb=" N1 CAN2436 " pdb=" C2 CAN2436 " ideal model delta sinusoidal sigma weight residual 200.00 38.60 161.40 1 1.50e+01 4.44e-03 8.31e+01 ... (remaining 98357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 28698 0.085 - 0.171: 793 0.171 - 0.256: 24 0.256 - 0.342: 4 0.342 - 0.427: 1 Chirality restraints: 29520 Sorted by residual: chirality pdb=" CG LEU 2 32 " pdb=" CB LEU 2 32 " pdb=" CD1 LEU 2 32 " pdb=" CD2 LEU 2 32 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.57e+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 2.24 0.30 2.00e-01 2.50e+01 2.31e+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 2.17 0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 29517 not shown) Planarity restraints: 12108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MGAN2065 " -0.057 2.00e-02 2.50e+03 6.08e-01 8.32e+03 pdb=" C4' 7MGAN2065 " -0.451 2.00e-02 2.50e+03 pdb=" O4' 7MGAN2065 " -0.693 2.00e-02 2.50e+03 pdb=" C3' 7MGAN2065 " 0.593 2.00e-02 2.50e+03 pdb=" O3' 7MGAN2065 " 0.629 2.00e-02 2.50e+03 pdb=" C2' 7MGAN2065 " 0.194 2.00e-02 2.50e+03 pdb=" O2' 7MGAN2065 " -0.956 2.00e-02 2.50e+03 pdb=" C1' 7MGAN2065 " -0.207 2.00e-02 2.50e+03 pdb=" N9 7MGAN2065 " 0.948 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MGAN2441 " -0.026 2.00e-02 2.50e+03 5.86e-01 7.73e+03 pdb=" C4' 2MGAN2441 " -0.446 2.00e-02 2.50e+03 pdb=" O4' 2MGAN2441 " -0.715 2.00e-02 2.50e+03 pdb=" C3' 2MGAN2441 " 0.586 2.00e-02 2.50e+03 pdb=" O3' 2MGAN2441 " 0.565 2.00e-02 2.50e+03 pdb=" C2' 2MGAN2441 " 0.226 2.00e-02 2.50e+03 pdb=" O2' 2MGAN2441 " -0.891 2.00e-02 2.50e+03 pdb=" C1' 2MGAN2441 " -0.209 2.00e-02 2.50e+03 pdb=" N9 2MGAN2441 " 0.910 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 7MGsN 524 " 0.031 2.00e-02 2.50e+03 5.64e-01 7.17e+03 pdb=" C4' 7MGsN 524 " 0.431 2.00e-02 2.50e+03 pdb=" O4' 7MGsN 524 " 0.616 2.00e-02 2.50e+03 pdb=" C3' 7MGsN 524 " -0.588 2.00e-02 2.50e+03 pdb=" O3' 7MGsN 524 " -0.558 2.00e-02 2.50e+03 pdb=" C2' 7MGsN 524 " -0.212 2.00e-02 2.50e+03 pdb=" O2' 7MGsN 524 " 0.903 2.00e-02 2.50e+03 pdb=" C1' 7MGsN 524 " 0.232 2.00e-02 2.50e+03 pdb=" N9 7MGsN 524 " -0.855 2.00e-02 2.50e+03 ... (remaining 12105 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 749 2.50 - 3.10: 89775 3.10 - 3.70: 251682 3.70 - 4.30: 388250 4.30 - 4.90: 526947 Nonbonded interactions: 1257403 Sorted by model distance: nonbonded pdb=" N7 GsN 320 " pdb="MG MGsN1604 " model vdw 1.898 2.250 nonbonded pdb=" N7 GsN 866 " pdb="MG MGsN1608 " model vdw 1.899 2.250 nonbonded pdb=" N7 GAN1366 " pdb="MG MGAN3010 " model vdw 1.900 2.250 nonbonded pdb=" N7 GsN 755 " pdb="MG MGsN1601 " model vdw 1.902 2.250 nonbonded pdb=" ND1 HIS C 53 " pdb="MG MGAN3050 " model vdw 1.903 2.250 ... (remaining 1257398 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: 5.850 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: 0.110 Extract box with map and model: 29.700 Check model and map are aligned: 1.600 Set scattering table: 0.980 Process input model: 583.490 Find NCS groups from input model: 2.790 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:11.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 637.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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 0.297 153917 Z= 0.146 Angle : 0.511 22.361 230667 Z= 0.276 Chirality : 0.029 0.427 29520 Planarity : 0.016 0.608 12108 Dihedral : 22.750 179.965 88363 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.76 % Favored : 97.16 % Rotamer: Outliers : 0.07 % Allowed : 2.75 % Favored : 97.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.23 (0.10), residues: 5361 helix: -0.34 (0.12), residues: 1705 sheet: -0.04 (0.16), residues: 1041 loop : -1.44 (0.10), residues: 2615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP b 106 HIS 0.007 0.001 HIS I 95 PHE 0.014 0.001 PHE F 77 TYR 0.013 0.001 TYR f 49 ARG 0.006 0.000 ARG C 269 *********************** 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 1089 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1086 time to evaluate : 5.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 LYS cc_start: 0.8144 (pttp) cc_final: 0.7828 (mttm) REVERT: D 34 ARG cc_start: 0.8034 (mtm-85) cc_final: 0.7727 (ptt180) REVERT: D 170 ASP cc_start: 0.7287 (t70) cc_final: 0.6918 (t0) REVERT: E 60 ARG cc_start: 0.6729 (mmp-170) cc_final: 0.6467 (mmp-170) REVERT: E 87 ARG cc_start: 0.7218 (mmt-90) cc_final: 0.6749 (mmt180) REVERT: F 130 MET cc_start: 0.4834 (ppp) cc_final: 0.4621 (ptm) REVERT: G 147 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7007 (mt-10) REVERT: J 37 ASP cc_start: 0.6683 (m-30) cc_final: 0.6418 (m-30) REVERT: L 3 GLN cc_start: 0.7685 (tt0) cc_final: 0.7465 (tt0) REVERT: M 1 MET cc_start: 0.9129 (mtm) cc_final: 0.8834 (mtp) REVERT: M 69 ARG cc_start: 0.7608 (mtt180) cc_final: 0.7221 (mtt-85) REVERT: N 9 LEU cc_start: 0.8870 (mm) cc_final: 0.8147 (mm) REVERT: T 31 ARG cc_start: 0.8813 (mmt180) cc_final: 0.8601 (mmt180) REVERT: Y 48 ASN cc_start: 0.6770 (t0) cc_final: 0.6501 (t160) REVERT: Z 38 ARG cc_start: 0.8196 (ttt-90) cc_final: 0.7973 (ttm110) REVERT: h 19 MET cc_start: 0.7265 (ttm) cc_final: 0.6857 (ttm) outliers start: 3 outliers final: 2 residues processed: 1088 average time/residue: 2.3058 time to fit residues: 3501.8739 Evaluate side-chains 828 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 826 time to evaluate : 5.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain b residue 144 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 986 random chunks: chunk 832 optimal weight: 6.9990 chunk 747 optimal weight: 10.0000 chunk 414 optimal weight: 7.9990 chunk 255 optimal weight: 6.9990 chunk 504 optimal weight: 2.9990 chunk 399 optimal weight: 1.9990 chunk 772 optimal weight: 5.9990 chunk 299 optimal weight: 4.9990 chunk 469 optimal weight: 6.9990 chunk 575 optimal weight: 3.9990 chunk 895 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 50 HIS C 48 HIS C 58 HIS C 60 GLN C 90 HIS C 120 ASN C 230 HIS C 250 GLN D 33 ASN D 108 GLN D 133 GLN D 137 HIS D 153 GLN E 45 HIS E 96 ASN E 114 GLN E 165 HIS I 40 HIS I 67 ASN I 77 HIS I 130 HIS I 135 GLN K 40 GLN N 99 HIS O 13 ASN O 78 GLN P 11 HIS P 71 GLN Q 6 GLN Q 87 GLN R 57 ASN T 38 ASN T 59 GLN T 72 ASN ** T 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 16 GLN ** U 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 29 GLN W 6 GLN Y 48 ASN Z 41 HIS Z 52 GLN b 17 HIS b 96 HIS b 105 ASN ** b 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 155 ASN b 197 ASN c 6 HIS c 19 ASN c 38 GLN c 176 HIS d 42 HIS ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 138 GLN d 154 GLN e 96 GLN ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 17 GLN ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 94 HIS g 32 GLN g 142 HIS h 18 GLN h 53 GLN i 73 GLN i 98 GLN j 35 GLN j 56 HIS k 27 ASN k 28 ASN l 5 ASN m 105 ASN o 20 ASN o 35 GLN o 42 HIS o 71 ASN p 44 ASN p 84 GLN q 31 GLN q 32 HIS r 31 GLN r 54 GLN r 61 GLN s 52 HIS t 6 GLN t 13 GLN t 75 HIS Total number of N/Q/H flips: 82 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.122 153917 Z= 0.398 Angle : 0.735 19.746 230667 Z= 0.381 Chirality : 0.042 0.407 29520 Planarity : 0.007 0.139 12108 Dihedral : 23.298 179.335 77745 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.66 % Favored : 96.27 % Rotamer: Outliers : 3.63 % Allowed : 13.84 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.51 (0.11), residues: 5361 helix: 0.60 (0.12), residues: 1730 sheet: 0.16 (0.16), residues: 1006 loop : -1.17 (0.11), residues: 2625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 248 HIS 0.012 0.002 HIS P 101 PHE 0.019 0.002 PHE K 66 TYR 0.019 0.002 TYR R 75 ARG 0.011 0.001 ARG I 27 *********************** 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 1052 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 891 time to evaluate : 6.001 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: 1 25 LYS cc_start: 0.8481 (ttmm) cc_final: 0.8267 (tttp) REVERT: 1 29 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7693 (mt0) REVERT: C 38 LYS cc_start: 0.8220 (pttp) cc_final: 0.7887 (mttm) REVERT: C 101 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7073 (mtm180) REVERT: C 175 ARG cc_start: 0.7296 (ttp-170) cc_final: 0.7082 (tpp80) REVERT: D 170 ASP cc_start: 0.7338 (t70) cc_final: 0.6939 (t0) REVERT: E 87 ARG cc_start: 0.7296 (mmt-90) cc_final: 0.6919 (mmt180) REVERT: E 139 ASP cc_start: 0.7289 (t0) cc_final: 0.6994 (t0) REVERT: F 59 LEU cc_start: 0.6307 (OUTLIER) cc_final: 0.6068 (tt) REVERT: F 133 LYS cc_start: 0.4978 (OUTLIER) cc_final: 0.4581 (pmmt) REVERT: J 37 ASP cc_start: 0.6901 (m-30) cc_final: 0.6698 (m-30) REVERT: L 3 GLN cc_start: 0.7750 (tt0) cc_final: 0.7533 (tt0) REVERT: M 81 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8677 (m) REVERT: O 32 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7417 (mt0) REVERT: O 97 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.7603 (mtp85) REVERT: Q 13 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7507 (ttt180) REVERT: R 1 MET cc_start: 0.3599 (ppp) cc_final: 0.3270 (ppp) REVERT: U 66 GLU cc_start: 0.6828 (tt0) cc_final: 0.6601 (tt0) REVERT: X 21 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8660 (mp10) REVERT: Y 48 ASN cc_start: 0.6947 (t0) cc_final: 0.6584 (t0) REVERT: Z 38 ARG cc_start: 0.8265 (ttt-90) cc_final: 0.8010 (ttm110) REVERT: b 76 ARG cc_start: 0.4528 (OUTLIER) cc_final: 0.4197 (tpt170) REVERT: b 97 ARG cc_start: 0.4583 (tmm160) cc_final: 0.3006 (ttt180) REVERT: d 118 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8099 (tt0) REVERT: g 53 LYS cc_start: 0.7091 (mmmm) cc_final: 0.6858 (mtpm) REVERT: h 19 MET cc_start: 0.7447 (ttm) cc_final: 0.7038 (ttm) REVERT: l 43 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7334 (tttt) REVERT: l 94 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.6424 (mtp85) REVERT: p 19 MET cc_start: 0.7700 (ptm) cc_final: 0.7500 (ptm) outliers start: 161 outliers final: 75 residues processed: 954 average time/residue: 2.2256 time to fit residues: 2984.6046 Evaluate side-chains 906 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 818 time to evaluate : 5.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 29 GLN Chi-restraints excluded: chain 1 residue 41 SER Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 101 ARG Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 137 ILE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 32 GLN Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 97 ARG Chi-restraints excluded: chain Q residue 13 ARG Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 62 GLU Chi-restraints excluded: chain R residue 68 ASP Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain T residue 39 LEU Chi-restraints excluded: chain T residue 65 ILE Chi-restraints excluded: chain T residue 101 VAL Chi-restraints excluded: chain U residue 7 ASN Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain V residue 11 LYS Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain X residue 21 GLN Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Z residue 45 ASP Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 57 ASN Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 76 ARG Chi-restraints excluded: chain b residue 102 MET Chi-restraints excluded: chain b residue 185 VAL Chi-restraints excluded: chain c residue 70 THR Chi-restraints excluded: chain c residue 92 THR Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 118 GLN Chi-restraints excluded: chain d residue 179 LYS Chi-restraints excluded: chain e residue 11 VAL Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain f residue 73 GLU Chi-restraints excluded: chain i residue 127 LYS Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain k residue 33 ILE Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain m residue 18 SER Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain n residue 26 GLU Chi-restraints excluded: chain o residue 79 THR Chi-restraints excluded: chain p residue 30 LYS Chi-restraints excluded: chain p residue 40 THR Chi-restraints excluded: chain p residue 42 SER Chi-restraints excluded: chain p residue 80 SER Chi-restraints excluded: chain s residue 18 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 986 random chunks: chunk 497 optimal weight: 6.9990 chunk 277 optimal weight: 4.9990 chunk 745 optimal weight: 10.0000 chunk 609 optimal weight: 8.9990 chunk 246 optimal weight: 6.9990 chunk 897 optimal weight: 5.9990 chunk 969 optimal weight: 0.8980 chunk 798 optimal weight: 0.0270 chunk 889 optimal weight: 10.0000 chunk 305 optimal weight: 5.9990 chunk 719 optimal weight: 6.9990 overall best weight: 3.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 41 GLN D 63 ASN I 67 ASN I 95 HIS I 136 GLN S 2 ASN T 38 ASN T 59 GLN T 76 GLN ** T 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 17 HIS b 155 ASN b 180 ASN c 21 ASN c 38 GLN ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 138 GLN d 154 GLN f 3 HIS f 11 HIS ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 37 HIS h 18 GLN l 5 ASN m 91 HIS o 35 GLN o 71 ASN q 31 GLN r 31 GLN r 54 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 153917 Z= 0.369 Angle : 0.702 15.129 230667 Z= 0.367 Chirality : 0.041 0.368 29520 Planarity : 0.007 0.142 12108 Dihedral : 23.337 179.858 77742 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.94 % Favored : 96.01 % Rotamer: Outliers : 4.33 % Allowed : 16.37 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.32 (0.11), residues: 5361 helix: 0.88 (0.12), residues: 1741 sheet: 0.14 (0.16), residues: 1014 loop : -1.11 (0.11), residues: 2606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 248 HIS 0.009 0.002 HIS I 40 PHE 0.024 0.002 PHE F 77 TYR 0.014 0.002 TYR H 25 ARG 0.008 0.001 ARG c 89 *********************** 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 1041 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 849 time to evaluate : 6.008 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: 1 25 LYS cc_start: 0.8440 (ttmm) cc_final: 0.8233 (tttp) REVERT: 1 29 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7666 (mt0) REVERT: C 38 LYS cc_start: 0.8295 (pttp) cc_final: 0.7904 (mttm) REVERT: D 170 ASP cc_start: 0.7274 (t70) cc_final: 0.6923 (t0) REVERT: G 147 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7360 (mt-10) REVERT: I 67 ASN cc_start: 0.8401 (t0) cc_final: 0.8148 (OUTLIER) REVERT: L 3 GLN cc_start: 0.7751 (tt0) cc_final: 0.7540 (tt0) REVERT: O 32 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7561 (mt0) REVERT: O 97 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.7563 (mtp85) REVERT: P 79 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.7666 (ttt) REVERT: Q 1 MET cc_start: 0.7111 (tpt) cc_final: 0.6871 (tpt) REVERT: Q 13 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7590 (ttt180) REVERT: R 60 HIS cc_start: 0.6352 (OUTLIER) cc_final: 0.6024 (t70) REVERT: S 34 ASP cc_start: 0.8353 (t70) cc_final: 0.7806 (t70) REVERT: W 65 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6702 (mp0) REVERT: X 21 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8656 (mp10) REVERT: Z 38 ARG cc_start: 0.8302 (ttt-90) cc_final: 0.8081 (ttm110) REVERT: b 72 VAL cc_start: 0.7378 (OUTLIER) cc_final: 0.7170 (m) REVERT: b 76 ARG cc_start: 0.4718 (OUTLIER) cc_final: 0.4011 (tpt170) REVERT: b 97 ARG cc_start: 0.4921 (tmm160) cc_final: 0.3066 (ttt180) REVERT: b 141 ARG cc_start: 0.3013 (tpp80) cc_final: 0.2788 (tpp80) REVERT: c 108 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7089 (mtp85) REVERT: f 54 ILE cc_start: 0.7397 (mp) cc_final: 0.7034 (tt) REVERT: g 53 LYS cc_start: 0.7218 (mmmm) cc_final: 0.6920 (mtpm) REVERT: h 19 MET cc_start: 0.7472 (ttm) cc_final: 0.7089 (ttm) REVERT: l 94 ARG cc_start: 0.6942 (OUTLIER) cc_final: 0.6471 (mtp85) REVERT: o 58 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7754 (ttt180) REVERT: q 19 ASP cc_start: 0.8039 (t0) cc_final: 0.7790 (t0) outliers start: 192 outliers final: 101 residues processed: 945 average time/residue: 2.2354 time to fit residues: 2981.7771 Evaluate side-chains 930 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 817 time to evaluate : 5.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 29 GLN Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 134 LYS Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 134 LYS Chi-restraints excluded: chain K residue 137 ILE Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 32 GLN Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 44 GLN Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 97 ARG Chi-restraints excluded: chain P residue 79 MET Chi-restraints excluded: chain Q residue 13 ARG Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 62 GLU Chi-restraints excluded: chain R residue 60 HIS Chi-restraints excluded: chain R residue 68 ASP Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain T residue 21 GLN Chi-restraints excluded: chain T residue 101 VAL Chi-restraints excluded: chain U residue 7 ASN Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain V residue 11 LYS Chi-restraints excluded: chain V residue 30 THR Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain W residue 53 THR Chi-restraints excluded: chain W residue 65 GLU Chi-restraints excluded: chain X residue 17 LEU Chi-restraints excluded: chain X residue 21 GLN Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 56 LEU Chi-restraints excluded: chain Y residue 4 ILE Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Z residue 29 VAL Chi-restraints excluded: chain Z residue 45 ASP Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 57 ASN Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 76 ARG Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 102 MET Chi-restraints excluded: chain b residue 114 ASN Chi-restraints excluded: chain b residue 165 VAL Chi-restraints excluded: chain b residue 185 VAL Chi-restraints excluded: chain c residue 70 THR Chi-restraints excluded: chain c residue 108 ARG Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 36 ASN Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 173 ILE Chi-restraints excluded: chain d residue 183 THR Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 91 SER Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain h residue 112 MET Chi-restraints excluded: chain i residue 64 THR Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain k residue 33 ILE Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 117 TYR Chi-restraints excluded: chain m residue 18 SER Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain o residue 58 ARG Chi-restraints excluded: chain p residue 30 LYS Chi-restraints excluded: chain p residue 40 THR Chi-restraints excluded: chain p residue 42 SER Chi-restraints excluded: chain p residue 70 LEU Chi-restraints excluded: chain p residue 80 SER Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain s residue 18 LYS Chi-restraints excluded: chain s residue 19 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 986 random chunks: chunk 886 optimal weight: 5.9990 chunk 674 optimal weight: 8.9990 chunk 465 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 428 optimal weight: 0.6980 chunk 602 optimal weight: 8.9990 chunk 900 optimal weight: 0.0070 chunk 953 optimal weight: 5.9990 chunk 470 optimal weight: 0.8980 chunk 853 optimal weight: 7.9990 chunk 256 optimal weight: 4.9990 overall best weight: 1.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 41 GLN C 163 GLN I 136 GLN T 59 GLN ** T 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 52 GLN c 21 ASN c 38 GLN d 102 ASN ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 18 GLN l 5 ASN o 61 ASN o 71 ASN q 31 GLN r 54 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 153917 Z= 0.217 Angle : 0.611 14.861 230667 Z= 0.327 Chirality : 0.036 0.392 29520 Planarity : 0.006 0.130 12108 Dihedral : 23.272 179.443 77742 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.88 % Favored : 96.05 % Rotamer: Outliers : 3.65 % Allowed : 18.55 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.04 (0.11), residues: 5361 helix: 1.28 (0.12), residues: 1744 sheet: 0.19 (0.16), residues: 1018 loop : -1.02 (0.11), residues: 2599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 248 HIS 0.006 0.001 HIS I 95 PHE 0.019 0.001 PHE F 138 TYR 0.012 0.001 TYR L 92 ARG 0.011 0.000 ARG b 115 *********************** 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 1006 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 844 time to evaluate : 6.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 3 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7548 (m-30) REVERT: 1 29 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7644 (mt0) REVERT: 2 64 ILE cc_start: 0.6222 (OUTLIER) cc_final: 0.5663 (tp) REVERT: C 38 LYS cc_start: 0.8270 (pttp) cc_final: 0.7839 (mttm) REVERT: C 101 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.6976 (mtm180) REVERT: D 170 ASP cc_start: 0.7228 (t70) cc_final: 0.6914 (t0) REVERT: E 87 ARG cc_start: 0.7310 (mmt180) cc_final: 0.6765 (mmt180) REVERT: G 147 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7317 (mt-10) REVERT: I 35 ARG cc_start: 0.8572 (mtt-85) cc_final: 0.8325 (mtt-85) REVERT: I 73 LYS cc_start: 0.8157 (mttm) cc_final: 0.7930 (mttm) REVERT: K 1 MET cc_start: 0.5733 (tpp) cc_final: 0.5487 (tpt) REVERT: M 69 ARG cc_start: 0.7452 (mtt90) cc_final: 0.7244 (mtt180) REVERT: M 81 THR cc_start: 0.8859 (m) cc_final: 0.8642 (m) REVERT: N 105 LEU cc_start: 0.8523 (tt) cc_final: 0.8298 (tt) REVERT: O 32 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.7425 (mt0) REVERT: P 79 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.7649 (ttt) REVERT: Q 1 MET cc_start: 0.6934 (tpt) cc_final: 0.6701 (tpt) REVERT: Q 13 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7521 (ttt180) REVERT: R 60 HIS cc_start: 0.6387 (OUTLIER) cc_final: 0.6044 (t70) REVERT: W 65 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6708 (mp0) REVERT: X 21 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8610 (mp10) REVERT: Z 38 ARG cc_start: 0.8205 (ttt-90) cc_final: 0.7994 (ttm110) REVERT: b 102 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.7025 (mtt) REVERT: c 108 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7109 (mtp85) REVERT: d 118 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8058 (tt0) REVERT: h 3 MET cc_start: 0.8387 (tpp) cc_final: 0.8109 (tmm) REVERT: h 19 MET cc_start: 0.7442 (ttm) cc_final: 0.7048 (ttm) REVERT: l 94 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.6417 (mtp85) REVERT: o 58 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7703 (ttt180) REVERT: o 73 LYS cc_start: 0.7875 (ttmt) cc_final: 0.7630 (tptt) outliers start: 162 outliers final: 85 residues processed: 915 average time/residue: 2.1542 time to fit residues: 2793.6909 Evaluate side-chains 917 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 817 time to evaluate : 5.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 ASP Chi-restraints excluded: chain 1 residue 29 GLN Chi-restraints excluded: chain 1 residue 41 SER Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 101 ARG Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain F residue 69 LEU Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 134 LYS Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 134 LYS Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 32 GLN Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 44 GLN Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain P residue 79 MET Chi-restraints excluded: chain Q residue 13 ARG Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 62 GLU Chi-restraints excluded: chain R residue 60 HIS Chi-restraints excluded: chain R residue 68 ASP Chi-restraints excluded: chain R residue 72 SER Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain T residue 21 GLN Chi-restraints excluded: chain U residue 7 ASN Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain W residue 65 GLU Chi-restraints excluded: chain X residue 17 LEU Chi-restraints excluded: chain X residue 21 GLN Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Z residue 45 ASP Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 57 ASN Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain b residue 102 MET Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 168 VAL Chi-restraints excluded: chain b residue 185 VAL Chi-restraints excluded: chain c residue 70 THR Chi-restraints excluded: chain c residue 108 ARG Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 118 GLN Chi-restraints excluded: chain d residue 173 ILE Chi-restraints excluded: chain d residue 183 THR Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain f residue 71 LEU Chi-restraints excluded: chain f residue 73 GLU Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain g residue 68 LYS Chi-restraints excluded: chain h residue 112 MET Chi-restraints excluded: chain i residue 64 THR Chi-restraints excluded: chain i residue 105 ASP Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain k residue 33 ILE Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 117 TYR Chi-restraints excluded: chain m residue 18 SER Chi-restraints excluded: chain o residue 58 ARG Chi-restraints excluded: chain p residue 30 LYS Chi-restraints excluded: chain p residue 40 THR Chi-restraints excluded: chain p residue 42 SER Chi-restraints excluded: chain p residue 80 SER Chi-restraints excluded: chain s residue 18 LYS Chi-restraints excluded: chain t residue 30 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 986 random chunks: chunk 793 optimal weight: 3.9990 chunk 541 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 709 optimal weight: 10.0000 chunk 393 optimal weight: 10.0000 chunk 813 optimal weight: 4.9990 chunk 658 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 486 optimal weight: 5.9990 chunk 855 optimal weight: 7.9990 chunk 240 optimal weight: 4.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 41 GLN C 163 GLN I 67 ASN I 136 GLN T 59 GLN T 76 GLN ** T 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 61 GLN c 21 ASN c 38 GLN ** c 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 18 GLN j 15 HIS l 5 ASN o 20 ASN ** o 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 61 ASN o 71 ASN q 31 GLN r 54 GLN r 61 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 153917 Z= 0.343 Angle : 0.684 14.614 230667 Z= 0.359 Chirality : 0.040 0.368 29520 Planarity : 0.006 0.137 12108 Dihedral : 23.312 179.320 77740 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.48 % Favored : 95.47 % Rotamer: Outliers : 4.37 % Allowed : 19.30 % Favored : 76.33 % 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: 1.23 (0.12), residues: 1745 sheet: 0.15 (0.16), residues: 1027 loop : -1.08 (0.11), residues: 2589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 248 HIS 0.009 0.001 HIS I 95 PHE 0.016 0.002 PHE F 138 TYR 0.014 0.002 TYR R 75 ARG 0.009 0.001 ARG L 57 *********************** 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 1017 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 823 time to evaluate : 5.957 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: 1 29 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7706 (mt0) REVERT: 2 64 ILE cc_start: 0.6300 (OUTLIER) cc_final: 0.5748 (tp) REVERT: C 38 LYS cc_start: 0.8331 (pttp) cc_final: 0.7931 (mttm) REVERT: C 101 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7154 (mtm180) REVERT: D 170 ASP cc_start: 0.7259 (t0) cc_final: 0.6933 (t0) REVERT: E 87 ARG cc_start: 0.7320 (mmt180) cc_final: 0.6905 (mmt180) REVERT: F 115 ARG cc_start: 0.5401 (tmm160) cc_final: 0.4692 (pmt170) REVERT: F 133 LYS cc_start: 0.5041 (OUTLIER) cc_final: 0.4781 (pmmt) REVERT: G 77 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.6949 (tppp) REVERT: G 147 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7357 (mt-10) REVERT: I 67 ASN cc_start: 0.8490 (t0) cc_final: 0.8181 (m110) REVERT: I 73 LYS cc_start: 0.8175 (mttm) cc_final: 0.7882 (mttp) REVERT: I 86 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7248 (tp30) REVERT: K 1 MET cc_start: 0.5881 (tpp) cc_final: 0.5659 (tpt) REVERT: L 10 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7508 (ptt180) REVERT: M 81 THR cc_start: 0.8922 (m) cc_final: 0.8715 (m) REVERT: O 32 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7433 (mt0) REVERT: O 97 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.7575 (mtp85) REVERT: P 79 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.7644 (ttt) REVERT: Q 13 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7571 (ttt180) REVERT: R 60 HIS cc_start: 0.6352 (OUTLIER) cc_final: 0.6002 (t70) REVERT: S 34 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.7883 (t70) REVERT: W 11 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7183 (ptt-90) REVERT: W 65 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6650 (mp0) REVERT: X 21 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8651 (mp10) REVERT: Z 38 ARG cc_start: 0.8245 (ttt-90) cc_final: 0.8027 (ttm110) REVERT: b 76 ARG cc_start: 0.4555 (OUTLIER) cc_final: 0.0690 (ttt180) REVERT: b 102 MET cc_start: 0.7215 (OUTLIER) cc_final: 0.6959 (mtt) REVERT: b 163 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7616 (tt) REVERT: c 108 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7181 (mtp85) REVERT: d 118 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8095 (tt0) REVERT: g 72 MET cc_start: 0.4364 (OUTLIER) cc_final: 0.3868 (ppp) REVERT: h 3 MET cc_start: 0.8469 (tpp) cc_final: 0.8192 (tmm) REVERT: h 19 MET cc_start: 0.7497 (ttm) cc_final: 0.7131 (ttm) REVERT: l 94 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.6486 (mtp85) REVERT: o 58 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7728 (ttt180) REVERT: o 73 LYS cc_start: 0.7900 (ttmt) cc_final: 0.7660 (tptt) outliers start: 194 outliers final: 117 residues processed: 919 average time/residue: 2.1583 time to fit residues: 2822.0950 Evaluate side-chains 943 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 802 time to evaluate : 5.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 23 LYS Chi-restraints excluded: chain 1 residue 29 GLN Chi-restraints excluded: chain 1 residue 41 SER Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 101 ARG Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 34 ARG Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 77 LYS Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 134 LYS Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 69 ILE Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 134 LYS Chi-restraints excluded: chain K residue 137 ILE Chi-restraints excluded: chain L residue 10 ARG Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 32 GLN Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 44 GLN Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 97 ARG Chi-restraints excluded: chain P residue 79 MET Chi-restraints excluded: chain Q residue 13 ARG Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 62 GLU Chi-restraints excluded: chain R residue 60 HIS Chi-restraints excluded: chain R residue 68 ASP Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain T residue 21 GLN Chi-restraints excluded: chain T residue 65 ILE Chi-restraints excluded: chain U residue 7 ASN Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 11 LYS Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain V residue 70 GLU Chi-restraints excluded: chain W residue 11 ARG Chi-restraints excluded: chain W residue 53 THR Chi-restraints excluded: chain W residue 65 GLU Chi-restraints excluded: chain X residue 17 LEU Chi-restraints excluded: chain X residue 21 GLN Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 56 LEU Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Z residue 45 ASP Chi-restraints excluded: chain b residue 6 VAL Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 57 ASN Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain b residue 76 ARG Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 102 MET Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 163 LEU Chi-restraints excluded: chain b residue 168 VAL Chi-restraints excluded: chain b residue 185 VAL Chi-restraints excluded: chain c residue 70 THR Chi-restraints excluded: chain c residue 108 ARG Chi-restraints excluded: chain c residue 123 GLN Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 70 LEU Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 118 GLN Chi-restraints excluded: chain d residue 173 ILE Chi-restraints excluded: chain d residue 183 THR Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 71 LEU Chi-restraints excluded: chain f residue 73 GLU Chi-restraints excluded: chain g residue 72 MET Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain h residue 112 MET Chi-restraints excluded: chain i residue 64 THR Chi-restraints excluded: chain i residue 105 ASP Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain k residue 33 ILE Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain l residue 15 LEU Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 117 TYR Chi-restraints excluded: chain m residue 18 SER Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain o residue 58 ARG Chi-restraints excluded: chain p residue 30 LYS Chi-restraints excluded: chain p residue 40 THR Chi-restraints excluded: chain p residue 42 SER Chi-restraints excluded: chain p residue 80 SER Chi-restraints excluded: chain p residue 92 LEU Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain s residue 4 SER Chi-restraints excluded: chain s residue 18 LYS Chi-restraints excluded: chain s residue 60 VAL Chi-restraints excluded: chain t residue 30 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 986 random chunks: chunk 320 optimal weight: 0.0670 chunk 858 optimal weight: 0.9980 chunk 188 optimal weight: 10.0000 chunk 559 optimal weight: 0.9980 chunk 235 optimal weight: 10.0000 chunk 953 optimal weight: 7.9990 chunk 791 optimal weight: 0.8980 chunk 441 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 315 optimal weight: 5.9990 chunk 500 optimal weight: 5.9990 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 41 GLN C 163 GLN D 50 GLN I 136 GLN T 38 ASN T 59 GLN ** T 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 21 ASN c 38 GLN ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 18 GLN l 5 ASN ** o 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 61 ASN o 71 ASN q 31 GLN r 54 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 153917 Z= 0.148 Angle : 0.595 14.838 230667 Z= 0.321 Chirality : 0.035 0.406 29520 Planarity : 0.005 0.124 12108 Dihedral : 23.314 179.219 77740 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.69 % Favored : 96.25 % Rotamer: Outliers : 3.31 % Allowed : 20.90 % Favored : 75.79 % 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: 1.46 (0.12), residues: 1748 sheet: 0.22 (0.16), residues: 1026 loop : -0.96 (0.12), residues: 2587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP c 201 HIS 0.005 0.001 HIS I 95 PHE 0.016 0.001 PHE F 138 TYR 0.019 0.001 TYR L 92 ARG 0.009 0.000 ARG r 50 *********************** 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 961 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 814 time to evaluate : 6.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 3 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7540 (m-30) REVERT: 1 29 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7565 (mt0) REVERT: C 38 LYS cc_start: 0.8337 (pttp) cc_final: 0.7951 (mttm) REVERT: C 101 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.6959 (mtm180) REVERT: D 170 ASP cc_start: 0.7150 (t0) cc_final: 0.6888 (t0) REVERT: E 87 ARG cc_start: 0.7231 (mmt180) cc_final: 0.6831 (mmt180) REVERT: F 115 ARG cc_start: 0.5307 (tmm160) cc_final: 0.4604 (pmt170) REVERT: F 133 LYS cc_start: 0.4945 (OUTLIER) cc_final: 0.4714 (pmmt) REVERT: I 73 LYS cc_start: 0.8127 (mttm) cc_final: 0.7855 (mttm) REVERT: I 86 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7195 (tp30) REVERT: K 1 MET cc_start: 0.5777 (tpp) cc_final: 0.5561 (tpt) REVERT: M 81 THR cc_start: 0.8869 (m) cc_final: 0.8667 (m) REVERT: O 32 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7365 (mt0) REVERT: O 97 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.7496 (mtp85) REVERT: P 79 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.7584 (ttt) REVERT: Q 13 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7485 (ttt180) REVERT: R 60 HIS cc_start: 0.6351 (OUTLIER) cc_final: 0.5975 (t70) REVERT: T 92 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.6600 (mtm-85) REVERT: X 21 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8613 (mp10) REVERT: Y 1 MET cc_start: 0.0483 (tmm) cc_final: -0.1010 (tmm) REVERT: Y 29 ARG cc_start: 0.8067 (mmt90) cc_final: 0.7830 (mmt180) REVERT: Z 38 ARG cc_start: 0.8185 (ttt-90) cc_final: 0.7968 (ttm110) REVERT: b 102 MET cc_start: 0.7284 (OUTLIER) cc_final: 0.7034 (mtt) REVERT: b 163 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7608 (tt) REVERT: c 108 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7165 (mtp85) REVERT: d 15 GLU cc_start: 0.5565 (OUTLIER) cc_final: 0.4401 (mp0) REVERT: f 54 ILE cc_start: 0.7305 (OUTLIER) cc_final: 0.7059 (mp) REVERT: g 72 MET cc_start: 0.4193 (OUTLIER) cc_final: 0.3734 (ppp) REVERT: h 3 MET cc_start: 0.8334 (tpp) cc_final: 0.8057 (tmm) REVERT: h 19 MET cc_start: 0.7417 (ttm) cc_final: 0.7030 (ttm) REVERT: j 74 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8620 (mt) REVERT: o 58 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7709 (ttt180) REVERT: o 73 LYS cc_start: 0.7878 (ttmt) cc_final: 0.7676 (tptt) outliers start: 147 outliers final: 75 residues processed: 884 average time/residue: 2.2141 time to fit residues: 2772.8100 Evaluate side-chains 884 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 789 time to evaluate : 5.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 ASP Chi-restraints excluded: chain 1 residue 29 GLN Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 101 ARG Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 151 TYR Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 137 ILE Chi-restraints excluded: chain L residue 6 ARG Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 32 GLN Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 44 GLN Chi-restraints excluded: chain O residue 97 ARG Chi-restraints excluded: chain P residue 79 MET Chi-restraints excluded: chain Q residue 13 ARG Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 62 GLU Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain R residue 59 GLU Chi-restraints excluded: chain R residue 60 HIS Chi-restraints excluded: chain R residue 68 ASP Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain T residue 21 GLN Chi-restraints excluded: chain T residue 92 ARG Chi-restraints excluded: chain U residue 7 ASN Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain V residue 11 LYS Chi-restraints excluded: chain X residue 17 LEU Chi-restraints excluded: chain X residue 21 GLN Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Z residue 45 ASP Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 57 ASN Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain b residue 102 MET Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 163 LEU Chi-restraints excluded: chain b residue 168 VAL Chi-restraints excluded: chain c residue 70 THR Chi-restraints excluded: chain c residue 108 ARG Chi-restraints excluded: chain c residue 123 GLN Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 15 GLU Chi-restraints excluded: chain d residue 70 LEU Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 173 ILE Chi-restraints excluded: chain d residue 183 THR Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 155 LYS Chi-restraints excluded: chain f residue 54 ILE Chi-restraints excluded: chain f residue 71 LEU Chi-restraints excluded: chain f residue 73 GLU Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 72 MET Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain h residue 112 MET Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 74 ILE Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain k residue 33 ILE Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain l residue 15 LEU Chi-restraints excluded: chain l residue 117 TYR Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain o residue 58 ARG Chi-restraints excluded: chain p residue 30 LYS Chi-restraints excluded: chain p residue 40 THR Chi-restraints excluded: chain s residue 18 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 986 random chunks: chunk 919 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 543 optimal weight: 4.9990 chunk 696 optimal weight: 6.9990 chunk 539 optimal weight: 3.9990 chunk 803 optimal weight: 3.9990 chunk 532 optimal weight: 4.9990 chunk 950 optimal weight: 10.0000 chunk 594 optimal weight: 6.9990 chunk 579 optimal weight: 0.5980 chunk 438 optimal weight: 3.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 41 GLN C 163 GLN D 50 GLN I 67 ASN I 136 GLN T 59 GLN T 76 GLN ** T 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 14 HIS c 21 ASN c 38 GLN ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 18 GLN l 5 ASN ** o 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 61 ASN o 71 ASN p 84 GLN q 31 GLN r 54 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 153917 Z= 0.369 Angle : 0.700 14.320 230667 Z= 0.366 Chirality : 0.041 0.353 29520 Planarity : 0.006 0.138 12108 Dihedral : 23.315 179.369 77740 Min Nonbonded Distance : 1.658 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.46 % Favored : 95.49 % Rotamer: Outliers : 4.17 % Allowed : 20.58 % Favored : 75.25 % 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: -0.02 (0.11), residues: 5361 helix: 1.34 (0.12), residues: 1745 sheet: 0.17 (0.16), residues: 1024 loop : -1.04 (0.11), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 248 HIS 0.009 0.001 HIS I 95 PHE 0.016 0.002 PHE K 66 TYR 0.019 0.002 TYR L 92 ARG 0.008 0.001 ARG L 52 *********************** 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 993 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 808 time to evaluate : 6.169 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 3 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7548 (m-30) REVERT: 1 29 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7706 (mt0) REVERT: 2 64 ILE cc_start: 0.6277 (OUTLIER) cc_final: 0.5732 (tp) REVERT: C 38 LYS cc_start: 0.8350 (pttp) cc_final: 0.7932 (mttm) REVERT: C 101 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7166 (mtm180) REVERT: D 170 ASP cc_start: 0.7227 (t0) cc_final: 0.6946 (t0) REVERT: E 87 ARG cc_start: 0.7291 (mmt180) cc_final: 0.6919 (mmt180) REVERT: F 115 ARG cc_start: 0.5609 (tmm160) cc_final: 0.4837 (pmt170) REVERT: F 133 LYS cc_start: 0.5106 (OUTLIER) cc_final: 0.4896 (pmmt) REVERT: G 77 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7006 (tppp) REVERT: I 67 ASN cc_start: 0.8434 (t0) cc_final: 0.8144 (m110) REVERT: I 86 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7263 (tp30) REVERT: M 69 ARG cc_start: 0.7585 (mtt180) cc_final: 0.7237 (mtt180) REVERT: O 32 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7225 (mt0) REVERT: O 86 LYS cc_start: 0.7908 (ttpt) cc_final: 0.7689 (ttpt) REVERT: O 97 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.7621 (mtp85) REVERT: P 79 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.7667 (ttt) REVERT: Q 13 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7575 (ttt180) REVERT: R 2 GLU cc_start: 0.6991 (mt-10) cc_final: 0.6698 (mt-10) REVERT: R 60 HIS cc_start: 0.6353 (OUTLIER) cc_final: 0.5980 (t70) REVERT: S 34 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.7846 (t70) REVERT: T 92 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.6610 (mtm-85) REVERT: U 40 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6550 (pp20) REVERT: U 67 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8688 (mp) REVERT: W 11 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7187 (ptt-90) REVERT: W 65 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6703 (mp0) REVERT: X 21 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8653 (mp10) REVERT: Y 29 ARG cc_start: 0.8158 (mmt90) cc_final: 0.7870 (mmt180) REVERT: Z 38 ARG cc_start: 0.8276 (ttt-90) cc_final: 0.8056 (ttm110) REVERT: b 76 ARG cc_start: 0.4615 (OUTLIER) cc_final: 0.0738 (ttt180) REVERT: b 163 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7634 (tt) REVERT: c 108 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7194 (mtp85) REVERT: d 15 GLU cc_start: 0.5708 (OUTLIER) cc_final: 0.4435 (mp0) REVERT: d 118 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8080 (tt0) REVERT: f 1 MET cc_start: 0.4913 (OUTLIER) cc_final: 0.4640 (mtp) REVERT: g 72 MET cc_start: 0.4288 (OUTLIER) cc_final: 0.3770 (ppp) REVERT: h 3 MET cc_start: 0.8462 (tpp) cc_final: 0.8203 (tmm) REVERT: h 19 MET cc_start: 0.7488 (ttm) cc_final: 0.7146 (ttm) REVERT: l 43 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7351 (tttt) REVERT: l 94 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.6487 (mtp85) REVERT: o 58 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7730 (ttt180) outliers start: 185 outliers final: 112 residues processed: 898 average time/residue: 2.2134 time to fit residues: 2824.3825 Evaluate side-chains 931 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 790 time to evaluate : 5.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 ASP Chi-restraints excluded: chain 1 residue 29 GLN Chi-restraints excluded: chain 1 residue 41 SER Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 101 ARG Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 77 LYS Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 134 LYS Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 134 LYS Chi-restraints excluded: chain K residue 137 ILE Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 32 GLN Chi-restraints excluded: chain O residue 44 GLN Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 97 ARG Chi-restraints excluded: chain P residue 79 MET Chi-restraints excluded: chain Q residue 13 ARG Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 62 GLU Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain R residue 59 GLU Chi-restraints excluded: chain R residue 60 HIS Chi-restraints excluded: chain R residue 68 ASP Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain T residue 21 GLN Chi-restraints excluded: chain T residue 65 ILE Chi-restraints excluded: chain T residue 74 THR Chi-restraints excluded: chain T residue 92 ARG Chi-restraints excluded: chain U residue 7 ASN Chi-restraints excluded: chain U residue 28 SER Chi-restraints excluded: chain U residue 40 GLU Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 11 LYS Chi-restraints excluded: chain W residue 11 ARG Chi-restraints excluded: chain W residue 65 GLU Chi-restraints excluded: chain X residue 17 LEU Chi-restraints excluded: chain X residue 21 GLN Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain Y residue 4 ILE Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Z residue 45 ASP Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 57 ASN Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain b residue 76 ARG Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 102 MET Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 163 LEU Chi-restraints excluded: chain b residue 168 VAL Chi-restraints excluded: chain c residue 70 THR Chi-restraints excluded: chain c residue 108 ARG Chi-restraints excluded: chain c residue 123 GLN Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 15 GLU Chi-restraints excluded: chain d residue 70 LEU Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 118 GLN Chi-restraints excluded: chain d residue 183 THR Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 71 LEU Chi-restraints excluded: chain f residue 73 GLU Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 72 MET Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain h residue 112 MET Chi-restraints excluded: chain i residue 64 THR Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain k residue 33 ILE Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain l residue 15 LEU Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 117 TYR Chi-restraints excluded: chain m residue 18 SER Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain o residue 7 ASP Chi-restraints excluded: chain o residue 58 ARG Chi-restraints excluded: chain p residue 30 LYS Chi-restraints excluded: chain p residue 40 THR Chi-restraints excluded: chain p residue 42 SER Chi-restraints excluded: chain p residue 80 SER Chi-restraints excluded: chain p residue 92 LEU Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain s residue 4 SER Chi-restraints excluded: chain s residue 18 LYS Chi-restraints excluded: chain s residue 23 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 986 random chunks: chunk 587 optimal weight: 0.1980 chunk 379 optimal weight: 0.8980 chunk 567 optimal weight: 3.9990 chunk 286 optimal weight: 4.9990 chunk 186 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 604 optimal weight: 7.9990 chunk 647 optimal weight: 20.0000 chunk 469 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 746 optimal weight: 10.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 41 GLN C 163 GLN I 136 GLN T 59 GLN ** T 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 21 ASN c 38 GLN ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 5 ASN ** o 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 61 ASN o 71 ASN q 31 GLN r 54 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 153917 Z= 0.259 Angle : 0.649 14.381 230667 Z= 0.346 Chirality : 0.038 0.364 29520 Planarity : 0.006 0.134 12108 Dihedral : 23.325 178.985 77740 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.44 % Favored : 95.50 % Rotamer: Outliers : 3.61 % Allowed : 21.51 % Favored : 74.89 % 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: -0.01 (0.11), residues: 5361 helix: 1.38 (0.12), residues: 1748 sheet: 0.13 (0.16), residues: 1021 loop : -1.03 (0.11), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 248 HIS 0.008 0.001 HIS I 95 PHE 0.015 0.002 PHE F 138 TYR 0.018 0.002 TYR L 92 ARG 0.014 0.001 ARG L 57 *********************** 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 962 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 802 time to evaluate : 6.143 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 3 ASP cc_start: 0.7828 (OUTLIER) cc_final: 0.7533 (m-30) REVERT: 1 29 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7656 (mt0) REVERT: 2 64 ILE cc_start: 0.6240 (OUTLIER) cc_final: 0.5697 (tp) REVERT: C 38 LYS cc_start: 0.8309 (pttp) cc_final: 0.7851 (mttm) REVERT: C 101 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7111 (mtm180) REVERT: D 170 ASP cc_start: 0.7206 (t0) cc_final: 0.6942 (t0) REVERT: F 115 ARG cc_start: 0.5498 (tmm160) cc_final: 0.4865 (pmt170) REVERT: F 133 LYS cc_start: 0.4944 (OUTLIER) cc_final: 0.4719 (pmmt) REVERT: G 77 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.6988 (tppp) REVERT: I 86 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7267 (tp30) REVERT: L 10 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7470 (ptt180) REVERT: M 69 ARG cc_start: 0.7558 (mtt180) cc_final: 0.7145 (mtt180) REVERT: O 32 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7361 (mt0) REVERT: O 97 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.7586 (mtp85) REVERT: P 79 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.7675 (ttt) REVERT: Q 13 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7547 (ttt180) REVERT: R 60 HIS cc_start: 0.6327 (OUTLIER) cc_final: 0.5954 (t70) REVERT: S 34 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.7839 (t70) REVERT: T 92 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.6588 (mtm-85) REVERT: U 40 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6455 (pp20) REVERT: U 67 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8675 (mp) REVERT: W 11 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.7197 (ptt-90) REVERT: W 65 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6698 (mp0) REVERT: X 21 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8639 (mp10) REVERT: Y 29 ARG cc_start: 0.8136 (mmt90) cc_final: 0.7849 (mmt180) REVERT: Z 38 ARG cc_start: 0.8233 (ttt-90) cc_final: 0.8016 (ttm110) REVERT: b 76 ARG cc_start: 0.4598 (OUTLIER) cc_final: 0.4180 (mtp85) REVERT: b 102 MET cc_start: 0.7271 (OUTLIER) cc_final: 0.6987 (mtt) REVERT: b 163 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7646 (tt) REVERT: c 108 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7186 (mtp85) REVERT: d 15 GLU cc_start: 0.5682 (OUTLIER) cc_final: 0.4417 (mp0) REVERT: f 1 MET cc_start: 0.4905 (OUTLIER) cc_final: 0.4628 (mtp) REVERT: g 72 MET cc_start: 0.4280 (OUTLIER) cc_final: 0.3798 (ppp) REVERT: h 3 MET cc_start: 0.8429 (tpp) cc_final: 0.8169 (tmm) REVERT: h 19 MET cc_start: 0.7469 (ttm) cc_final: 0.7125 (ttm) REVERT: l 43 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7279 (tttt) REVERT: o 58 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7720 (ttt180) outliers start: 160 outliers final: 107 residues processed: 875 average time/residue: 2.2050 time to fit residues: 2731.7596 Evaluate side-chains 932 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 796 time to evaluate : 6.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 ASP Chi-restraints excluded: chain 0 residue 23 LYS Chi-restraints excluded: chain 1 residue 29 GLN Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 101 ARG Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 77 LYS Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 134 LYS Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 134 LYS Chi-restraints excluded: chain K residue 137 ILE Chi-restraints excluded: chain L residue 10 ARG Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain N residue 37 TYR Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 32 GLN Chi-restraints excluded: chain O residue 44 GLN Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 97 ARG Chi-restraints excluded: chain P residue 79 MET Chi-restraints excluded: chain Q residue 13 ARG Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 62 GLU Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain R residue 59 GLU Chi-restraints excluded: chain R residue 60 HIS Chi-restraints excluded: chain R residue 68 ASP Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain T residue 21 GLN Chi-restraints excluded: chain T residue 65 ILE Chi-restraints excluded: chain T residue 68 VAL Chi-restraints excluded: chain T residue 74 THR Chi-restraints excluded: chain T residue 92 ARG Chi-restraints excluded: chain U residue 7 ASN Chi-restraints excluded: chain U residue 28 SER Chi-restraints excluded: chain U residue 40 GLU Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 11 LYS Chi-restraints excluded: chain W residue 11 ARG Chi-restraints excluded: chain W residue 53 THR Chi-restraints excluded: chain W residue 65 GLU Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain X residue 17 LEU Chi-restraints excluded: chain X residue 21 GLN Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain Y residue 4 ILE Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Z residue 45 ASP Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 57 ASN Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain b residue 76 ARG Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 102 MET Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 163 LEU Chi-restraints excluded: chain b residue 168 VAL Chi-restraints excluded: chain c residue 70 THR Chi-restraints excluded: chain c residue 108 ARG Chi-restraints excluded: chain c residue 123 GLN Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 15 GLU Chi-restraints excluded: chain d residue 70 LEU Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 183 THR Chi-restraints excluded: chain d residue 189 ASP Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 71 LEU Chi-restraints excluded: chain f residue 73 GLU Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 72 MET Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain h residue 112 MET Chi-restraints excluded: chain i residue 64 THR Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain k residue 33 ILE Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain l residue 15 LEU Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 117 TYR Chi-restraints excluded: chain m residue 18 SER Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain o residue 58 ARG Chi-restraints excluded: chain p residue 30 LYS Chi-restraints excluded: chain p residue 40 THR Chi-restraints excluded: chain p residue 80 SER Chi-restraints excluded: chain p residue 92 LEU Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain s residue 4 SER Chi-restraints excluded: chain s residue 18 LYS Chi-restraints excluded: chain t residue 30 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 986 random chunks: chunk 864 optimal weight: 2.9990 chunk 910 optimal weight: 10.0000 chunk 830 optimal weight: 9.9990 chunk 885 optimal weight: 4.9990 chunk 533 optimal weight: 2.9990 chunk 385 optimal weight: 6.9990 chunk 695 optimal weight: 6.9990 chunk 271 optimal weight: 4.9990 chunk 800 optimal weight: 4.9990 chunk 837 optimal weight: 9.9990 chunk 882 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 41 GLN C 163 GLN I 67 ASN I 136 GLN T 38 ASN T 59 GLN ** T 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 52 GLN b 17 HIS b 96 HIS c 21 ASN c 38 GLN d 102 ASN f 28 GLN ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 5 ASN ** o 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 61 ASN o 71 ASN q 31 GLN ** r 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.119 153917 Z= 0.396 Angle : 0.731 13.972 230667 Z= 0.381 Chirality : 0.043 0.343 29520 Planarity : 0.007 0.140 12108 Dihedral : 23.398 179.713 77740 Min Nonbonded Distance : 1.643 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.98 % Favored : 94.96 % Rotamer: Outliers : 3.94 % Allowed : 21.24 % Favored : 74.82 % 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: -0.18 (0.11), residues: 5361 helix: 1.19 (0.12), residues: 1749 sheet: 0.06 (0.16), residues: 1015 loop : -1.11 (0.11), residues: 2597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP b 25 HIS 0.010 0.001 HIS I 95 PHE 0.018 0.002 PHE K 66 TYR 0.018 0.002 TYR G 115 ARG 0.011 0.001 ARG L 57 *********************** 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 985 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 810 time to evaluate : 6.101 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: 1 29 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7727 (mt0) REVERT: 2 64 ILE cc_start: 0.6349 (OUTLIER) cc_final: 0.5827 (tp) REVERT: C 38 LYS cc_start: 0.8313 (pttp) cc_final: 0.7833 (mttm) REVERT: C 95 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8591 (ttmt) REVERT: C 101 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7158 (mtm180) REVERT: D 170 ASP cc_start: 0.7238 (t0) cc_final: 0.6948 (t0) REVERT: E 139 ASP cc_start: 0.7340 (t0) cc_final: 0.7111 (t0) REVERT: F 115 ARG cc_start: 0.5629 (tmm160) cc_final: 0.4958 (pmt170) REVERT: G 77 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7063 (tppp) REVERT: G 153 SER cc_start: 0.8667 (p) cc_final: 0.8418 (t) REVERT: I 67 ASN cc_start: 0.8449 (t0) cc_final: 0.8189 (m110) REVERT: I 86 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7321 (tp30) REVERT: K 143 LYS cc_start: 0.7582 (mtmp) cc_final: 0.7349 (ptpp) REVERT: L 10 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7546 (ptt180) REVERT: N 105 LEU cc_start: 0.8532 (tt) cc_final: 0.8316 (tt) REVERT: O 32 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7425 (mt0) REVERT: O 97 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.7646 (mtp85) REVERT: P 79 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.7700 (ttt) REVERT: Q 13 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7569 (ttt180) REVERT: R 60 HIS cc_start: 0.6508 (OUTLIER) cc_final: 0.6066 (t70) REVERT: S 34 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.7813 (t70) REVERT: T 92 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.6455 (mtm-85) REVERT: U 40 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6649 (pp20) REVERT: U 67 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8684 (mp) REVERT: W 11 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7191 (ptt-90) REVERT: W 65 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6758 (mp0) REVERT: X 21 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8663 (mp10) REVERT: Y 1 MET cc_start: 0.0480 (tmm) cc_final: -0.1375 (tmm) REVERT: b 76 ARG cc_start: 0.4643 (tpt170) cc_final: 0.4261 (mtp85) REVERT: c 108 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7357 (mtp85) REVERT: d 15 GLU cc_start: 0.5740 (OUTLIER) cc_final: 0.4519 (mp0) REVERT: d 118 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8092 (tt0) REVERT: g 72 MET cc_start: 0.4270 (OUTLIER) cc_final: 0.3793 (ppp) REVERT: h 3 MET cc_start: 0.8442 (tpp) cc_final: 0.8187 (tmm) REVERT: h 19 MET cc_start: 0.7473 (ttm) cc_final: 0.7140 (ttm) REVERT: l 43 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7321 (tttt) REVERT: l 94 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6482 (mtp85) REVERT: o 58 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7754 (ttt180) outliers start: 175 outliers final: 110 residues processed: 905 average time/residue: 2.1771 time to fit residues: 2804.9851 Evaluate side-chains 921 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 785 time to evaluate : 5.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 23 LYS Chi-restraints excluded: chain 1 residue 29 GLN Chi-restraints excluded: chain 1 residue 41 SER Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 ARG Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 77 LYS Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 134 LYS Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 134 LYS Chi-restraints excluded: chain K residue 137 ILE Chi-restraints excluded: chain L residue 10 ARG Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain N residue 55 LEU Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 32 GLN Chi-restraints excluded: chain O residue 67 ILE Chi-restraints excluded: chain O residue 97 ARG Chi-restraints excluded: chain P residue 79 MET Chi-restraints excluded: chain Q residue 13 ARG Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 62 GLU Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain R residue 59 GLU Chi-restraints excluded: chain R residue 60 HIS Chi-restraints excluded: chain R residue 68 ASP Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain T residue 21 GLN Chi-restraints excluded: chain T residue 74 THR Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain T residue 92 ARG Chi-restraints excluded: chain U residue 7 ASN Chi-restraints excluded: chain U residue 28 SER Chi-restraints excluded: chain U residue 40 GLU Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 11 LYS Chi-restraints excluded: chain W residue 11 ARG Chi-restraints excluded: chain W residue 53 THR Chi-restraints excluded: chain W residue 65 GLU Chi-restraints excluded: chain X residue 21 GLN Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Z residue 45 ASP Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 57 ASN Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 102 MET Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain c residue 70 THR Chi-restraints excluded: chain c residue 108 ARG Chi-restraints excluded: chain c residue 123 GLN Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 15 GLU Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 118 GLN Chi-restraints excluded: chain d residue 183 THR Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain f residue 22 VAL Chi-restraints excluded: chain f residue 71 LEU Chi-restraints excluded: chain f residue 73 GLU Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 72 MET Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain h residue 112 MET Chi-restraints excluded: chain i residue 64 THR Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain k residue 33 ILE Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain l residue 15 LEU Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 94 ARG Chi-restraints excluded: chain l residue 117 TYR Chi-restraints excluded: chain m residue 18 SER Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain o residue 58 ARG Chi-restraints excluded: chain p residue 30 LYS Chi-restraints excluded: chain p residue 40 THR Chi-restraints excluded: chain p residue 42 SER Chi-restraints excluded: chain p residue 80 SER Chi-restraints excluded: chain p residue 92 LEU Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 30 VAL Chi-restraints excluded: chain s residue 4 SER Chi-restraints excluded: chain s residue 18 LYS Chi-restraints excluded: chain t residue 30 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 986 random chunks: chunk 581 optimal weight: 2.9990 chunk 936 optimal weight: 0.7980 chunk 571 optimal weight: 0.9990 chunk 444 optimal weight: 0.9980 chunk 651 optimal weight: 9.9990 chunk 982 optimal weight: 8.9990 chunk 904 optimal weight: 2.9990 chunk 782 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 604 optimal weight: 7.9990 chunk 479 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 41 GLN C 163 GLN D 50 GLN I 136 GLN Q 69 HIS T 38 ASN T 59 GLN ** T 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 4 GLN b 67 ASN c 21 ASN c 38 GLN c 140 ASN e 96 GLN ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 5 ASN l 72 HIS ** o 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 61 ASN o 71 ASN q 31 GLN ** r 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 153917 Z= 0.167 Angle : 0.600 14.414 230667 Z= 0.323 Chirality : 0.035 0.371 29520 Planarity : 0.005 0.127 12108 Dihedral : 23.316 179.335 77740 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.94 % Favored : 96.01 % Rotamer: Outliers : 2.86 % Allowed : 22.86 % Favored : 74.28 % 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: 0.09 (0.11), residues: 5361 helix: 1.48 (0.12), residues: 1750 sheet: 0.16 (0.16), residues: 1006 loop : -0.97 (0.12), residues: 2605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 201 HIS 0.006 0.001 HIS I 95 PHE 0.014 0.001 PHE Z 47 TYR 0.033 0.001 TYR F 97 ARG 0.012 0.000 ARG L 57 ********************** 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 948 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 821 time to evaluate : 6.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 29 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7591 (mt0) REVERT: C 38 LYS cc_start: 0.8377 (pttp) cc_final: 0.7919 (mttm) REVERT: C 101 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.6964 (mtm180) REVERT: D 170 ASP cc_start: 0.7164 (t0) cc_final: 0.6876 (t0) REVERT: F 115 ARG cc_start: 0.5564 (tmm160) cc_final: 0.4811 (pmt170) REVERT: G 153 SER cc_start: 0.8605 (p) cc_final: 0.8363 (t) REVERT: I 86 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7309 (tp30) REVERT: I 96 LYS cc_start: 0.7708 (mtmm) cc_final: 0.7326 (mtmm) REVERT: O 32 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7450 (mt0) REVERT: O 97 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.7510 (mtp85) REVERT: P 79 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.7653 (ttt) REVERT: Q 13 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7486 (ttt180) REVERT: R 60 HIS cc_start: 0.6482 (OUTLIER) cc_final: 0.6028 (t70) REVERT: T 92 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.6339 (mtm-85) REVERT: U 40 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6431 (pp20) REVERT: W 11 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7258 (ptt-90) REVERT: Y 29 ARG cc_start: 0.8119 (mmt90) cc_final: 0.7915 (mmt180) REVERT: b 76 ARG cc_start: 0.4638 (tpt170) cc_final: 0.4278 (mtp85) REVERT: b 102 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.7118 (mtt) REVERT: c 108 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7281 (mtp85) REVERT: d 15 GLU cc_start: 0.5632 (OUTLIER) cc_final: 0.4393 (mp0) REVERT: g 72 MET cc_start: 0.4290 (OUTLIER) cc_final: 0.3883 (ppp) REVERT: h 19 MET cc_start: 0.7429 (ttm) cc_final: 0.7091 (ttm) REVERT: l 43 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7228 (tttt) REVERT: o 58 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7728 (ttt180) outliers start: 127 outliers final: 77 residues processed: 892 average time/residue: 2.1927 time to fit residues: 2784.6652 Evaluate side-chains 889 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 795 time to evaluate : 5.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 29 GLN Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 101 ARG Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 60 ASP Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 32 GLN Chi-restraints excluded: chain O residue 97 ARG Chi-restraints excluded: chain P residue 79 MET Chi-restraints excluded: chain Q residue 13 ARG Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 62 GLU Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain R residue 59 GLU Chi-restraints excluded: chain R residue 60 HIS Chi-restraints excluded: chain R residue 68 ASP Chi-restraints excluded: chain S residue 78 ASP Chi-restraints excluded: chain T residue 21 GLN Chi-restraints excluded: chain T residue 74 THR Chi-restraints excluded: chain T residue 92 ARG Chi-restraints excluded: chain U residue 7 ASN Chi-restraints excluded: chain U residue 40 GLU Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 11 LYS Chi-restraints excluded: chain W residue 11 ARG Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain Y residue 4 ILE Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Z residue 45 ASP Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 57 ASN Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 102 MET Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 189 VAL Chi-restraints excluded: chain b residue 201 VAL Chi-restraints excluded: chain c residue 70 THR Chi-restraints excluded: chain c residue 108 ARG Chi-restraints excluded: chain c residue 123 GLN Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain d residue 15 GLU Chi-restraints excluded: chain d residue 70 LEU Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 183 THR Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain f residue 71 LEU Chi-restraints excluded: chain f residue 73 GLU Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 72 MET Chi-restraints excluded: chain g residue 91 VAL Chi-restraints excluded: chain g residue 129 GLU Chi-restraints excluded: chain h residue 112 MET Chi-restraints excluded: chain i residue 64 THR Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain k residue 33 ILE Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain l residue 15 LEU Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 117 TYR Chi-restraints excluded: chain m residue 18 SER Chi-restraints excluded: chain o residue 58 ARG Chi-restraints excluded: chain p residue 30 LYS Chi-restraints excluded: chain p residue 40 THR Chi-restraints excluded: chain p residue 42 SER Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain s residue 4 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 986 random chunks: chunk 621 optimal weight: 8.9990 chunk 833 optimal weight: 30.0000 chunk 239 optimal weight: 6.9990 chunk 721 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 217 optimal weight: 4.9990 chunk 783 optimal weight: 5.9990 chunk 327 optimal weight: 0.0770 chunk 804 optimal weight: 0.5980 chunk 99 optimal weight: 4.9990 chunk 144 optimal weight: 6.9990 overall best weight: 3.1344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 41 GLN C 163 GLN D 50 GLN I 67 ASN I 136 GLN T 59 GLN ** T 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 4 GLN c 21 ASN c 38 GLN e 85 ASN e 96 GLN ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 5 ASN o 61 ASN o 71 ASN q 31 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.145497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.098794 restraints weight = 185761.477| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.01 r_work: 0.2828 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 153917 Z= 0.331 Angle : 0.680 14.015 230667 Z= 0.358 Chirality : 0.040 0.340 29520 Planarity : 0.006 0.136 12108 Dihedral : 23.323 179.285 77740 Min Nonbonded Distance : 1.658 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.79 % Favored : 95.15 % Rotamer: Outliers : 2.77 % Allowed : 22.99 % Favored : 74.23 % 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: -0.01 (0.11), residues: 5361 helix: 1.38 (0.12), residues: 1744 sheet: 0.10 (0.16), residues: 1022 loop : -1.01 (0.12), residues: 2595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 248 HIS 0.011 0.001 HIS l 72 PHE 0.016 0.002 PHE P 57 TYR 0.019 0.002 TYR L 92 ARG 0.010 0.001 ARG L 57 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 42375.32 seconds wall clock time: 735 minutes 24.56 seconds (44124.56 seconds total)