Starting phenix.real_space_refine on Fri Dec 15 21:04:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3b_21032/12_2023/6v3b_21032_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3b_21032/12_2023/6v3b_21032.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3b_21032/12_2023/6v3b_21032_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3b_21032/12_2023/6v3b_21032_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3b_21032/12_2023/6v3b_21032_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3b_21032/12_2023/6v3b_21032.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3b_21032/12_2023/6v3b_21032.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3b_21032/12_2023/6v3b_21032_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v3b_21032/12_2023/6v3b_21032_updated.pdb" } resolution = 2.91 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= 0.106 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 4533 5.49 5 Mg 93 5.21 5 S 138 5.16 5 Na 1 4.78 5 C 69995 2.51 5 N 25995 2.21 5 O 39534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 23": "NH1" <-> "NH2" Residue "2 ARG 39": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "2 ARG 58": "NH1" <-> "NH2" Residue "3 ARG 18": "NH1" <-> "NH2" Residue "3 ARG 24": "NH1" <-> "NH2" Residue "3 ARG 32": "NH1" <-> "NH2" Residue "3 ARG 36": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C ARG 87": "NH1" <-> "NH2" Residue "C ARG 111": "NH1" <-> "NH2" Residue "C ARG 133": "NH1" <-> "NH2" Residue "C ARG 167": "NH1" <-> "NH2" Residue "C ASP 168": "OD1" <-> "OD2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "C ARG 238": "NH1" <-> "NH2" Residue "C ARG 258": "NH1" <-> "NH2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "D ARG 8": "NH1" <-> "NH2" Residue "D ARG 14": "NH1" <-> "NH2" Residue "D ASP 18": "OD1" <-> "OD2" Residue "D ARG 56": "NH1" <-> "NH2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D ARG 93": "NH1" <-> "NH2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D ARG 157": "NH1" <-> "NH2" Residue "D ASP 170": "OD1" <-> "OD2" Residue "D ASP 184": "OD1" <-> "OD2" Residue "D ARG 207": "NH1" <-> "NH2" Residue "E ARG 20": "NH1" <-> "NH2" Residue "E GLU 24": "OE1" <-> "OE2" Residue "E TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 48": "NH1" <-> "NH2" Residue "E PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "E ARG 68": "NH1" <-> "NH2" Residue "E ASP 90": "OD1" <-> "OD2" Residue "E ARG 113": "NH1" <-> "NH2" Residue "E ASP 115": "OD1" <-> "OD2" Residue "E GLU 132": "OE1" <-> "OE2" Residue "E ARG 161": "NH1" <-> "NH2" Residue "E ASP 175": "OD1" <-> "OD2" Residue "E PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 144": "OD1" <-> "OD2" Residue "F ARG 150": "NH1" <-> "NH2" Residue "F ASP 153": "OD1" <-> "OD2" 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 GLU 46": "OE1" <-> "OE2" Residue "G ARG 69": "NH1" <-> "NH2" Residue "G ARG 163": "NH1" <-> "NH2" Residue "G ARG 171": "NH1" <-> "NH2" Residue "H GLU 58": "OE1" <-> "OE2" Residue "I GLU 10": "OE1" <-> "OE2" Residue "I PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 27": "NH1" <-> "NH2" Residue "I ARG 34": "NH1" <-> "NH2" Residue "I ARG 35": "NH1" <-> "NH2" Residue "I TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 76": "NH1" <-> "NH2" Residue "I PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 71": "NH1" <-> "NH2" Residue "J ASP 73": "OD1" <-> "OD2" Residue "J ARG 104": "NH1" <-> "NH2" Residue "J GLU 105": "OE1" <-> "OE2" Residue "J GLU 109": "OE1" <-> "OE2" Residue "J GLU 120": "OE1" <-> "OE2" 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 145": "OE1" <-> "OE2" 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 GLU 91": "OE1" <-> "OE2" Residue "L TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 111": "OE1" <-> "OE2" 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 GLU 32": "OE1" <-> "OE2" Residue "M ARG 46": "NH1" <-> "NH2" Residue "M ARG 63": "NH1" <-> "NH2" Residue "M ARG 64": "NH1" <-> "NH2" Residue "M PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 110": "NH1" <-> "NH2" Residue "N PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 56": "NH1" <-> "NH2" Residue "O ARG 91": "NH1" <-> "NH2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O ARG 97": "NH1" <-> "NH2" Residue "O ARG 112": "NH1" <-> "NH2" Residue "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 ARG 51": "NH1" <-> "NH2" Residue "P ARG 70": "NH1" <-> "NH2" Residue "P TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 78": "NH1" <-> "NH2" Residue "P PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 111": "OE1" <-> "OE2" Residue "Q TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 16": "OE1" <-> "OE2" Residue "Q GLU 23": "OE1" <-> "OE2" Residue "Q ASP 36": "OD1" <-> "OD2" Residue "Q ARG 68": "NH1" <-> "NH2" 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 GLU 52": "OE1" <-> "OE2" Residue "R GLU 59": "OE1" <-> "OE2" Residue "R ASP 67": "OD1" <-> "OD2" Residue "R ASP 94": "OD1" <-> "OD2" Residue "R ARG 95": "NH1" <-> "NH2" Residue "S ARG 5": "NH1" <-> "NH2" Residue "S ASP 34": "OD1" <-> "OD2" Residue "S ARG 68": "NH1" <-> "NH2" Residue "S ARG 76": "NH1" <-> "NH2" Residue "S ASP 91": "OD1" <-> "OD2" Residue "T GLU 17": "OE1" <-> "OE2" Residue "T ARG 31": "NH1" <-> "NH2" Residue "T TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 87": "OD1" <-> "OD2" Residue "U PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 11": "NH1" <-> "NH2" Residue "U ASP 14": "OD1" <-> "OD2" Residue "U ARG 22": "NH1" <-> "NH2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "U ARG 49": "NH1" <-> "NH2" Residue "U PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 44": "OE1" <-> "OE2" Residue "V PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 64": "OD1" <-> "OD2" Residue "W ARG 37": "NH1" <-> "NH2" Residue "W ARG 48": "NH1" <-> "NH2" Residue "W GLU 65": "OE1" <-> "OE2" Residue "X ASP 5": "OD1" <-> "OD2" Residue "X GLU 8": "OE1" <-> "OE2" 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 PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 37": "NH1" <-> "NH2" Residue "b ASP 54": "OD1" <-> "OD2" Residue "b PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 76": "NH1" <-> "NH2" Residue "b ARG 83": "NH1" <-> "NH2" Residue "b ARG 88": "NH1" <-> "NH2" Residue "b TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 110": "NH1" <-> "NH2" Residue "b PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 134": "NH1" <-> "NH2" Residue "b ARG 141": "NH1" <-> "NH2" Residue "b GLU 147": "OE1" <-> "OE2" Residue "b ARG 148": "NH1" <-> "NH2" Residue "b ASP 167": "OD1" <-> "OD2" Residue "b ASP 190": "OD1" <-> "OD2" Residue "b ASP 207": "OD1" <-> "OD2" Residue "b ARG 210": "NH1" <-> "NH2" Residue "b TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 11": "NH1" <-> "NH2" Residue "c TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 31": "OE1" <-> "OE2" Residue "c ASP 83": "OD1" <-> "OD2" Residue "c ARG 108": "NH1" <-> "NH2" Residue "c ASP 110": "OD1" <-> "OD2" Residue "c ARG 114": "NH1" <-> "NH2" Residue "c GLU 118": "OE1" <-> "OE2" Residue "c GLU 125": "OE1" <-> "OE2" Residue "c PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 169": "NH1" <-> "NH2" Residue "c GLU 170": "OE1" <-> "OE2" Residue "c ASP 183": "OD1" <-> "OD2" 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 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 GLU 90": "OE1" <-> "OE2" Residue "d GLU 97": "OE1" <-> "OE2" Residue "d ARG 106": "NH1" <-> "NH2" Residue "d ARG 113": "NH1" <-> "NH2" Residue "d GLU 115": "OE1" <-> "OE2" Residue "d ARG 123": "NH1" <-> "NH2" Residue "d ARG 130": "NH1" <-> "NH2" Residue "e ASP 18": "OD1" <-> "OD2" Residue "e PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "f GLU 40": "OE1" <-> "OE2" Residue "f ASP 72": "OD1" <-> "OD2" 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 GLU 60": "OE1" <-> "OE2" Residue "g PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 90": "OE1" <-> "OE2" Residue "g ARG 95": "NH1" <-> "NH2" Residue "g ARG 102": "NH1" <-> "NH2" Residue "g GLU 113": "OE1" <-> "OE2" Residue "g ARG 119": "NH1" <-> "NH2" Residue "g ARG 138": "NH1" <-> "NH2" Residue "h ARG 13": "NH1" <-> "NH2" Residue "h TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 88": "NH1" <-> "NH2" Residue "h ASP 114": "OD1" <-> "OD2" Residue "h ARG 115": "NH1" <-> "NH2" Residue "h ARG 118": "NH1" <-> "NH2" Residue "i ARG 9": "NH1" <-> "NH2" Residue "i PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 57": "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 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 91": "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 PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 67": "OE1" <-> "OE2" Residue "k ARG 97": "NH1" <-> "NH2" 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 ASP 89": "OD1" <-> "OD2" Residue "l TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 99": "NH1" <-> "NH2" 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 GLU 47": "OE1" <-> "OE2" Residue "m ASP 49": "OD1" <-> "OD2" Residue "m ARG 57": "NH1" <-> "NH2" Residue "m GLU 59": "OE1" <-> "OE2" Residue "m GLU 72": "OE1" <-> "OE2" 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 ASP 38": "OD1" <-> "OD2" Residue "n ARG 59": "NH1" <-> "NH2" Residue "n ARG 61": "NH1" <-> "NH2" 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 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 16": "OD1" <-> "OD2" Residue "q ARG 40": "NH1" <-> "NH2" Residue "q ARG 41": "NH1" <-> "NH2" Residue "q ASP 49": "OD1" <-> "OD2" Residue "q GLU 81": "OE1" <-> "OE2" Residue "r TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 22": "OD1" <-> "OD2" Residue "r TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 25": "OD1" <-> "OD2" Residue "r ASP 27": "OD1" <-> "OD2" Residue "r ARG 43": "NH1" <-> "NH2" Residue "r ARG 53": "NH1" <-> "NH2" Residue "r ARG 63": "NH1" <-> "NH2" Residue "r ASP 72": "OD1" <-> "OD2" 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 TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 78": "NH1" <-> "NH2" Residue "u ARG 35": "NH1" <-> "NH2" Residue "u ARG 45": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 140290 Number of models: 1 Model: "" Number of chains: 76 Chain: "0" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 427 Classifications: {'peptide': 51} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "1" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "2" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "3" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 295 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "AN" Number of atoms: 62023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2892, 62023 Classifications: {'RNA': 2892} Modifications used: {'5*END': 1, 'rna2p': 3, 'rna2p_pur': 257, 'rna2p_pyr': 144, 'rna3p': 12, 'rna3p_pur': 1391, 'rna3p_pyr': 1085} Link IDs: {'rna2p': 404, 'rna3p': 2487} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2450 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 54, 'rna3p_pyr': 48} Link IDs: {'rna2p': 13, 'rna3p': 101} Chain: "C" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2096 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 16, 'TRANS': 253} Chain: "D" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1572 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 205} Chain: "E" Number of atoms: 1419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1419 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 6, 'TRANS': 179} Chain: "F" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1381 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 6, 'TRANS': 168} Chain: "G" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1318 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 8, 'TRANS': 165} Chain: "H" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 458 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "I" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1125 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "J" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "K" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1089 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 142} Chain: "L" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1087 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 130} Chain: "M" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "N" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 857 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "O" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 919 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "P" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 934 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "Q" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 807 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "R" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 826 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain: "S" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 702 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "T" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 749 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "U" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 760 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "V" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 598 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "W" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 632 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "X" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 498 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "Y" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 463 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "Z" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 456 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "sN" Number of atoms: 32782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1528, 32782 Classifications: {'RNA': 1528} Modifications used: {'5*END': 1, 'rna2p': 1, 'rna2p_pur': 108, 'rna2p_pyr': 83, 'rna3p': 8, 'rna3p_pur': 755, 'rna3p_pyr': 573} Link IDs: {'rna2p': 191, 'rna3p': 1336} 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: "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: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Unusual residues: {' MG': 52, ' NA': 1} Classifications: {'undetermined': 53} Link IDs: {None: 52} Chain: "sN" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Unusual residues: {' MG': 41} Classifications: {'undetermined': 41} Link IDs: {None: 40} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "AN" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} 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: "M" 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "sN" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 107 Classifications: {'water': 107} Link IDs: {None: 106} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "i" 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "s" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1382 SG CYS 3 11 180.614 126.111 135.027 1.00 31.25 S ATOM 1398 SG CYS 3 14 179.279 124.261 132.174 1.00 30.12 S ATOM 1503 SG CYS 3 27 180.713 121.690 134.818 1.00 30.86 S Time building chain proxies: 54.17, per 1000 atoms: 0.39 Number of scatterers: 140290 At special positions: 0 Unit cell: (228.76, 246.848, 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 138 16.00 P 4533 15.00 Mg 93 11.99 Na 1 11.00 O 39534 8.00 N 25995 7.00 C 69995 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=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 56.20 Conformation dependent library (CDL) restraints added in 7.4 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 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 14 " 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 66 sheets defined 38.9% alpha, 19.1% beta 1393 base pairs and 2339 stacking pairs defined. Time for finding SS restraints: 65.35 Creating SS restraints... Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 25 removed outlier: 3.863A pdb=" N THR 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LYS 1 25 " --> pdb=" O ARG 1 21 " (cutoff:3.500A) Processing helix chain '1' and resid 26 through 38 Processing helix chain '2' and resid 7 through 14 Processing helix chain '2' and resid 31 through 36 removed outlier: 4.472A pdb=" N LYS 2 35 " --> pdb=" O ILE 2 31 " (cutoff:3.500A) removed outlier: 5.066A 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: 4.099A pdb=" N ARG 2 44 " --> pdb=" O ILE 2 40 " (cutoff:3.500A) Processing helix chain '2' and resid 50 through 62 removed outlier: 4.624A pdb=" N ALA 2 55 " --> pdb=" O VAL 2 51 " (cutoff:3.500A) removed outlier: 4.868A 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: 5.233A pdb=" N PHE C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.653A pdb=" N VAL C 34 " --> pdb=" O TYR C 30 " (cutoff:3.500A) removed outlier: 5.514A 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: 3.937A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 3.944A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.457A 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 'D' and resid 57 through 62 removed outlier: 3.504A pdb=" N VAL D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N THR D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 57 through 62' Processing helix chain 'D' and resid 63 through 73 Processing helix chain 'D' and resid 86 through 91 removed outlier: 3.971A pdb=" N GLU D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'E' and resid 15 through 20 removed outlier: 3.714A pdb=" N ARG E 20 " --> pdb=" O VAL E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 39 removed outlier: 3.750A pdb=" N GLY E 38 " --> pdb=" O TYR E 34 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ARG E 39 " --> pdb=" O LEU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 52 removed outlier: 6.206A 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: 3.609A pdb=" N LEU E 133 " --> pdb=" O LYS E 129 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU E 140 " --> pdb=" O LYS E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 164 removed outlier: 3.570A pdb=" N TYR E 157 " --> pdb=" O ASP E 153 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASN E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 4.506A 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: 3.551A 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: 4.092A pdb=" N ASP F 10 " --> pdb=" O ALA F 6 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU F 11 " --> pdb=" O ARG F 7 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER F 21 " --> pdb=" O GLN F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 removed outlier: 4.469A pdb=" N ASP F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 61 removed outlier: 3.850A pdb=" N GLY F 52 " --> pdb=" O LYS F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 110 removed outlier: 3.675A pdb=" N TYR F 97 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ILE F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Proline residue: F 109 - end of helix Processing helix chain 'F' and resid 162 through 174 removed outlier: 4.317A 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: 3.700A pdb=" N LEU G 141 " --> pdb=" O ASN G 137 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG G 152 " --> pdb=" O ILE G 148 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 Processing helix chain 'H' and resid 40 through 47 Processing helix chain 'H' and resid 50 through 59 removed outlier: 5.181A pdb=" N GLU H 58 " --> pdb=" O LEU H 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 12 removed outlier: 5.921A pdb=" N GLN I 12 " --> pdb=" O PRO I 8 " (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: 3.636A pdb=" N LYS I 120 " --> pdb=" O TYR I 116 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYS I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N MET I 122 " --> pdb=" O MET I 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 118 removed outlier: 3.576A pdb=" N ILE J 115 " --> pdb=" O PHE J 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 44 removed outlier: 3.664A pdb=" N ARG K 43 " --> pdb=" O GLY K 39 " (cutoff:3.500A) removed outlier: 5.790A 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: 3.562A pdb=" N LEU K 63 " --> pdb=" O ILE K 59 " (cutoff:3.500A) Proline residue: K 64 - end of helix Processing helix chain 'K' and resid 70 through 77 removed outlier: 4.082A pdb=" N LEU K 74 " --> pdb=" O SER K 70 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS K 75 " --> pdb=" O GLN K 71 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR K 76 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.027A 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: 4.087A pdb=" N LEU K 84 " --> pdb=" O ARG K 80 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N SER K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LYS K 86 " --> pdb=" O SER K 82 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL K 87 " --> pdb=" O GLU K 83 " (cutoff:3.500A) removed outlier: 5.840A 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: 3.565A pdb=" N ASN K 101 " --> pdb=" O LEU K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 141 removed outlier: 3.648A pdb=" N GLY K 141 " --> pdb=" O ILE K 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 59 removed outlier: 3.527A pdb=" N LYS L 59 " --> pdb=" O SER L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 126 removed outlier: 3.850A pdb=" N ALA L 123 " --> pdb=" O ALA L 119 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS L 124 " --> pdb=" O LEU L 120 " (cutoff:3.500A) removed outlier: 3.530A 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: 3.873A pdb=" N ARG M 45 " --> pdb=" O ALA M 41 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ARG M 46 " --> pdb=" O LYS M 42 " (cutoff:3.500A) removed outlier: 3.918A 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: 4.773A pdb=" N GLY M 84 " --> pdb=" O PHE M 80 " (cutoff:3.500A) Proline residue: M 85 - end of helix Processing helix chain 'N' and resid 3 through 23 removed outlier: 3.788A pdb=" N SER N 7 " --> pdb=" O GLU N 3 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER N 14 " --> pdb=" O ARG N 10 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N THR N 15 " --> pdb=" O ARG N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 66 through 85 Processing helix chain 'N' and resid 100 through 113 removed outlier: 3.802A pdb=" N GLY N 113 " --> pdb=" O ALA N 109 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 16 removed outlier: 3.938A pdb=" N SER O 14 " --> pdb=" O ALA O 10 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLN O 15 " --> pdb=" O ILE O 11 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU O 16 " --> pdb=" O GLU O 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 107 removed outlier: 4.761A pdb=" N ASP O 105 " --> pdb=" O TYR O 101 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU O 106 " --> pdb=" O TYR O 102 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N SER O 107 " --> pdb=" O LEU O 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 101 through 107' Processing helix chain 'P' and resid 7 through 22 removed outlier: 3.514A pdb=" N ALA P 21 " --> pdb=" O ILE P 17 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS P 22 " --> pdb=" O LEU P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 31 removed outlier: 3.763A pdb=" N ARG P 30 " --> pdb=" O GLY P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 73 removed outlier: 3.901A pdb=" N ARG P 51 " --> pdb=" O TYR P 47 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS P 54 " --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 4.107A 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: 3.972A pdb=" N LEU R 19 " --> pdb=" O GLN R 15 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL R 20 " --> pdb=" O LYS R 16 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU R 23 " --> pdb=" O LEU R 19 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE R 24 " --> pdb=" O VAL R 20 " (cutoff:3.500A) removed outlier: 3.713A 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: 4.440A pdb=" N VAL R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU R 46 " --> pdb=" O LYS R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 70 removed outlier: 4.057A pdb=" N LEU R 69 " --> pdb=" O ASP R 65 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LYS R 70 " --> pdb=" O VAL R 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 65 through 70' Processing helix chain 'S' and resid 3 through 10 removed outlier: 4.390A pdb=" N TYR S 7 " --> pdb=" O ASN S 3 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN S 8 " --> pdb=" O GLU S 4 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU S 10 " --> pdb=" O ILE S 6 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 26 Processing helix chain 'S' and resid 38 through 50 Processing helix chain 'T' and resid 64 through 69 removed outlier: 3.794A pdb=" N VAL T 68 " --> pdb=" O HIS T 64 " (cutoff:3.500A) removed outlier: 5.461A 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: 5.396A pdb=" N GLY U 17 " --> pdb=" O GLU U 13 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 28 removed outlier: 3.701A pdb=" N SER U 28 " --> pdb=" O LEU U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 57 removed outlier: 4.038A pdb=" N SER U 57 " --> pdb=" O LYS U 53 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 63 removed outlier: 4.587A pdb=" N GLU U 62 " --> pdb=" O ASN U 58 " (cutoff:3.500A) Processing helix chain 'W' and resid 52 through 63 Processing helix chain 'W' and resid 64 through 75 removed outlier: 3.818A pdb=" N GLN W 74 " --> pdb=" O ASP W 70 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLY W 75 " --> pdb=" O LEU W 71 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 9 removed outlier: 4.221A pdb=" N GLU X 8 " --> pdb=" O LYS X 4 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYS X 9 " --> pdb=" O ASP X 5 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 35 Processing helix chain 'X' and resid 39 through 63 removed outlier: 4.163A pdb=" N VAL X 43 " --> pdb=" O LYS X 39 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLN X 44 " --> pdb=" O SER X 40 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN X 63 " --> pdb=" O GLU X 59 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 27 removed outlier: 3.572A pdb=" N LEU Y 26 " --> pdb=" O CYS Y 22 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY Y 27 " --> pdb=" O LEU Y 23 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 51 removed outlier: 3.500A pdb=" N MET Y 46 " --> pdb=" O SER Y 42 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL Y 50 " --> pdb=" O MET Y 46 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 19 removed outlier: 5.174A pdb=" N HIS Z 19 " --> pdb=" O MET Z 15 " (cutoff:3.500A) Processing helix chain 'b' and resid 7 through 15 removed outlier: 3.571A pdb=" N GLY b 15 " --> pdb=" O LEU b 11 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 34 removed outlier: 4.183A pdb=" N ILE b 33 " --> pdb=" O MET b 29 " (cutoff:3.500A) removed outlier: 5.831A 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: 3.909A pdb=" N THR b 48 " --> pdb=" O ASN b 44 " (cutoff:3.500A) Proline residue: b 50 - end of helix Processing helix chain 'b' and resid 76 through 90 removed outlier: 3.755A pdb=" N ASN b 80 " --> pdb=" O ARG b 76 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE b 81 " --> pdb=" O ALA b 77 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG b 83 " --> pdb=" O SER b 79 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLU b 84 " --> pdb=" O ASN b 80 " (cutoff:3.500A) Processing helix chain 'b' and resid 101 through 106 Processing helix chain 'b' and resid 107 through 126 removed outlier: 4.822A pdb=" N GLN b 111 " --> pdb=" O LYS b 107 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N SER b 112 " --> pdb=" O THR b 108 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE b 113 " --> pdb=" O LEU b 109 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER b 123 " --> pdb=" O LEU b 119 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLN b 124 " --> pdb=" O GLN b 120 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP b 125 " --> pdb=" O THR b 121 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLY b 126 " --> pdb=" O GLN b 122 " (cutoff:3.500A) Processing helix chain 'b' and resid 127 through 132 removed outlier: 6.247A pdb=" N LEU b 131 " --> pdb=" O THR b 127 " (cutoff:3.500A) removed outlier: 6.360A 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 151 removed outlier: 4.187A pdb=" N SER b 149 " --> pdb=" O LYS b 145 " (cutoff:3.500A) Processing helix chain 'b' and resid 167 through 172 removed outlier: 4.210A pdb=" N GLU b 171 " --> pdb=" O ASP b 167 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA b 172 " --> pdb=" O VAL b 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 167 through 172' Processing helix chain 'b' and resid 173 through 182 Processing helix chain 'b' and resid 208 through 226 removed outlier: 3.730A pdb=" N GLY b 226 " --> pdb=" O ALA b 222 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.656A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 25 through 48 removed outlier: 5.002A pdb=" N ALA c 30 " --> pdb=" O PRO c 26 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N GLU c 31 " --> pdb=" O LYS c 27 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LYS c 48 " --> pdb=" O THR c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 78 removed outlier: 3.527A pdb=" N VAL c 76 " --> pdb=" O ARG c 72 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY c 78 " --> pdb=" O GLY c 74 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 96 removed outlier: 4.263A pdb=" N GLY c 96 " --> pdb=" O THR c 92 " (cutoff:3.500A) Processing helix chain 'c' and resid 112 through 127 removed outlier: 4.243A pdb=" N ARG c 127 " --> pdb=" O GLN c 123 " (cutoff:3.500A) Processing helix chain 'c' and resid 129 through 145 removed outlier: 3.795A pdb=" N GLY c 145 " --> pdb=" O THR c 141 " (cutoff:3.500A) Processing helix chain 'c' and resid 210 through 215 removed outlier: 4.621A pdb=" N VAL c 214 " --> pdb=" O GLY c 210 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 16 removed outlier: 3.727A 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: 3.683A pdb=" N VAL d 84 " --> pdb=" O GLU d 80 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LYS d 85 " --> pdb=" O ALA d 81 " (cutoff:3.500A) Processing helix chain 'd' and resid 87 through 99 removed outlier: 4.000A 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: 3.786A pdb=" N ARG d 123 " --> pdb=" O LEU d 119 " (cutoff:3.500A) Processing helix chain 'd' and resid 148 through 153 removed outlier: 4.373A pdb=" N GLN d 153 " --> pdb=" O GLU d 149 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 168 removed outlier: 3.707A pdb=" N LYS d 158 " --> pdb=" O GLN d 154 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU d 162 " --> pdb=" O LYS d 158 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU d 163 " --> pdb=" O ASN d 159 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG d 167 " --> pdb=" O LEU d 163 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N GLY d 168 " --> pdb=" O ALA d 164 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 194 removed outlier: 3.504A 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: 3.858A pdb=" N ILE d 202 " --> pdb=" O ASN d 198 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LYS d 208 " --> pdb=" O GLU d 204 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 3.509A pdb=" N ASN e 69 " --> pdb=" O ALA e 65 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N MET e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 107 through 118 removed outlier: 3.802A pdb=" N VAL e 113 " --> pdb=" O ALA e 109 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 146 removed outlier: 3.710A pdb=" N ARG e 144 " --> pdb=" O PHE e 140 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP e 145 " --> pdb=" O LYS e 141 " (cutoff:3.500A) removed outlier: 3.964A 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: 3.629A pdb=" N ILE e 163 " --> pdb=" O SER e 159 " (cutoff:3.500A) removed outlier: 4.083A 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 22 removed outlier: 3.578A pdb=" N SER f 15 " --> pdb=" O HIS f 11 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP f 16 " --> pdb=" O PRO f 12 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLN f 17 " --> pdb=" O ASP f 13 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY f 20 " --> pdb=" O ASP f 16 " (cutoff:3.500A) Processing helix chain 'f' and resid 23 through 30 removed outlier: 3.915A pdb=" N GLN f 28 " --> pdb=" O ARG f 24 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE f 29 " --> pdb=" O TYR f 25 " (cutoff:3.500A) Processing helix chain 'f' and resid 70 through 81 removed outlier: 3.800A pdb=" N PHE f 78 " --> pdb=" O LEU f 74 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR f 80 " --> pdb=" O GLU f 76 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASN f 81 " --> pdb=" O LEU f 77 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 Processing helix chain 'g' and resid 35 through 55 removed outlier: 3.653A pdb=" N ALA g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS g 53 " --> pdb=" O ARG g 49 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN g 54 " --> pdb=" O VAL g 50 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.719A pdb=" N PHE g 61 " --> pdb=" O ASP g 57 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS g 68 " --> pdb=" O THR g 64 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL g 69 " --> pdb=" O THR g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 112 removed outlier: 3.573A pdb=" N ARG g 111 " --> pdb=" O ALA g 107 " (cutoff:3.500A) removed outlier: 5.736A 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: 3.995A pdb=" N LYS g 136 " --> pdb=" O GLY g 132 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLU g 139 " --> pdb=" O ILE g 135 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 removed outlier: 3.735A 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: 4.678A pdb=" N GLY i 38 " --> pdb=" O GLU i 34 " (cutoff:3.500A) Processing helix chain 'i' and resid 39 through 54 removed outlier: 3.712A pdb=" N ARG i 43 " --> pdb=" O ARG i 39 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN i 48 " --> pdb=" O MET i 44 " (cutoff:3.500A) Proline residue: i 49 - end of helix Processing helix chain 'i' and resid 69 through 90 Processing helix chain 'i' and resid 91 through 100 removed outlier: 5.087A pdb=" N VAL i 95 " --> pdb=" O THR i 91 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA i 99 " --> pdb=" O VAL i 95 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 3.745A pdb=" N ILE j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY j 33 " --> pdb=" O ALA j 29 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 3.723A pdb=" N VAL j 84 " --> pdb=" O THR j 80 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP j 85 " --> pdb=" O ASP j 81 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 3.579A pdb=" N GLY k 50 " --> pdb=" O SER k 46 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 59 removed outlier: 4.621A pdb=" N SER k 57 " --> pdb=" O GLY k 53 " (cutoff:3.500A) removed outlier: 4.166A 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: 3.937A pdb=" N VAL k 64 " --> pdb=" O PHE k 60 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP k 75 " --> pdb=" O LYS k 71 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N TYR k 76 " --> pdb=" O ALA k 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 103 removed outlier: 4.028A pdb=" N ALA k 95 " --> pdb=" O GLY k 91 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N VAL k 96 " --> pdb=" O ARG k 92 " (cutoff:3.500A) removed outlier: 3.635A 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: 4.921A pdb=" N TYR l 117 " --> pdb=" O SER l 113 " (cutoff:3.500A) removed outlier: 3.758A 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: 3.724A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.766A 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: 3.611A pdb=" N LEU m 48 " --> pdb=" O LYS m 44 " (cutoff:3.500A) removed outlier: 5.415A 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: 4.218A pdb=" N ALA m 55 " --> pdb=" O ALA m 51 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS m 62 " --> pdb=" O ALA m 58 " (cutoff:3.500A) removed outlier: 3.854A 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 67 through 84 removed outlier: 3.690A pdb=" N GLY m 84 " --> pdb=" O LEU m 80 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 94 removed outlier: 4.918A pdb=" N ARG m 93 " --> pdb=" O LEU m 89 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER m 94 " --> pdb=" O ARG m 90 " (cutoff:3.500A) Processing helix chain 'm' and resid 106 through 111 removed outlier: 4.290A pdb=" N GLY m 111 " --> pdb=" O ALA m 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 106 through 111' Processing helix chain 'n' and resid 3 through 21 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: 4.487A pdb=" N LEU n 60 " --> pdb=" O SER n 56 " (cutoff:3.500A) removed outlier: 5.744A 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: 3.947A pdb=" N ASP n 86 " --> pdb=" O ASN n 82 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY n 91 " --> pdb=" O THR n 87 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 16 Processing helix chain 'o' and resid 24 through 44 removed outlier: 4.062A pdb=" N GLY o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS o 42 " --> pdb=" O ASP o 38 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 4.136A 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: 3.587A pdb=" N GLY p 82 " --> pdb=" O TRP p 78 " (cutoff:3.500A) Processing helix chain 'p' and resid 86 through 101 removed outlier: 3.626A pdb=" N ALA p 101 " --> pdb=" O LYS p 97 " (cutoff:3.500A) Processing helix chain 'r' and resid 25 through 34 removed outlier: 3.621A pdb=" N LEU r 29 " --> pdb=" O ASP r 25 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR r 32 " --> pdb=" O THR r 28 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N THR r 34 " --> pdb=" O LYS r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 46 removed outlier: 3.603A 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: 4.509A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.164A 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: 3.616A pdb=" N LEU t 24 " --> pdb=" O HIS t 20 " (cutoff:3.500A) removed outlier: 3.732A 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: 3.660A pdb=" N GLY t 65 " --> pdb=" O MET t 61 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 87 removed outlier: 3.774A pdb=" N LEU t 86 " --> pdb=" O GLN t 82 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA t 87 " --> pdb=" O VAL t 83 " (cutoff:3.500A) Processing helix chain 'u' and resid 39 through 54 removed outlier: 4.467A pdb=" N GLN u 43 " --> pdb=" O GLU u 39 " (cutoff:3.500A) removed outlier: 3.675A 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: 6.461A pdb=" N TYR 0 15 " --> pdb=" O SER 0 9 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ILE 0 44 " --> pdb=" O SER 0 10 " (cutoff:3.500A) removed outlier: 5.830A 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 removed outlier: 3.898A pdb=" N VAL 3 25 " --> pdb=" O GLN 3 35 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N CYS 3 27 " --> pdb=" O HIS 3 33 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N HIS 3 33 " --> pdb=" O CYS 3 27 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 80 through 83 removed outlier: 3.890A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N VAL C 74 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N SER C 118 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASP C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLY C 127 " --> pdb=" O LYS C 115 " (cutoff:3.500A) removed outlier: 5.017A 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: 4.462A pdb=" N SER C 139 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.097A 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: 5.373A pdb=" N HIS C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 4.470A 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: 4.543A pdb=" N VAL D 21 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL D 27 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLY D 202 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 13.600A pdb=" N GLY D 201 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 11.886A pdb=" N LYS D 117 " --> pdb=" O GLY D 201 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ASP D 203 " --> pdb=" O GLN D 115 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLN D 115 " --> pdb=" O ASP D 203 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU D 171 " --> pdb=" O SER D 116 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N GLY D 118 " --> pdb=" O GLY D 169 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY D 169 " --> pdb=" O GLY D 118 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLY D 120 " --> pdb=" O HIS D 167 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N HIS D 167 " --> pdb=" O GLY D 120 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 37 through 41 removed outlier: 3.971A pdb=" N LEU D 41 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TYR D 46 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLN D 50 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 4.288A 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: 5.494A pdb=" N SER D 188 " --> pdb=" O VAL D 30 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 48 through 52 Processing sheet with id= 12, first strand: chain 'D' and resid 111 through 114 Processing sheet with id= 13, first strand: chain 'E' and resid 116 through 119 removed outlier: 5.759A pdb=" N ARG E 116 " --> pdb=" O ASP E 183 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS E 184 " --> pdb=" O ARG E 144 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP E 167 " --> pdb=" O ALA E 145 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'F' and resid 66 through 71 removed outlier: 6.921A pdb=" N VAL F 66 " --> pdb=" O CYS F 87 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N CYS F 87 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N THR F 68 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N TRP F 83 " --> pdb=" O ALA F 70 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N CYS F 87 " --> pdb=" O MET F 38 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N MET F 38 " --> pdb=" O CYS F 87 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS F 33 " --> pdb=" O THR F 157 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR F 155 " --> pdb=" O THR F 35 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET F 152 " --> pdb=" O LEU F 132 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE F 156 " --> pdb=" O TYR F 128 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N TYR F 128 " --> pdb=" O ILE F 156 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'G' and resid 16 through 19 Processing sheet with id= 16, first strand: chain 'G' and resid 41 through 45 removed outlier: 4.386A pdb=" N GLU G 42 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ALA G 53 " --> pdb=" O GLU G 42 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'G' and resid 82 through 89 removed outlier: 6.435A pdb=" N LEU G 133 " --> pdb=" O ARG G 85 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS G 134 " --> pdb=" O THR G 122 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR G 122 " --> pdb=" O LYS G 134 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'G' and resid 94 through 98 Processing sheet with id= 19, first strand: chain 'H' and resid 2 through 6 removed outlier: 7.601A pdb=" N ASP H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA H 39 " --> pdb=" O ASP H 2 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'I' and resid 52 through 57 removed outlier: 5.285A pdb=" N ASP I 19 " --> pdb=" O LEU I 140 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'I' and resid 74 through 78 removed outlier: 4.156A pdb=" N GLY I 83 " --> pdb=" O THR I 78 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'J' and resid 18 through 21 removed outlier: 3.612A pdb=" N VAL J 19 " --> pdb=" O LEU J 8 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR J 6 " --> pdb=" O CYS J 21 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ASN J 82 " --> pdb=" O MET J 7 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'J' and resid 39 through 42 Processing sheet with id= 24, first strand: chain 'L' and resid 38 through 41 removed outlier: 6.435A pdb=" N GLU L 38 " --> pdb=" O PRO L 99 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'L' and resid 63 through 66 removed outlier: 3.626A pdb=" N TYR L 104 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE L 34 " --> pdb=" O LEU L 103 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS L 101 " --> pdb=" O ALA L 36 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'L' and resid 31 through 37 removed outlier: 7.943A pdb=" N SER L 31 " --> pdb=" O ARG L 134 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LYS L 128 " --> pdb=" O THR L 37 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'M' and resid 33 through 37 Processing sheet with id= 28, first strand: chain 'N' and resid 50 through 53 removed outlier: 3.530A pdb=" N ALA N 50 " --> pdb=" O VAL N 40 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL N 29 " --> pdb=" O ASP N 92 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'O' and resid 41 through 48 removed outlier: 3.737A pdb=" N LYS O 86 " --> pdb=" O GLN O 32 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'O' and resid 52 through 55 removed outlier: 3.853A pdb=" N ALA O 52 " --> pdb=" O THR O 63 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N SER O 60 " --> pdb=" O THR O 79 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'Q' and resid 11 through 15 removed outlier: 3.881A pdb=" N MET Q 40 " --> pdb=" O VAL Q 4 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LEU Q 39 " --> pdb=" O GLY Q 50 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY Q 50 " --> pdb=" O LEU Q 39 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'Q' and resid 18 through 23 removed outlier: 4.126A pdb=" N GLU Q 18 " --> pdb=" O ILE Q 98 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLU Q 95 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR Q 60 " --> pdb=" O THR Q 99 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ALA Q 31 " --> pdb=" O VAL Q 63 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'Q' and resid 57 through 60 removed outlier: 3.579A pdb=" N SER Q 102 " --> pdb=" O LYS Q 58 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'Q' and resid 65 through 74 removed outlier: 3.859A pdb=" N GLY Q 65 " --> pdb=" O GLU Q 95 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLN Q 91 " --> pdb=" O HIS Q 69 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LYS Q 71 " --> pdb=" O HIS Q 89 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N HIS Q 89 " --> pdb=" O LYS Q 71 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ARG Q 73 " --> pdb=" O GLN Q 87 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLN Q 87 " --> pdb=" O ARG Q 73 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'R' and resid 2 through 8 removed outlier: 4.999A pdb=" N THR R 100 " --> pdb=" O GLY R 79 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'S' and resid 28 through 32 removed outlier: 4.906A pdb=" N LYS S 65 " --> pdb=" O ARG S 76 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASP S 78 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LYS S 63 " --> pdb=" O ASP S 78 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LYS S 80 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE S 61 " --> pdb=" O LYS S 80 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ALA S 82 " --> pdb=" O THR S 59 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N THR S 59 " --> pdb=" O ALA S 82 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL S 84 " --> pdb=" O VAL S 57 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N VAL S 57 " --> pdb=" O VAL S 84 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'T' and resid 8 through 12 removed outlier: 5.182A pdb=" N ASP T 8 " --> pdb=" O VAL T 24 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS T 20 " --> pdb=" O VAL T 12 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'T' and resid 38 through 45 removed outlier: 5.443A pdb=" N ASN T 38 " --> pdb=" O ALA T 61 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN T 44 " --> pdb=" O GLY T 55 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'U' and resid 73 through 76 removed outlier: 3.572A pdb=" N GLU U 66 " --> pdb=" O PHE U 4 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS U 68 " --> pdb=" O LEU U 6 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA U 93 " --> pdb=" O PRO U 31 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG U 97 " --> pdb=" O TYR U 35 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'U' and resid 82 through 85 removed outlier: 6.566A pdb=" N GLN U 82 " --> pdb=" O MET U 91 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR U 89 " --> pdb=" O HIS U 84 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'V' and resid 45 through 48 Processing sheet with id= 42, first strand: chain 'V' and resid 50 through 54 removed outlier: 7.322A pdb=" N ASN V 50 " --> pdb=" O THR V 62 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N THR V 58 " --> pdb=" O GLY V 54 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'W' and resid 12 through 19 removed outlier: 4.731A pdb=" N ASN W 23 " --> pdb=" O SER W 19 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'W' and resid 34 through 41 Processing sheet with id= 45, first strand: chain 'Y' and resid 34 through 38 removed outlier: 3.615A pdb=" N VAL Y 6 " --> pdb=" O VAL Y 35 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS Y 5 " --> pdb=" O GLU Y 57 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU Y 57 " --> pdb=" O LYS Y 5 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N MET Y 53 " --> pdb=" O THR Y 9 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'Z' and resid 28 through 31 removed outlier: 3.959A pdb=" N GLU Z 35 " --> pdb=" O ASP Z 30 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'b' and resid 69 through 73 removed outlier: 3.527A pdb=" N LEU b 70 " --> pdb=" O ALA b 162 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'c' and resid 53 through 59 removed outlier: 3.665A pdb=" N ASN c 54 " --> pdb=" O SER c 69 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'c' and resid 167 through 170 removed outlier: 3.603A pdb=" N GLY c 194 " --> pdb=" O THR c 191 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'd' and resid 142 through 146 removed outlier: 3.583A pdb=" N ASP d 143 " --> pdb=" O PHE d 184 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'e' and resid 10 through 15 removed outlier: 7.005A pdb=" N LEU e 35 " --> pdb=" O VAL e 15 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'e' and resid 83 through 87 Processing sheet with id= 53, first strand: chain 'e' and resid 31 through 40 removed outlier: 7.114A pdb=" N ARG e 44 " --> pdb=" O ASP e 40 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'f' and resid 36 through 42 removed outlier: 4.301A pdb=" N ILE f 36 " --> pdb=" O GLU f 65 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG f 38 " --> pdb=" O ASN f 63 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN f 63 " --> pdb=" O ARG f 38 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU f 40 " --> pdb=" O LEU f 61 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL f 10 " --> pdb=" O HIS f 58 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE f 60 " --> pdb=" O LEU f 8 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS f 3 " --> pdb=" O ARG f 92 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'h' and resid 23 through 29 removed outlier: 6.865A pdb=" N GLN h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N SER h 58 " --> pdb=" O SER h 29 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN h 48 " --> pdb=" O THR h 63 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'h' and resid 75 through 78 removed outlier: 5.075A pdb=" N MET h 75 " --> pdb=" O SER h 131 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA h 128 " --> pdb=" O ILE h 104 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ILE h 104 " --> pdb=" O ILE h 127 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'i' and resid 4 through 9 removed outlier: 3.586A pdb=" N THR i 14 " --> pdb=" O LYS i 66 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LYS i 58 " --> pdb=" O GLY i 22 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS i 25 " --> pdb=" O TYR i 59 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'j' and resid 39 through 42 removed outlier: 4.792A pdb=" N LYS j 71 " --> pdb=" O MET j 42 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ARG j 7 " --> pdb=" O ALA j 101 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'j' and resid 44 through 53 removed outlier: 8.324A pdb=" N ALA j 61 " --> pdb=" O THR j 53 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'k' and resid 28 through 34 removed outlier: 3.714A pdb=" N ASN k 28 " --> pdb=" O SER k 25 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY k 18 " --> pdb=" O ASN k 80 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASP k 82 " --> pdb=" O GLY k 18 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'l' and resid 29 through 32 Processing sheet with id= 62, first strand: chain 'l' and resid 36 through 41 removed outlier: 3.605A pdb=" N ARG l 36 " --> pdb=" O ARG l 54 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR l 40 " --> pdb=" O ARG l 50 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG l 50 " --> pdb=" O THR l 40 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU l 57 " --> pdb=" O PHE l 61 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N PHE l 61 " --> pdb=" O LEU l 57 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'p' and resid 22 through 28 removed outlier: 5.316A pdb=" N LYS p 67 " --> pdb=" O ASN p 58 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'q' and resid 7 through 12 removed outlier: 5.994A pdb=" N ARG q 7 " --> pdb=" O GLU q 64 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N THR q 61 " --> pdb=" O VAL q 77 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'q' and resid 20 through 31 No H-bonds generated for sheet with id= 65 Processing sheet with id= 66, first strand: chain 's' and resid 30 through 34 1702 hydrogen bonds defined for protein. 5052 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3484 hydrogen bonds 5428 hydrogen bond angles 0 basepair planarities 1393 basepair parallelities 2339 stacking parallelities Total time for adding SS restraints: 228.92 Time building geometry restraints manager: 60.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 12576 1.31 - 1.44: 68373 1.44 - 1.57: 61754 1.57 - 1.70: 9066 1.70 - 1.83: 248 Bond restraints: 152017 Sorted by residual: bond pdb=" C5 5MUAN1935 " pdb=" C6 5MUAN1935 " ideal model delta sigma weight residual 1.155 1.451 -0.296 2.00e-02 2.50e+03 2.20e+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 9.27e+01 bond pdb=" N1 5MUAN1935 " pdb=" C2 5MUAN1935 " ideal model delta sigma weight residual 1.436 1.561 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" N6 MA6sN1516 " pdb=" C9 MA6sN1516 " ideal model delta sigma weight residual 1.517 1.443 0.074 2.00e-02 2.50e+03 1.39e+01 bond pdb=" N6 MA6sN1515 " pdb=" C9 MA6sN1515 " ideal model delta sigma weight residual 1.517 1.443 0.074 2.00e-02 2.50e+03 1.38e+01 ... (remaining 152012 not shown) Histogram of bond angle deviations from ideal: 99.46 - 109.25: 60137 109.25 - 119.05: 91663 119.05 - 128.84: 71547 128.84 - 138.63: 4362 138.63 - 148.43: 2 Bond angle restraints: 227711 Sorted by residual: angle pdb=" C1' 2MGsN1204 " pdb=" N9 2MGsN1204 " pdb=" C8 2MGsN1204 " ideal model delta sigma weight residual 110.07 132.72 -22.65 3.00e+00 1.11e-01 5.70e+01 angle pdb=" C1' 2MGsN 963 " pdb=" N9 2MGsN 963 " pdb=" C8 2MGsN 963 " ideal model delta sigma weight residual 110.07 132.67 -22.60 3.00e+00 1.11e-01 5.68e+01 angle pdb=" C1' 6MZAN2026 " pdb=" N9 6MZAN2026 " pdb=" C8 6MZAN2026 " ideal model delta sigma weight residual 126.23 148.43 -22.20 3.00e+00 1.11e-01 5.48e+01 angle pdb=" C1' OMGAN2247 " pdb=" N9 OMGAN2247 " pdb=" C4 OMGAN2247 " ideal model delta sigma weight residual 108.29 129.78 -21.49 3.00e+00 1.11e-01 5.13e+01 angle pdb=" C1' 2MGAN2441 " pdb=" N9 2MGAN2441 " pdb=" C8 2MGAN2441 " ideal model delta sigma weight residual 110.07 131.50 -21.43 3.00e+00 1.11e-01 5.10e+01 ... (remaining 227706 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 83786 35.99 - 71.99: 8253 71.99 - 107.98: 1129 107.98 - 143.97: 21 143.97 - 179.97: 48 Dihedral angle restraints: 93237 sinusoidal: 77713 harmonic: 15524 Sorted by residual: dihedral pdb=" O4' UAN2880 " pdb=" C1' UAN2880 " pdb=" N1 UAN2880 " pdb=" C2 UAN2880 " ideal model delta sinusoidal sigma weight residual 200.00 26.62 173.38 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' CsN 326 " pdb=" C1' CsN 326 " pdb=" N1 CsN 326 " pdb=" C2 CsN 326 " ideal model delta sinusoidal sigma weight residual 200.00 29.73 170.27 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' CAN 912 " pdb=" C1' CAN 912 " pdb=" N1 CAN 912 " pdb=" C2 CAN 912 " ideal model delta sinusoidal sigma weight residual -160.00 10.20 -170.20 1 1.50e+01 4.44e-03 8.47e+01 ... (remaining 93234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 28348 0.086 - 0.172: 761 0.172 - 0.258: 20 0.258 - 0.343: 3 0.343 - 0.429: 1 Chirality restraints: 29133 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 4.61e+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 2.26 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C1' AAN 980 " pdb=" O4' AAN 980 " pdb=" C2' AAN 980 " pdb=" N9 AAN 980 " both_signs ideal model delta sigma weight residual False 2.46 2.18 0.28 2.00e-01 2.50e+01 1.89e+00 ... (remaining 29130 not shown) Planarity restraints: 12026 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MGAN2065 " -0.064 2.00e-02 2.50e+03 6.20e-01 8.64e+03 pdb=" C4' 7MGAN2065 " -0.457 2.00e-02 2.50e+03 pdb=" O4' 7MGAN2065 " -0.714 2.00e-02 2.50e+03 pdb=" C3' 7MGAN2065 " 0.592 2.00e-02 2.50e+03 pdb=" O3' 7MGAN2065 " 0.646 2.00e-02 2.50e+03 pdb=" C2' 7MGAN2065 " 0.189 2.00e-02 2.50e+03 pdb=" O2' 7MGAN2065 " -0.968 2.00e-02 2.50e+03 pdb=" C1' 7MGAN2065 " -0.199 2.00e-02 2.50e+03 pdb=" N9 7MGAN2065 " 0.975 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MGAN2441 " -0.029 2.00e-02 2.50e+03 5.75e-01 7.44e+03 pdb=" C4' 2MGAN2441 " -0.438 2.00e-02 2.50e+03 pdb=" O4' 2MGAN2441 " -0.663 2.00e-02 2.50e+03 pdb=" C3' 2MGAN2441 " 0.589 2.00e-02 2.50e+03 pdb=" O3' 2MGAN2441 " 0.563 2.00e-02 2.50e+03 pdb=" C2' 2MGAN2441 " 0.219 2.00e-02 2.50e+03 pdb=" O2' 2MGAN2441 " -0.900 2.00e-02 2.50e+03 pdb=" C1' 2MGAN2441 " -0.220 2.00e-02 2.50e+03 pdb=" N9 2MGAN2441 " 0.878 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MGsN1204 " -0.037 2.00e-02 2.50e+03 5.72e-01 7.36e+03 pdb=" C4' 2MGsN1204 " -0.433 2.00e-02 2.50e+03 pdb=" O4' 2MGsN1204 " -0.623 2.00e-02 2.50e+03 pdb=" C3' 2MGsN1204 " 0.591 2.00e-02 2.50e+03 pdb=" O3' 2MGsN1204 " 0.574 2.00e-02 2.50e+03 pdb=" C2' 2MGsN1204 " 0.208 2.00e-02 2.50e+03 pdb=" O2' 2MGsN1204 " -0.917 2.00e-02 2.50e+03 pdb=" C1' 2MGsN1204 " -0.228 2.00e-02 2.50e+03 pdb=" N9 2MGsN1204 " 0.866 2.00e-02 2.50e+03 ... (remaining 12023 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.50: 738 2.50 - 3.10: 88197 3.10 - 3.70: 246935 3.70 - 4.30: 381554 4.30 - 4.90: 519736 Nonbonded interactions: 1237160 Sorted by model distance: nonbonded pdb=" N7 GAN 731 " pdb="MG MGAN3005 " model vdw 1.895 2.250 nonbonded pdb=" N1 AsN 325 " pdb="MG MGsN1606 " model vdw 1.895 2.250 nonbonded pdb=" N7 GsN1263 " pdb="MG MGsN1639 " model vdw 1.896 2.250 nonbonded pdb=" N7 GsN 320 " pdb="MG MGsN1609 " model vdw 1.897 2.250 nonbonded pdb=" N7 AAN2430 " pdb="MG MGAN3020 " model vdw 1.898 2.250 ... (remaining 1237155 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: 0.010 Normalize map: mean=0, sd=1: 6.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.660 Construct map_model_manager: 0.140 Extract box with map and model: 29.720 Check model and map are aligned: 1.510 Set scattering table: 0.960 Process input model: 521.090 Find NCS groups from input model: 2.670 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:13.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 577.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 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 0.296 152017 Z= 0.137 Angle : 0.506 22.648 227711 Z= 0.275 Chirality : 0.029 0.429 29133 Planarity : 0.015 0.620 12026 Dihedral : 21.757 179.968 83240 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.89 % Favored : 97.05 % Rotamer: Outliers : 0.05 % Allowed : 2.61 % Favored : 97.34 % 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: -1.21 (0.10), residues: 5361 helix: -0.34 (0.11), residues: 1712 sheet: -0.05 (0.15), residues: 1055 loop : -1.42 (0.11), residues: 2594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 106 HIS 0.005 0.001 HIS I 95 PHE 0.015 0.001 PHE F 138 TYR 0.017 0.001 TYR F 8 ARG 0.006 0.000 ARG J 51 *********************** 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 1112 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1110 time to evaluate : 5.869 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 4 residues processed: 1112 average time/residue: 2.3612 time to fit residues: 3626.4247 Evaluate side-chains 831 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 827 time to evaluate : 5.766 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 2 average time/residue: 0.9798 time to fit residues: 9.9103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 979 random chunks: chunk 826 optimal weight: 9.9990 chunk 742 optimal weight: 10.0000 chunk 411 optimal weight: 2.9990 chunk 253 optimal weight: 6.9990 chunk 500 optimal weight: 0.0040 chunk 396 optimal weight: 20.0000 chunk 767 optimal weight: 3.9990 chunk 296 optimal weight: 10.0000 chunk 466 optimal weight: 5.9990 chunk 571 optimal weight: 0.8980 chunk 889 optimal weight: 20.0000 overall best weight: 2.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 41 GLN 2 19 ASN 2 42 GLN 2 50 HIS 3 35 GLN C 48 HIS C 58 HIS C 60 GLN C 90 HIS C 117 GLN C 230 HIS C 243 GLN C 260 ASN D 50 GLN D 65 GLN D 108 GLN D 139 ASN D 153 GLN E 96 ASN E 114 GLN E 138 ASN E 165 HIS F 63 GLN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 GLN G 74 ASN ** H 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 ASN I 13 HIS I 40 HIS I 77 HIS I 130 HIS I 135 GLN J 59 ASN J 110 GLN K 40 GLN K 56 GLN K 107 GLN K 125 GLN N 39 GLN O 78 GLN P 11 HIS Q 82 HIS Q 87 GLN R 57 ASN R 60 HIS R 61 ASN S 3 ASN S 8 GLN T 38 ASN U 16 GLN U 75 ASN U 79 GLN U 84 HIS W 6 GLN X 24 ASN X 61 GLN Z 25 ASN Z 41 HIS Z 52 GLN ** b 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 80 ASN b 85 GLN b 96 HIS b 170 HIS c 6 HIS c 19 ASN c 123 GLN c 176 HIS d 42 HIS ** d 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 118 GLN d 138 GLN e 121 ASN f 11 HIS ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 94 HIS g 32 GLN h 18 GLN h 38 ASN i 4 ASN i 35 GLN i 73 GLN i 79 HIS j 56 HIS j 64 GLN k 49 GLN l 96 HIS m 105 ASN o 35 GLN o 37 ASN ** o 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 42 HIS p 44 ASN q 31 GLN q 32 HIS s 52 HIS t 13 GLN t 75 HIS Total number of N/Q/H flips: 93 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 152017 Z= 0.302 Angle : 0.656 14.564 227711 Z= 0.344 Chirality : 0.038 0.395 29133 Planarity : 0.006 0.138 12026 Dihedral : 22.286 179.276 72617 Min Nonbonded Distance : 1.667 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.38 % Favored : 96.57 % Rotamer: Outliers : 3.54 % Allowed : 14.63 % Favored : 81.83 % 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: -0.42 (0.11), residues: 5361 helix: 0.59 (0.12), residues: 1740 sheet: 0.20 (0.16), residues: 1025 loop : -1.06 (0.11), residues: 2596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP b 106 HIS 0.009 0.002 HIS C 61 PHE 0.020 0.002 PHE D 121 TYR 0.029 0.002 TYR F 128 ARG 0.008 0.001 ARG c 143 *********************** 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 1036 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 879 time to evaluate : 5.809 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: symmetry clash revert: symmetry clash outliers start: 157 outliers final: 74 residues processed: 946 average time/residue: 2.2209 time to fit residues: 2962.1312 Evaluate side-chains 885 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 811 time to evaluate : 5.768 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 34 residues processed: 45 average time/residue: 1.1334 time to fit residues: 94.6204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 979 random chunks: chunk 494 optimal weight: 3.9990 chunk 275 optimal weight: 5.9990 chunk 739 optimal weight: 10.0000 chunk 605 optimal weight: 8.9990 chunk 245 optimal weight: 5.9990 chunk 890 optimal weight: 5.9990 chunk 962 optimal weight: 5.9990 chunk 793 optimal weight: 7.9990 chunk 883 optimal weight: 3.9990 chunk 303 optimal weight: 5.9990 chunk 714 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 41 GLN 2 19 ASN 2 42 GLN D 139 ASN F 95 GLN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN J 110 GLN N 39 GLN S 8 GLN T 59 GLN X 24 ASN ** b 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 67 ASN ** d 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 88 HIS e 121 ASN ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 32 GLN i 35 GLN k 63 GLN m 91 HIS n 90 GLN o 35 GLN q 31 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.093 152017 Z= 0.533 Angle : 0.825 13.930 227711 Z= 0.421 Chirality : 0.048 0.394 29133 Planarity : 0.007 0.148 12026 Dihedral : 22.599 179.306 72617 Min Nonbonded Distance : 1.665 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.16 % Favored : 95.78 % Rotamer: Outliers : 5.52 % Allowed : 16.68 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.66 (0.11), residues: 5361 helix: 0.39 (0.12), residues: 1761 sheet: 0.05 (0.16), residues: 1028 loop : -1.21 (0.11), residues: 2572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 248 HIS 0.012 0.002 HIS I 130 PHE 0.024 0.003 PHE K 66 TYR 0.034 0.003 TYR Q 2 ARG 0.011 0.001 ARG C 39 *********************** 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 1049 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 804 time to evaluate : 5.885 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 outliers start: 245 outliers final: 116 residues processed: 926 average time/residue: 2.2367 time to fit residues: 2944.7710 Evaluate side-chains 884 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 768 time to evaluate : 5.830 Switching outliers to nearest non-outliers outliers start: 116 outliers final: 59 residues processed: 58 average time/residue: 1.2208 time to fit residues: 129.9444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 979 random chunks: chunk 879 optimal weight: 0.5980 chunk 669 optimal weight: 20.0000 chunk 462 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 425 optimal weight: 1.9990 chunk 598 optimal weight: 0.8980 chunk 893 optimal weight: 3.9990 chunk 946 optimal weight: 5.9990 chunk 466 optimal weight: 2.9990 chunk 847 optimal weight: 8.9990 chunk 255 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 22 ASN 0 41 GLN 2 42 GLN G 74 ASN J 110 GLN N 39 GLN R 61 ASN T 59 GLN X 24 ASN ** b 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 105 ASN e 88 HIS e 121 ASN ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 35 GLN j 56 HIS k 117 HIS t 80 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 152017 Z= 0.148 Angle : 0.568 12.970 227711 Z= 0.306 Chirality : 0.034 0.389 29133 Planarity : 0.005 0.123 12026 Dihedral : 22.318 179.574 72617 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.28 % Favored : 96.66 % Rotamer: Outliers : 4.10 % Allowed : 19.32 % Favored : 76.58 % 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: -0.05 (0.11), residues: 5361 helix: 1.09 (0.12), residues: 1748 sheet: 0.33 (0.16), residues: 1013 loop : -0.96 (0.11), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 201 HIS 0.005 0.001 HIS I 95 PHE 0.018 0.001 PHE b 71 TYR 0.021 0.001 TYR Q 2 ARG 0.007 0.000 ARG X 29 *********************** 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 1010 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 828 time to evaluate : 5.924 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 outliers start: 182 outliers final: 102 residues processed: 933 average time/residue: 2.1355 time to fit residues: 2856.4443 Evaluate side-chains 891 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 789 time to evaluate : 5.877 Switching outliers to nearest non-outliers outliers start: 102 outliers final: 65 residues processed: 39 average time/residue: 1.5301 time to fit residues: 103.1210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 979 random chunks: chunk 788 optimal weight: 8.9990 chunk 537 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 704 optimal weight: 8.9990 chunk 390 optimal weight: 6.9990 chunk 807 optimal weight: 1.9990 chunk 654 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 483 optimal weight: 3.9990 chunk 849 optimal weight: 4.9990 chunk 238 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 41 GLN 2 19 ASN 2 42 GLN F 63 GLN ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 13 HIS I 61 GLN J 110 GLN N 35 HIS N 39 GLN O 55 ASN P 101 HIS R 61 ASN S 8 GLN T 59 GLN X 24 ASN ** b 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 118 GLN ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 35 GLN m 8 ASN n 90 GLN q 31 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 152017 Z= 0.473 Angle : 0.766 14.019 227711 Z= 0.393 Chirality : 0.045 0.382 29133 Planarity : 0.007 0.143 12026 Dihedral : 22.478 178.891 72617 Min Nonbonded Distance : 1.694 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.48 % Favored : 95.47 % Rotamer: Outliers : 5.30 % Allowed : 19.18 % Favored : 75.52 % 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: -0.39 (0.11), residues: 5361 helix: 0.76 (0.12), residues: 1765 sheet: 0.09 (0.16), residues: 1019 loop : -1.12 (0.11), residues: 2577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP c 201 HIS 0.010 0.002 HIS C 61 PHE 0.023 0.002 PHE K 66 TYR 0.035 0.002 TYR Q 2 ARG 0.010 0.001 ARG X 29 *********************** 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 1029 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 794 time to evaluate : 5.878 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 outliers start: 235 outliers final: 148 residues processed: 926 average time/residue: 2.1836 time to fit residues: 2880.0271 Evaluate side-chains 909 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 761 time to evaluate : 5.809 Switching outliers to nearest non-outliers outliers start: 148 outliers final: 90 residues processed: 60 average time/residue: 1.3203 time to fit residues: 140.6204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 979 random chunks: chunk 318 optimal weight: 4.9990 chunk 852 optimal weight: 0.9980 chunk 187 optimal weight: 2.9990 chunk 555 optimal weight: 5.9990 chunk 233 optimal weight: 20.0000 chunk 947 optimal weight: 1.9990 chunk 786 optimal weight: 4.9990 chunk 438 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 313 optimal weight: 9.9990 chunk 497 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 41 GLN 2 42 GLN ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 13 HIS J 110 GLN T 44 GLN T 59 GLN X 24 ASN ** b 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 90 GLN q 31 GLN t 80 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 152017 Z= 0.253 Angle : 0.616 13.805 227711 Z= 0.328 Chirality : 0.037 0.375 29133 Planarity : 0.006 0.130 12026 Dihedral : 22.379 179.084 72617 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.95 % Favored : 95.99 % Rotamer: Outliers : 4.60 % Allowed : 20.60 % Favored : 74.80 % 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: -0.16 (0.11), residues: 5361 helix: 1.07 (0.12), residues: 1755 sheet: 0.14 (0.16), residues: 1022 loop : -1.03 (0.11), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP c 201 HIS 0.007 0.001 HIS C 61 PHE 0.018 0.002 PHE b 71 TYR 0.034 0.001 TYR Q 2 ARG 0.011 0.000 ARG X 29 *********************** 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 1003 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 799 time to evaluate : 5.944 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: symmetry clash revert: symmetry clash outliers start: 204 outliers final: 142 residues processed: 921 average time/residue: 2.1721 time to fit residues: 2860.8175 Evaluate side-chains 927 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 785 time to evaluate : 5.789 Switching outliers to nearest non-outliers outliers start: 142 outliers final: 92 residues processed: 53 average time/residue: 1.4502 time to fit residues: 131.5883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 979 random chunks: chunk 913 optimal weight: 5.9990 chunk 106 optimal weight: 20.0000 chunk 539 optimal weight: 0.0980 chunk 691 optimal weight: 6.9990 chunk 535 optimal weight: 3.9990 chunk 797 optimal weight: 8.9990 chunk 528 optimal weight: 0.9980 chunk 943 optimal weight: 5.9990 chunk 590 optimal weight: 0.5980 chunk 575 optimal weight: 0.6980 chunk 435 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 41 GLN 2 42 GLN C 53 HIS E 138 ASN J 110 GLN O 55 ASN R 61 ASN S 8 GLN T 59 GLN V 29 GLN X 24 ASN ** b 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 49 GLN m 8 ASN n 90 GLN o 40 GLN q 31 GLN t 80 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 152017 Z= 0.130 Angle : 0.578 16.090 227711 Z= 0.312 Chirality : 0.034 0.375 29133 Planarity : 0.005 0.121 12026 Dihedral : 22.398 179.982 72617 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.69 % Favored : 96.25 % Rotamer: Outliers : 3.97 % Allowed : 21.46 % Favored : 74.57 % 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: 0.04 (0.11), residues: 5361 helix: 1.24 (0.12), residues: 1760 sheet: 0.22 (0.16), residues: 1022 loop : -0.90 (0.12), residues: 2579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP c 201 HIS 0.005 0.001 HIS f 3 PHE 0.018 0.001 PHE b 71 TYR 0.039 0.001 TYR Q 2 ARG 0.038 0.000 ARG G 69 *********************** 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 970 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 794 time to evaluate : 6.006 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 176 outliers final: 118 residues processed: 909 average time/residue: 2.1224 time to fit residues: 2769.3809 Evaluate side-chains 896 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 778 time to evaluate : 5.838 Switching outliers to nearest non-outliers outliers start: 118 outliers final: 86 residues processed: 34 average time/residue: 1.3246 time to fit residues: 82.3457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 979 random chunks: chunk 583 optimal weight: 3.9990 chunk 376 optimal weight: 7.9990 chunk 563 optimal weight: 3.9990 chunk 284 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 chunk 599 optimal weight: 4.9990 chunk 642 optimal weight: 20.0000 chunk 466 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 741 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 41 GLN 2 42 GLN ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 GLN R 61 ASN T 59 GLN V 29 GLN X 24 ASN ** b 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 21 GLN q 31 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 152017 Z= 0.493 Angle : 0.780 15.715 227711 Z= 0.399 Chirality : 0.046 0.369 29133 Planarity : 0.007 0.144 12026 Dihedral : 22.504 179.960 72617 Min Nonbonded Distance : 1.660 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.94 % Favored : 95.00 % Rotamer: Outliers : 4.46 % Allowed : 21.60 % Favored : 73.94 % 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: -0.33 (0.11), residues: 5361 helix: 0.88 (0.12), residues: 1755 sheet: 0.05 (0.16), residues: 1011 loop : -1.10 (0.11), residues: 2595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP c 201 HIS 0.009 0.002 HIS I 130 PHE 0.024 0.002 PHE K 66 TYR 0.044 0.002 TYR Q 2 ARG 0.013 0.001 ARG X 29 *********************** 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 992 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 794 time to evaluate : 5.999 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 outliers start: 198 outliers final: 141 residues processed: 908 average time/residue: 2.2372 time to fit residues: 2897.7759 Evaluate side-chains 921 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 780 time to evaluate : 6.044 Switching outliers to nearest non-outliers outliers start: 141 outliers final: 89 residues processed: 56 average time/residue: 1.3314 time to fit residues: 131.9167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 979 random chunks: chunk 858 optimal weight: 5.9990 chunk 903 optimal weight: 10.0000 chunk 824 optimal weight: 10.0000 chunk 879 optimal weight: 0.4980 chunk 529 optimal weight: 0.9980 chunk 383 optimal weight: 3.9990 chunk 690 optimal weight: 7.9990 chunk 269 optimal weight: 4.9990 chunk 794 optimal weight: 0.8980 chunk 831 optimal weight: 10.0000 chunk 876 optimal weight: 3.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 41 GLN 2 42 GLN E 138 ASN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 GLN O 55 ASN R 61 ASN T 59 GLN X 24 ASN ** b 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 8 ASN n 90 GLN o 40 GLN q 31 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 152017 Z= 0.241 Angle : 0.637 16.326 227711 Z= 0.339 Chirality : 0.038 0.367 29133 Planarity : 0.006 0.128 12026 Dihedral : 22.463 179.161 72617 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.16 % Favored : 95.78 % Rotamer: Outliers : 3.40 % Allowed : 23.13 % Favored : 73.47 % 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: -0.21 (0.11), residues: 5361 helix: 1.02 (0.12), residues: 1759 sheet: 0.09 (0.16), residues: 995 loop : -1.02 (0.11), residues: 2607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP c 201 HIS 0.007 0.001 HIS I 95 PHE 0.023 0.002 PHE I 16 TYR 0.037 0.002 TYR Q 2 ARG 0.012 0.000 ARG X 29 *********************** 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 951 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 800 time to evaluate : 6.000 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 outliers start: 151 outliers final: 112 residues processed: 903 average time/residue: 2.2033 time to fit residues: 2839.0057 Evaluate side-chains 898 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 786 time to evaluate : 5.893 Switching outliers to nearest non-outliers outliers start: 112 outliers final: 86 residues processed: 28 average time/residue: 1.4027 time to fit residues: 71.5865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 979 random chunks: chunk 577 optimal weight: 0.9980 chunk 929 optimal weight: 0.1980 chunk 567 optimal weight: 0.5980 chunk 441 optimal weight: 3.9990 chunk 646 optimal weight: 30.0000 chunk 975 optimal weight: 4.9990 chunk 897 optimal weight: 6.9990 chunk 776 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 599 optimal weight: 3.9990 chunk 476 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 41 GLN 2 42 GLN I 61 GLN J 110 GLN O 55 ASN T 59 GLN V 29 GLN X 24 ASN ** b 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 27 ASN q 31 GLN t 80 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 152017 Z= 0.129 Angle : 0.554 16.618 227711 Z= 0.298 Chirality : 0.033 0.360 29133 Planarity : 0.005 0.123 12026 Dihedral : 22.314 179.462 72617 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.66 % Favored : 96.29 % Rotamer: Outliers : 2.68 % Allowed : 24.01 % Favored : 73.31 % 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: 0.14 (0.11), residues: 5361 helix: 1.38 (0.13), residues: 1759 sheet: 0.28 (0.16), residues: 1000 loop : -0.87 (0.12), residues: 2602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP F 83 HIS 0.005 0.001 HIS j 56 PHE 0.019 0.001 PHE I 16 TYR 0.026 0.001 TYR T 94 ARG 0.018 0.000 ARG F 80 ********************** 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 941 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 822 time to evaluate : 5.936 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 outliers start: 119 outliers final: 96 residues processed: 910 average time/residue: 2.1698 time to fit residues: 2838.2977 Evaluate side-chains 889 residues out of total 4436 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 793 time to evaluate : 5.842 Switching outliers to nearest non-outliers outliers start: 96 outliers final: 78 residues processed: 22 average time/residue: 1.4983 time to fit residues: 60.4823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 979 random chunks: chunk 616 optimal weight: 8.9990 chunk 827 optimal weight: 1.9990 chunk 237 optimal weight: 7.9990 chunk 716 optimal weight: 30.0000 chunk 114 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 777 optimal weight: 0.1980 chunk 325 optimal weight: 5.9990 chunk 798 optimal weight: 0.0050 chunk 98 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 overall best weight: 2.4400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 41 GLN 2 42 GLN E 29 GLN E 138 ASN ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 GLN T 59 GLN V 29 GLN X 24 ASN ** b 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 38 GLN d 148 HIS h 86 GLN m 8 ASN q 31 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.141193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.091708 restraints weight = 193277.069| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 0.98 r_work: 0.2824 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 152017 Z= 0.265 Angle : 0.624 15.755 227711 Z= 0.329 Chirality : 0.037 0.351 29133 Planarity : 0.006 0.131 12026 Dihedral : 22.316 178.981 72617 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.42 % Favored : 95.52 % Rotamer: Outliers : 2.77 % Allowed : 24.21 % Favored : 73.02 % 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: 0.03 (0.11), residues: 5361 helix: 1.22 (0.12), residues: 1774 sheet: 0.25 (0.16), residues: 995 loop : -0.91 (0.12), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 83 HIS 0.006 0.001 HIS I 95 PHE 0.014 0.002 PHE K 66 TYR 0.024 0.002 TYR d 4 ARG 0.013 0.001 ARG e 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 42825.37 seconds wall clock time: 743 minutes 3.79 seconds (44583.79 seconds total)