Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 23:21:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xxb_6778/04_2023/5xxb_6778_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xxb_6778/04_2023/5xxb_6778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xxb_6778/04_2023/5xxb_6778.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xxb_6778/04_2023/5xxb_6778.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xxb_6778/04_2023/5xxb_6778_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xxb_6778/04_2023/5xxb_6778_neut.pdb" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3352 5.49 5 S 251 5.16 5 C 63425 2.51 5 N 22510 2.21 5 O 31895 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 38": "NH1" <-> "NH2" Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 54": "NH1" <-> "NH2" Residue "A ASP 65": "OD1" <-> "OD2" Residue "A GLU 80": "OE1" <-> "OE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A ARG 227": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 10": "NH1" <-> "NH2" Residue "B PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 26": "NH1" <-> "NH2" Residue "B ASP 35": "OD1" <-> "OD2" Residue "B TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 210": "OE1" <-> "OE2" Residue "B ARG 231": "NH1" <-> "NH2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "B ARG 239": "NH1" <-> "NH2" Residue "B ARG 258": "NH1" <-> "NH2" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B ARG 291": "NH1" <-> "NH2" Residue "B ARG 303": "NH1" <-> "NH2" Residue "B PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B ARG 347": "NH1" <-> "NH2" Residue "B ARG 348": "NH1" <-> "NH2" Residue "B ARG 368": "NH1" <-> "NH2" Residue "B TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "C TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 267": "NH1" <-> "NH2" Residue "C ARG 294": "NH1" <-> "NH2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C ARG 331": "NH1" <-> "NH2" Residue "C ARG 372": "NH1" <-> "NH2" Residue "C PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 15": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 24": "NH1" <-> "NH2" Residue "D ARG 41": "NH1" <-> "NH2" Residue "D TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 107": "NH1" <-> "NH2" Residue "D ARG 138": "NH1" <-> "NH2" Residue "D ARG 139": "NH1" <-> "NH2" Residue "D ARG 151": "NH1" <-> "NH2" Residue "D ARG 201": "NH1" <-> "NH2" Residue "D TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 283": "NH1" <-> "NH2" Residue "E ARG 57": "NH1" <-> "NH2" Residue "E ARG 85": "NH1" <-> "NH2" Residue "E ARG 89": "NH1" <-> "NH2" Residue "E ASP 169": "OD1" <-> "OD2" Residue "E ARG 187": "NH1" <-> "NH2" Residue "F ARG 21": "NH1" <-> "NH2" Residue "F ARG 66": "NH1" <-> "NH2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 155": "NH1" <-> "NH2" Residue "F TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 225": "NH1" <-> "NH2" Residue "F ARG 232": "NH1" <-> "NH2" Residue "F GLU 237": "OE1" <-> "OE2" Residue "F ARG 239": "NH1" <-> "NH2" Residue "G ARG 45": "NH1" <-> "NH2" Residue "G ARG 56": "NH1" <-> "NH2" Residue "G ARG 57": "NH1" <-> "NH2" Residue "G ARG 61": "NH1" <-> "NH2" Residue "G TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 75": "NH1" <-> "NH2" Residue "G ARG 76": "NH1" <-> "NH2" Residue "G PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 105": "NH1" <-> "NH2" Residue "G TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 240": "NH1" <-> "NH2" Residue "G ARG 241": "NH1" <-> "NH2" Residue "H ASP 19": "OD1" <-> "OD2" Residue "H ARG 23": "NH1" <-> "NH2" Residue "H TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 121": "NH1" <-> "NH2" Residue "H ARG 167": "NH1" <-> "NH2" Residue "H ARG 168": "NH1" <-> "NH2" Residue "I ARG 32": "NH1" <-> "NH2" Residue "I TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 69": "NH1" <-> "NH2" Residue "I PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 154": "NH1" <-> "NH2" Residue "J ARG 33": "NH1" <-> "NH2" Residue "J ARG 36": "NH1" <-> "NH2" Residue "J ARG 56": "NH1" <-> "NH2" Residue "J ARG 62": "NH1" <-> "NH2" Residue "J TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 73": "NH1" <-> "NH2" Residue "J PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 154": "NH1" <-> "NH2" Residue "K ARG 19": "NH1" <-> "NH2" Residue "K ARG 30": "NH1" <-> "NH2" Residue "K PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 100": "NH1" <-> "NH2" Residue "K ARG 103": "NH1" <-> "NH2" Residue "K ARG 114": "NH1" <-> "NH2" Residue "K PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 127": "NH1" <-> "NH2" Residue "K PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 191": "NH1" <-> "NH2" Residue "L ARG 12": "NH1" <-> "NH2" Residue "L ARG 36": "NH1" <-> "NH2" Residue "L ARG 49": "NH1" <-> "NH2" Residue "L ARG 55": "NH1" <-> "NH2" Residue "L TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 68": "NH1" <-> "NH2" Residue "L ARG 103": "NH1" <-> "NH2" Residue "L ASP 110": "OD1" <-> "OD2" Residue "L ARG 111": "NH1" <-> "NH2" Residue "L ARG 121": "NH1" <-> "NH2" Residue "M GLU 8": "OE1" <-> "OE2" Residue "M ARG 20": "NH1" <-> "NH2" Residue "M ARG 26": "NH1" <-> "NH2" Residue "M TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 68": "NH1" <-> "NH2" Residue "M ARG 71": "NH1" <-> "NH2" Residue "M TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 176": "NH1" <-> "NH2" Residue "M ARG 184": "NH1" <-> "NH2" Residue "M ARG 189": "NH1" <-> "NH2" Residue "M ARG 202": "NH1" <-> "NH2" Residue "N ARG 103": "NH1" <-> "NH2" Residue "N ARG 125": "NH1" <-> "NH2" Residue "N ARG 133": "NH1" <-> "NH2" Residue "N ARG 144": "NH1" <-> "NH2" Residue "N ARG 148": "NH1" <-> "NH2" Residue "N ARG 155": "NH1" <-> "NH2" Residue "N GLU 159": "OE1" <-> "OE2" Residue "N GLU 172": "OE1" <-> "OE2" Residue "N ARG 183": "NH1" <-> "NH2" Residue "N ARG 194": "NH1" <-> "NH2" Residue "N PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 203": "NH1" <-> "NH2" Residue "N ARG 221": "NH1" <-> "NH2" Residue "O TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 21": "OD1" <-> "OD2" Residue "O ARG 23": "NH1" <-> "NH2" Residue "O ARG 62": "NH1" <-> "NH2" Residue "O PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 153": "OE1" <-> "OE2" Residue "P TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P ARG 43": "NH1" <-> "NH2" Residue "P PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 57": "NH1" <-> "NH2" Residue "P ARG 90": "NH1" <-> "NH2" Residue "P PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 128": "NH1" <-> "NH2" Residue "P ARG 139": "NH1" <-> "NH2" Residue "P ARG 179": "NH1" <-> "NH2" Residue "P ARG 180": "NH1" <-> "NH2" Residue "P TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 8": "NH1" <-> "NH2" Residue "Q ARG 19": "NH1" <-> "NH2" Residue "Q ARG 20": "NH1" <-> "NH2" Residue "Q ASP 24": "OD1" <-> "OD2" Residue "Q ARG 73": "NH1" <-> "NH2" Residue "Q ARG 80": "NH1" <-> "NH2" Residue "Q TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 135": "NH1" <-> "NH2" Residue "R ARG 39": "NH1" <-> "NH2" Residue "R GLU 73": "OE1" <-> "OE2" Residue "R PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 87": "NH1" <-> "NH2" Residue "R TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 75": "OE1" <-> "OE2" Residue "S ARG 83": "NH1" <-> "NH2" Residue "S ARG 108": "NH1" <-> "NH2" Residue "S PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 41": "NH1" <-> "NH2" Residue "V ARG 64": "NH1" <-> "NH2" Residue "W ARG 44": "NH1" <-> "NH2" Residue "W ARG 51": "NH1" <-> "NH2" Residue "W ARG 65": "NH1" <-> "NH2" Residue "W ARG 66": "NH1" <-> "NH2" Residue "W PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 149": "NH1" <-> "NH2" Residue "X ARG 11": "NH1" <-> "NH2" Residue "X PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 65": "NH1" <-> "NH2" Residue "X ARG 74": "NH1" <-> "NH2" Residue "X ASP 113": "OD1" <-> "OD2" Residue "X ARG 120": "NH1" <-> "NH2" Residue "Y ARG 66": "NH1" <-> "NH2" Residue "Y PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 83": "NH1" <-> "NH2" Residue "Y ARG 141": "NH1" <-> "NH2" Residue "Z TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 115": "OD1" <-> "OD2" Residue "Z GLU 133": "OE1" <-> "OE2" Residue "a ARG 18": "NH1" <-> "NH2" Residue "a ARG 28": "NH1" <-> "NH2" Residue "a ARG 41": "NH1" <-> "NH2" Residue "b ARG 55": "NH1" <-> "NH2" Residue "b TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 89": "NH1" <-> "NH2" Residue "c TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 39": "NH1" <-> "NH2" Residue "c ARG 78": "NH1" <-> "NH2" Residue "c ARG 82": "NH1" <-> "NH2" Residue "c ARG 85": "NH1" <-> "NH2" Residue "c ARG 87": "NH1" <-> "NH2" Residue "c GLU 95": "OE1" <-> "OE2" Residue "c TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 119": "OE1" <-> "OE2" Residue "d ARG 15": "NH1" <-> "NH2" Residue "d ARG 29": "NH1" <-> "NH2" Residue "d ARG 35": "NH1" <-> "NH2" Residue "d TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 107": "NH1" <-> "NH2" Residue "d ARG 108": "NH1" <-> "NH2" Residue "d ARG 113": "NH1" <-> "NH2" Residue "e ARG 11": "NH1" <-> "NH2" Residue "e TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 43": "NH1" <-> "NH2" Residue "e TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 70": "NH1" <-> "NH2" Residue "e ARG 75": "NH1" <-> "NH2" Residue "e ARG 77": "NH1" <-> "NH2" Residue "e PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 9": "NH1" <-> "NH2" Residue "f ARG 19": "NH1" <-> "NH2" Residue "f ARG 24": "NH1" <-> "NH2" Residue "f ARG 68": "NH1" <-> "NH2" Residue "f ARG 86": "NH1" <-> "NH2" Residue "f ARG 88": "NH1" <-> "NH2" Residue "f ARG 91": "NH1" <-> "NH2" Residue "g ARG 93": "NH1" <-> "NH2" Residue "g ARG 94": "NH1" <-> "NH2" Residue "g ARG 110": "NH1" <-> "NH2" Residue "g PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 10": "NH1" <-> "NH2" Residue "h ARG 42": "NH1" <-> "NH2" Residue "h TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 87": "NH1" <-> "NH2" Residue "h ARG 98": "NH1" <-> "NH2" Residue "i ARG 14": "NH1" <-> "NH2" Residue "i ARG 27": "NH1" <-> "NH2" Residue "i ARG 48": "NH1" <-> "NH2" Residue "i ARG 58": "NH1" <-> "NH2" Residue "i ARG 59": "NH1" <-> "NH2" Residue "i ARG 75": "NH1" <-> "NH2" Residue "i ARG 76": "NH1" <-> "NH2" Residue "i GLU 83": "OE1" <-> "OE2" Residue "j ARG 6": "NH1" <-> "NH2" Residue "j ARG 22": "NH1" <-> "NH2" Residue "j PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 15": "NH1" <-> "NH2" Residue "k ARG 28": "NH1" <-> "NH2" Residue "k ARG 36": "NH1" <-> "NH2" Residue "n ARG 42": "NH1" <-> "NH2" Residue "n ARG 45": "NH1" <-> "NH2" Residue "o ARG 23": "NH1" <-> "NH2" Residue "o TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 85": "NH1" <-> "NH2" Residue "p ARG 30": "NH1" <-> "NH2" Residue "p ARG 72": "NH1" <-> "NH2" Residue "p ARG 103": "NH1" <-> "NH2" Residue "p ARG 104": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 121433 Number of models: 1 Model: "" Number of chains: 44 Chain: "1" Number of atoms: 65598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3077, 65598 Classifications: {'RNA': 3077} Modifications used: {'rna2p_pur': 301, 'rna2p_pyr': 220, 'rna3p_pur': 1318, 'rna3p_pyr': 1238} Link IDs: {'rna2p': 520, 'rna3p': 2556} Chain breaks: 23 Chain: "3" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2519 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 55, 'rna3p_pyr': 50} Link IDs: {'rna2p': 12, 'rna3p': 105} Chain breaks: 2 Chain: "4" Number of atoms: 3339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 3339 Classifications: {'RNA': 157} Modifications used: {'rna2p_pur': 18, 'rna2p_pyr': 9, 'rna3p_pur': 62, 'rna3p_pyr': 68} Link IDs: {'rna2p': 27, 'rna3p': 129} Chain breaks: 1 Chain: "A" Number of atoms: 1882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1882 Classifications: {'peptide': 246} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 233} Chain: "B" Number of atoms: 2942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2942 Classifications: {'peptide': 369} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 346} Chain breaks: 8 Chain: "C" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3060 Classifications: {'peptide': 394} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 374} Chain breaks: 6 Chain: "D" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2123 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain breaks: 3 Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 971 Classifications: {'peptide': 124} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 116} Chain breaks: 4 Chain: "F" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2059 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 12, 'TRANS': 237} Chain breaks: 1 Chain: "G" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1877 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 12, 'TRANS': 220} Chain breaks: 3 Chain: "H" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 181} Chain: "I" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1540 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 183} Chain breaks: 3 Chain: "J" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1343 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 4, 'TRANS': 161} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1593 Classifications: {'peptide': 199} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 186} Chain breaks: 2 Chain: "L" Number of atoms: 1063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1063 Classifications: {'peptide': 131} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 125} Chain: "M" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1683 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 194} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1645 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 7, 'TRANS': 192} Chain breaks: 1 Chain: "O" Number of atoms: 1286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1286 Classifications: {'peptide': 158} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 150} Chain breaks: 1 Chain: "P" Number of atoms: 1477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1477 Classifications: {'peptide': 186} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 176} Chain: "Q" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1473 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain: "R" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1492 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 10, 'TRANS': 171} Chain: "S" Number of atoms: 1231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1231 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 8, 'TRANS': 145} Chain: "T" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 827 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain breaks: 1 Chain: "U" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 968 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "V" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 533 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "W" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1038 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 120} Chain: "X" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1011 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "Y" Number of atoms: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1163 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "Z" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1136 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain breaks: 1 Chain: "a" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 404 Classifications: {'peptide': 49} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 45} Chain breaks: 1 Chain: "b" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 725 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 1, 'TRANS': 94} Chain breaks: 1 Chain: "c" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 908 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain breaks: 1 Chain: "d" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1011 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "e" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 854 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} Chain breaks: 1 Chain: "f" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 863 Classifications: {'peptide': 107} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 98} Chain: "g" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 981 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "h" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 772 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain breaks: 1 Chain: "i" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 688 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 3, 'TRANS': 83} Chain breaks: 2 Chain: "j" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 591 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 4, 'TRANS': 67} Chain breaks: 1 Chain: "k" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 419 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "l" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 419 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 5, 'TRANS': 46} Chain: "n" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 790 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "o" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 684 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "p" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 974 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain breaks: 1 Time building chain proxies: 45.90, per 1000 atoms: 0.38 Number of scatterers: 121433 At special positions: 0 Unit cell: (212.52, 232.32, 260.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 251 16.00 P 3352 15.00 O 31895 8.00 N 22510 7.00 C 63425 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS i 22 " - pdb=" SG CYS i 25 " distance=2.01 Simple disulfide: pdb=" SG CYS i 22 " - pdb=" SG CYS i 40 " distance=2.23 Simple disulfide: pdb=" SG CYS i 25 " - pdb=" SG CYS i 37 " distance=2.52 Simple disulfide: pdb=" SG CYS i 25 " - pdb=" SG CYS i 40 " distance=1.71 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 45.12 Conformation dependent library (CDL) restraints added in 6.1 seconds 12082 Ramachandran restraints generated. 6041 Oldfield, 0 Emsley, 6041 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11574 Finding SS restraints... Secondary structure from input PDB file: 200 helices and 68 sheets defined 36.3% alpha, 14.1% beta 933 base pairs and 1779 stacking pairs defined. Time for finding SS restraints: 34.15 Creating SS restraints... Processing helix chain 'A' and resid 7 through 11 removed outlier: 3.562A pdb=" N LYS A 10 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY A 11 " --> pdb=" O GLN A 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 7 through 11' Processing helix chain 'A' and resid 33 through 38 removed outlier: 3.837A pdb=" N ARG A 37 " --> pdb=" O ASP A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 191 removed outlier: 3.506A pdb=" N ALA A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS A 188 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 116 Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 131 through 139 removed outlier: 3.633A pdb=" N LYS B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 153 removed outlier: 3.642A pdb=" N ARG B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 196 removed outlier: 3.753A pdb=" N VAL B 191 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 233 Processing helix chain 'B' and resid 371 through 380 Processing helix chain 'C' and resid 34 through 46 removed outlier: 3.594A pdb=" N PHE C 39 " --> pdb=" O ASP C 35 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS C 46 " --> pdb=" O THR C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 49 No H-bonds generated for 'chain 'C' and resid 47 through 49' Processing helix chain 'C' and resid 116 through 130 Processing helix chain 'C' and resid 133 through 140 removed outlier: 3.548A pdb=" N VAL C 137 " --> pdb=" O LEU C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 159 Processing helix chain 'C' and resid 163 through 175 removed outlier: 3.560A pdb=" N LYS C 169 " --> pdb=" O ARG C 165 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU C 171 " --> pdb=" O ALA C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 186 removed outlier: 3.845A pdb=" N VAL C 183 " --> pdb=" O GLU C 179 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 197 removed outlier: 3.528A pdb=" N LYS C 196 " --> pdb=" O GLY C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 224 removed outlier: 3.858A pdb=" N ARG C 223 " --> pdb=" O THR C 219 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASN C 224 " --> pdb=" O ARG C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 242 removed outlier: 3.592A pdb=" N LEU C 241 " --> pdb=" O ASN C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 266 removed outlier: 3.601A pdb=" N LEU C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLN C 262 " --> pdb=" O PHE C 258 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU C 263 " --> pdb=" O LYS C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 297 Processing helix chain 'C' and resid 298 through 303 removed outlier: 3.599A pdb=" N ARG C 303 " --> pdb=" O GLU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 348 Processing helix chain 'C' and resid 350 through 405 removed outlier: 3.691A pdb=" N ARG C 354 " --> pdb=" O GLY C 350 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU C 356 " --> pdb=" O LYS C 352 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU C 367 " --> pdb=" O ALA C 363 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS C 369 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS C 371 " --> pdb=" O GLU C 367 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG C 372 " --> pdb=" O HIS C 368 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N GLN C 373 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N SER C 374 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG C 376 " --> pdb=" O ARG C 372 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG C 377 " --> pdb=" O GLN C 373 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA C 385 " --> pdb=" O GLU C 381 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU C 394 " --> pdb=" O MET C 390 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA C 405 " --> pdb=" O LYS C 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 16 removed outlier: 3.783A pdb=" N PHE D 13 " --> pdb=" O ASN D 9 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS D 14 " --> pdb=" O LYS D 10 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG D 15 " --> pdb=" O ALA D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 38 removed outlier: 3.766A pdb=" N ALA D 35 " --> pdb=" O ALA D 31 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU D 38 " --> pdb=" O ARG D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 94 through 114 removed outlier: 4.028A pdb=" N ARG D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU D 110 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN D 112 " --> pdb=" O ARG D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 169 Processing helix chain 'D' and resid 194 through 203 removed outlier: 4.056A pdb=" N HIS D 198 " --> pdb=" O ASP D 194 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG D 201 " --> pdb=" O ALA D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 218 removed outlier: 4.301A pdb=" N GLU D 216 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU D 217 " --> pdb=" O GLN D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 225 Processing helix chain 'D' and resid 226 through 232 Processing helix chain 'D' and resid 238 through 251 removed outlier: 3.560A pdb=" N TYR D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS D 244 " --> pdb=" O GLU D 240 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N HIS D 247 " --> pdb=" O TYR D 243 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA D 248 " --> pdb=" O LYS D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 299 removed outlier: 3.745A pdb=" N ARG D 295 " --> pdb=" O GLN D 291 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN D 298 " --> pdb=" O GLU D 294 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS D 299 " --> pdb=" O ARG D 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 89 No H-bonds generated for 'chain 'E' and resid 87 through 89' Processing helix chain 'E' and resid 149 through 159 removed outlier: 3.719A pdb=" N GLN E 153 " --> pdb=" O ALA E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 166 removed outlier: 3.970A pdb=" N LEU E 163 " --> pdb=" O ASP E 159 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA E 164 " --> pdb=" O LYS E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 178 Processing helix chain 'F' and resid 21 through 83 removed outlier: 3.739A pdb=" N LYS F 25 " --> pdb=" O ARG F 21 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP F 29 " --> pdb=" O LYS F 25 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS F 31 " --> pdb=" O ALA F 27 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS F 52 " --> pdb=" O HIS F 48 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR F 59 " --> pdb=" O LYS F 55 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS F 60 " --> pdb=" O MET F 56 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR F 61 " --> pdb=" O ARG F 57 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE F 73 " --> pdb=" O ARG F 69 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS F 76 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS F 80 " --> pdb=" O LYS F 76 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY F 83 " --> pdb=" O ALA F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 116 removed outlier: 3.509A pdb=" N ARG F 114 " --> pdb=" O LYS F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 141 removed outlier: 4.241A pdb=" N ALA F 139 " --> pdb=" O GLU F 135 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL F 140 " --> pdb=" O MET F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 161 Processing helix chain 'F' and resid 179 through 188 removed outlier: 4.397A pdb=" N VAL F 183 " --> pdb=" O ALA F 179 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS F 186 " --> pdb=" O ILE F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 204 removed outlier: 3.629A pdb=" N VAL F 199 " --> pdb=" O VAL F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 215 removed outlier: 3.640A pdb=" N ALA F 212 " --> pdb=" O TYR F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 258 removed outlier: 3.943A pdb=" N ARG F 256 " --> pdb=" O GLU F 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 82 removed outlier: 4.531A pdb=" N ARG G 76 " --> pdb=" O GLN G 72 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN G 80 " --> pdb=" O ARG G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 93 removed outlier: 3.732A pdb=" N PHE G 91 " --> pdb=" O ILE G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 108 removed outlier: 3.512A pdb=" N GLN G 102 " --> pdb=" O ASN G 98 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU G 103 " --> pdb=" O GLN G 99 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU G 106 " --> pdb=" O GLN G 102 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA G 108 " --> pdb=" O MET G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 111 No H-bonds generated for 'chain 'G' and resid 109 through 111' Processing helix chain 'G' and resid 116 through 126 removed outlier: 3.885A pdb=" N GLN G 120 " --> pdb=" O ALA G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 137 removed outlier: 3.624A pdb=" N ALA G 135 " --> pdb=" O GLY G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 156 removed outlier: 4.212A pdb=" N ASP G 152 " --> pdb=" O ASN G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 176 removed outlier: 4.778A pdb=" N PHE G 176 " --> pdb=" O GLU G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 185 Processing helix chain 'G' and resid 193 through 202 removed outlier: 3.655A pdb=" N LEU G 197 " --> pdb=" O GLY G 193 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU G 200 " --> pdb=" O ARG G 196 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL G 201 " --> pdb=" O LEU G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 218 through 233 removed outlier: 3.640A pdb=" N LYS G 227 " --> pdb=" O GLU G 223 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ILE G 228 " --> pdb=" O ALA G 224 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR G 229 " --> pdb=" O GLN G 225 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA G 231 " --> pdb=" O LYS G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 271 removed outlier: 3.745A pdb=" N LYS G 258 " --> pdb=" O HIS G 254 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN G 264 " --> pdb=" O GLU G 260 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS G 269 " --> pdb=" O ILE G 265 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing helix chain 'H' and resid 67 through 86 removed outlier: 3.940A pdb=" N THR H 71 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS H 73 " --> pdb=" O ILE H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 164 removed outlier: 3.839A pdb=" N VAL H 153 " --> pdb=" O ASP H 149 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE H 160 " --> pdb=" O SER H 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 81 removed outlier: 3.561A pdb=" N LYS I 74 " --> pdb=" O VAL I 70 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS I 78 " --> pdb=" O LYS I 74 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY I 81 " --> pdb=" O ILE I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 156 removed outlier: 3.651A pdb=" N THR I 150 " --> pdb=" O ALA I 146 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU I 152 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG I 154 " --> pdb=" O THR I 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 159 No H-bonds generated for 'chain 'I' and resid 157 through 159' Processing helix chain 'I' and resid 177 through 183 removed outlier: 4.094A pdb=" N LYS I 182 " --> pdb=" O LYS I 178 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS I 183 " --> pdb=" O VAL I 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 43 removed outlier: 3.583A pdb=" N ARG J 33 " --> pdb=" O ASP J 29 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA J 34 " --> pdb=" O ARG J 30 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL J 37 " --> pdb=" O ARG J 33 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU J 38 " --> pdb=" O ALA J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 89 removed outlier: 3.879A pdb=" N VAL J 87 " --> pdb=" O LYS J 83 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS J 88 " --> pdb=" O GLY J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 113 Processing helix chain 'J' and resid 137 through 142 removed outlier: 4.249A pdb=" N HIS J 141 " --> pdb=" O ASN J 137 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 167 removed outlier: 3.575A pdb=" N SER J 160 " --> pdb=" O THR J 156 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS J 162 " --> pdb=" O GLU J 158 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN J 166 " --> pdb=" O LYS J 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 46 removed outlier: 3.547A pdb=" N GLN K 39 " --> pdb=" O ARG K 35 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS K 44 " --> pdb=" O GLU K 40 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 83 removed outlier: 3.619A pdb=" N VAL K 82 " --> pdb=" O GLU K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 93 removed outlier: 3.966A pdb=" N ILE K 92 " --> pdb=" O VAL K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 121 removed outlier: 3.838A pdb=" N LEU K 108 " --> pdb=" O SER K 104 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN K 111 " --> pdb=" O SER K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 195 removed outlier: 3.712A pdb=" N LEU K 186 " --> pdb=" O ALA K 182 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG K 191 " --> pdb=" O ARG K 187 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS K 193 " --> pdb=" O ALA K 189 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN K 195 " --> pdb=" O ARG K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 204 removed outlier: 3.627A pdb=" N LYS K 202 " --> pdb=" O LYS K 198 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 83 removed outlier: 3.962A pdb=" N LYS L 76 " --> pdb=" O SER L 72 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA L 78 " --> pdb=" O THR L 74 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS L 81 " --> pdb=" O LYS L 77 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP L 82 " --> pdb=" O ALA L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 91 removed outlier: 3.560A pdb=" N ASN L 89 " --> pdb=" O ILE L 85 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER L 91 " --> pdb=" O LYS L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 93 through 105 removed outlier: 3.611A pdb=" N LEU L 98 " --> pdb=" O GLY L 94 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA L 104 " --> pdb=" O LYS L 100 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN L 105 " --> pdb=" O GLU L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 132 removed outlier: 3.539A pdb=" N LEU L 114 " --> pdb=" O ASP L 110 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET L 115 " --> pdb=" O ARG L 111 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL L 124 " --> pdb=" O GLN L 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 12 Processing helix chain 'M' and resid 16 through 33 removed outlier: 3.529A pdb=" N TRP M 28 " --> pdb=" O ARG M 24 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG M 31 " --> pdb=" O THR M 27 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN M 32 " --> pdb=" O TRP M 28 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU M 33 " --> pdb=" O GLU M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 51 removed outlier: 3.635A pdb=" N ARG M 50 " --> pdb=" O ASP M 46 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 79 removed outlier: 3.615A pdb=" N GLY M 78 " --> pdb=" O VAL M 75 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 106 Processing helix chain 'M' and resid 109 through 111 No H-bonds generated for 'chain 'M' and resid 109 through 111' Processing helix chain 'M' and resid 140 through 146 removed outlier: 3.867A pdb=" N ASP M 146 " --> pdb=" O ALA M 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 158 removed outlier: 5.296A pdb=" N TRP M 151 " --> pdb=" O ARG M 148 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU M 152 " --> pdb=" O ILE M 149 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS M 154 " --> pdb=" O TRP M 151 " (cutoff:3.500A) Proline residue: M 155 - end of helix removed outlier: 3.770A pdb=" N LYS M 158 " --> pdb=" O PRO M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 166 through 174 removed outlier: 3.586A pdb=" N LYS M 170 " --> pdb=" O THR M 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR M 172 " --> pdb=" O ALA M 168 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY M 174 " --> pdb=" O LYS M 170 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 196 Processing helix chain 'N' and resid 81 through 95 removed outlier: 3.730A pdb=" N VAL N 88 " --> pdb=" O ARG N 84 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS N 91 " --> pdb=" O SER N 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 106 removed outlier: 3.580A pdb=" N ASP N 106 " --> pdb=" O ARG N 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 103 through 106' Processing helix chain 'N' and resid 112 through 126 removed outlier: 3.832A pdb=" N LEU N 126 " --> pdb=" O ARG N 122 " (cutoff:3.500A) Processing helix chain 'N' and resid 141 through 152 removed outlier: 3.505A pdb=" N THR N 149 " --> pdb=" O ILE N 145 " (cutoff:3.500A) Processing helix chain 'N' and resid 158 through 168 removed outlier: 3.542A pdb=" N LEU N 165 " --> pdb=" O GLY N 161 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU N 168 " --> pdb=" O ALA N 164 " (cutoff:3.500A) Processing helix chain 'N' and resid 190 through 195 Processing helix chain 'N' and resid 204 through 211 removed outlier: 3.537A pdb=" N VAL N 211 " --> pdb=" O LEU N 207 " (cutoff:3.500A) Processing helix chain 'N' and resid 215 through 255 removed outlier: 3.961A pdb=" N VAL N 219 " --> pdb=" O HIS N 215 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU N 223 " --> pdb=" O VAL N 219 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR N 228 " --> pdb=" O GLU N 224 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS N 236 " --> pdb=" O ALA N 232 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN N 244 " --> pdb=" O ARG N 240 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN N 249 " --> pdb=" O THR N 245 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE N 250 " --> pdb=" O GLU N 246 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR N 253 " --> pdb=" O GLN N 249 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU N 255 " --> pdb=" O ALA N 251 " (cutoff:3.500A) Processing helix chain 'N' and resid 256 through 264 removed outlier: 3.702A pdb=" N VAL N 260 " --> pdb=" O PRO N 256 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA N 261 " --> pdb=" O LYS N 257 " (cutoff:3.500A) Processing helix chain 'O' and resid 25 through 37 removed outlier: 3.531A pdb=" N ALA O 31 " --> pdb=" O LYS O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 59 removed outlier: 3.609A pdb=" N ASP O 56 " --> pdb=" O LYS O 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 83 removed outlier: 3.520A pdb=" N ALA O 79 " --> pdb=" O LYS O 76 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU O 81 " --> pdb=" O GLN O 78 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 111 removed outlier: 3.512A pdb=" N PHE O 96 " --> pdb=" O LYS O 92 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET O 110 " --> pdb=" O SER O 106 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS O 111 " --> pdb=" O ASN O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 138 through 140 No H-bonds generated for 'chain 'O' and resid 138 through 140' Processing helix chain 'P' and resid 23 through 41 removed outlier: 3.894A pdb=" N ASN P 41 " --> pdb=" O ALA P 37 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 53 removed outlier: 3.702A pdb=" N ALA P 46 " --> pdb=" O SER P 42 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) Processing helix chain 'P' and resid 64 through 71 removed outlier: 3.897A pdb=" N ARG P 69 " --> pdb=" O SER P 65 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET P 71 " --> pdb=" O LEU P 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 105 through 116 Processing helix chain 'P' and resid 121 through 129 removed outlier: 3.680A pdb=" N LEU P 127 " --> pdb=" O ASP P 123 " (cutoff:3.500A) Processing helix chain 'P' and resid 145 through 150 removed outlier: 4.068A pdb=" N HIS P 150 " --> pdb=" O GLU P 146 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 14 Processing helix chain 'Q' and resid 27 through 34 removed outlier: 3.588A pdb=" N SER Q 32 " --> pdb=" O ALA Q 28 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET Q 33 " --> pdb=" O SER Q 29 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA Q 34 " --> pdb=" O ASP Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 36 through 46 removed outlier: 3.720A pdb=" N LYS Q 42 " --> pdb=" O PHE Q 38 " (cutoff:3.500A) Processing helix chain 'Q' and resid 59 through 71 removed outlier: 3.508A pdb=" N ALA Q 71 " --> pdb=" O GLU Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 83 through 88 Processing helix chain 'Q' and resid 89 through 111 removed outlier: 3.534A pdb=" N ARG Q 97 " --> pdb=" O LEU Q 93 " (cutoff:3.500A) Processing helix chain 'Q' and resid 115 through 129 removed outlier: 3.503A pdb=" N HIS Q 120 " --> pdb=" O LYS Q 116 " (cutoff:3.500A) Processing helix chain 'Q' and resid 133 through 175 removed outlier: 3.879A pdb=" N LEU Q 137 " --> pdb=" O ASN Q 133 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS Q 148 " --> pdb=" O GLU Q 144 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS Q 150 " --> pdb=" O ASN Q 146 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU Q 154 " --> pdb=" O LYS Q 150 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN Q 157 " --> pdb=" O ALA Q 153 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA Q 166 " --> pdb=" O LYS Q 162 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS Q 175 " --> pdb=" O LYS Q 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 56 removed outlier: 3.978A pdb=" N VAL R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS R 54 " --> pdb=" O TYR R 50 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET R 55 " --> pdb=" O LEU R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 122 removed outlier: 3.532A pdb=" N ALA R 115 " --> pdb=" O SER R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 143 through 148 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.895A pdb=" N VAL S 32 " --> pdb=" O ARG S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 54 through 58 Processing helix chain 'S' and resid 102 through 118 removed outlier: 3.764A pdb=" N LYS S 110 " --> pdb=" O LEU S 106 " (cutoff:3.500A) Processing helix chain 'T' and resid 34 through 39 Processing helix chain 'T' and resid 44 through 56 removed outlier: 3.713A pdb=" N LEU T 48 " --> pdb=" O GLU T 44 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU T 49 " --> pdb=" O ALA T 45 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE T 56 " --> pdb=" O LEU T 52 " (cutoff:3.500A) Processing helix chain 'T' and resid 87 through 102 removed outlier: 3.907A pdb=" N ILE T 91 " --> pdb=" O SER T 87 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS T 92 " --> pdb=" O LYS T 88 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS T 101 " --> pdb=" O LYS T 97 " (cutoff:3.500A) Processing helix chain 'U' and resid 68 through 72 removed outlier: 3.621A pdb=" N ARG U 72 " --> pdb=" O PRO U 69 " (cutoff:3.500A) Processing helix chain 'U' and resid 121 through 128 removed outlier: 3.658A pdb=" N ALA U 125 " --> pdb=" O GLY U 121 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU U 127 " --> pdb=" O GLU U 123 " (cutoff:3.500A) Processing helix chain 'U' and resid 128 through 135 removed outlier: 3.600A pdb=" N SER U 132 " --> pdb=" O TRP U 128 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA U 133 " --> pdb=" O PRO U 129 " (cutoff:3.500A) Processing helix chain 'V' and resid 40 through 50 removed outlier: 3.602A pdb=" N LEU V 46 " --> pdb=" O LYS V 42 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN V 49 " --> pdb=" O SER V 45 " (cutoff:3.500A) Processing helix chain 'V' and resid 52 through 56 removed outlier: 3.585A pdb=" N LYS V 55 " --> pdb=" O LYS V 52 " (cutoff:3.500A) Processing helix chain 'V' and resid 59 through 66 Processing helix chain 'W' and resid 82 through 86 removed outlier: 3.660A pdb=" N ILE W 86 " --> pdb=" O ASP W 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 82 through 86' Processing helix chain 'W' and resid 93 through 103 removed outlier: 3.627A pdb=" N LYS W 98 " --> pdb=" O GLU W 94 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS W 99 " --> pdb=" O SER W 95 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE W 100 " --> pdb=" O ALA W 96 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU W 101 " --> pdb=" O MET W 97 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU W 102 " --> pdb=" O LYS W 98 " (cutoff:3.500A) Processing helix chain 'W' and resid 115 through 127 Processing helix chain 'W' and resid 155 through 164 removed outlier: 3.784A pdb=" N VAL W 159 " --> pdb=" O ASP W 155 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN W 161 " --> pdb=" O LEU W 157 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 21 Processing helix chain 'X' and resid 22 through 30 removed outlier: 3.644A pdb=" N ARG X 27 " --> pdb=" O SER X 23 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS X 28 " --> pdb=" O SER X 24 " (cutoff:3.500A) Processing helix chain 'X' and resid 37 through 42 removed outlier: 3.582A pdb=" N LYS X 41 " --> pdb=" O GLU X 37 " (cutoff:3.500A) Processing helix chain 'X' and resid 111 through 122 removed outlier: 3.581A pdb=" N LEU X 118 " --> pdb=" O ARG X 114 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU X 119 " --> pdb=" O LYS X 115 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG X 120 " --> pdb=" O ALA X 116 " (cutoff:3.500A) Processing helix chain 'Y' and resid 57 through 65 removed outlier: 3.506A pdb=" N MET Y 65 " --> pdb=" O ILE Y 61 " (cutoff:3.500A) Processing helix chain 'Y' and resid 86 through 91 removed outlier: 4.014A pdb=" N MET Y 90 " --> pdb=" O VAL Y 86 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP Y 91 " --> pdb=" O SER Y 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 86 through 91' Processing helix chain 'Y' and resid 102 through 105 Processing helix chain 'Y' and resid 106 through 123 removed outlier: 3.571A pdb=" N LYS Y 112 " --> pdb=" O LYS Y 108 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY Y 113 " --> pdb=" O ALA Y 109 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS Y 116 " --> pdb=" O LYS Y 112 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU Y 120 " --> pdb=" O LYS Y 116 " (cutoff:3.500A) Processing helix chain 'Y' and resid 134 through 142 removed outlier: 3.766A pdb=" N LEU Y 138 " --> pdb=" O SER Y 134 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU Y 140 " --> pdb=" O ASP Y 136 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG Y 141 " --> pdb=" O LEU Y 137 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS Y 142 " --> pdb=" O LEU Y 138 " (cutoff:3.500A) Processing helix chain 'Z' and resid 6 through 12 removed outlier: 4.060A pdb=" N LYS Z 10 " --> pdb=" O ARG Z 6 " (cutoff:3.500A) Processing helix chain 'Z' and resid 41 through 46 Processing helix chain 'Z' and resid 78 through 82 Processing helix chain 'Z' and resid 85 through 92 removed outlier: 3.973A pdb=" N GLN Z 92 " --> pdb=" O GLU Z 88 " (cutoff:3.500A) Processing helix chain 'Z' and resid 102 through 106 Processing helix chain 'Z' and resid 129 through 139 removed outlier: 3.552A pdb=" N LYS Z 134 " --> pdb=" O LYS Z 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 11 through 17 Processing helix chain 'a' and resid 36 through 50 removed outlier: 3.564A pdb=" N ARG a 44 " --> pdb=" O LEU a 40 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET a 50 " --> pdb=" O CYS a 46 " (cutoff:3.500A) Processing helix chain 'b' and resid 12 through 24 removed outlier: 4.195A pdb=" N GLN b 18 " --> pdb=" O ASN b 14 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU b 19 " --> pdb=" O SER b 15 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL b 20 " --> pdb=" O ARG b 16 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET b 21 " --> pdb=" O LEU b 17 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS b 22 " --> pdb=" O GLN b 18 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER b 23 " --> pdb=" O LEU b 19 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 40 Processing helix chain 'b' and resid 52 through 67 removed outlier: 3.500A pdb=" N MET b 64 " --> pdb=" O GLU b 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 85 removed outlier: 3.809A pdb=" N GLY b 81 " --> pdb=" O ASN b 77 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR b 82 " --> pdb=" O ASN b 78 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 107 removed outlier: 4.480A pdb=" N SER b 106 " --> pdb=" O ASP b 102 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL b 107 " --> pdb=" O ILE b 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 102 through 107' Processing helix chain 'c' and resid 24 through 28 Processing helix chain 'c' and resid 37 through 53 removed outlier: 3.614A pdb=" N LEU c 41 " --> pdb=" O ALA c 37 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU c 43 " --> pdb=" O ARG c 39 " (cutoff:3.500A) Processing helix chain 'c' and resid 60 through 68 removed outlier: 3.520A pdb=" N PHE c 66 " --> pdb=" O LYS c 62 " (cutoff:3.500A) Processing helix chain 'c' and resid 69 through 71 No H-bonds generated for 'chain 'c' and resid 69 through 71' Processing helix chain 'd' and resid 42 through 47 Processing helix chain 'd' and resid 56 through 60 removed outlier: 3.500A pdb=" N TYR d 59 " --> pdb=" O ASN d 56 " (cutoff:3.500A) Processing helix chain 'd' and resid 81 through 88 removed outlier: 3.647A pdb=" N ILE d 84 " --> pdb=" O PRO d 81 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU d 86 " --> pdb=" O ASP d 83 " (cutoff:3.500A) Processing helix chain 'd' and resid 103 through 117 removed outlier: 3.797A pdb=" N GLU d 112 " --> pdb=" O ARG d 108 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN d 116 " --> pdb=" O GLU d 112 " (cutoff:3.500A) Processing helix chain 'e' and resid 42 through 47 removed outlier: 3.717A pdb=" N GLN e 47 " --> pdb=" O ARG e 43 " (cutoff:3.500A) Processing helix chain 'f' and resid 66 through 71 removed outlier: 3.778A pdb=" N THR f 71 " --> pdb=" O ARG f 68 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 106 removed outlier: 3.521A pdb=" N GLU f 87 " --> pdb=" O ALA f 83 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU f 96 " --> pdb=" O ALA f 92 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS f 99 " --> pdb=" O VAL f 95 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN f 103 " --> pdb=" O LYS f 99 " (cutoff:3.500A) Processing helix chain 'g' and resid 5 through 10 removed outlier: 3.560A pdb=" N LEU g 9 " --> pdb=" O ARG g 5 " (cutoff:3.500A) Processing helix chain 'g' and resid 15 through 38 removed outlier: 3.648A pdb=" N ALA g 34 " --> pdb=" O GLN g 30 " (cutoff:3.500A) Processing helix chain 'g' and resid 40 through 45 removed outlier: 3.623A pdb=" N LEU g 44 " --> pdb=" O ALA g 40 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER g 45 " --> pdb=" O ALA g 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 40 through 45' Processing helix chain 'g' and resid 45 through 73 removed outlier: 3.917A pdb=" N GLU g 49 " --> pdb=" O SER g 45 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS g 52 " --> pdb=" O THR g 48 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA g 69 " --> pdb=" O GLN g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 88 through 93 Processing helix chain 'g' and resid 96 through 102 Processing helix chain 'g' and resid 104 through 114 removed outlier: 3.546A pdb=" N LYS g 109 " --> pdb=" O VAL g 105 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL g 114 " --> pdb=" O ARG g 110 " (cutoff:3.500A) Processing helix chain 'h' and resid 31 through 46 removed outlier: 3.799A pdb=" N SER h 36 " --> pdb=" O PRO h 32 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG h 38 " --> pdb=" O MET h 34 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE h 40 " --> pdb=" O SER h 36 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN h 43 " --> pdb=" O GLU h 39 " (cutoff:3.500A) Processing helix chain 'h' and resid 48 through 60 removed outlier: 3.520A pdb=" N ARG h 53 " --> pdb=" O PRO h 49 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 77 removed outlier: 3.566A pdb=" N LYS h 67 " --> pdb=" O ALA h 63 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG h 68 " --> pdb=" O ALA h 64 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU h 70 " --> pdb=" O THR h 66 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU h 77 " --> pdb=" O ALA h 73 " (cutoff:3.500A) Processing helix chain 'h' and resid 79 through 99 removed outlier: 3.553A pdb=" N ASN h 92 " --> pdb=" O GLU h 88 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ARG h 99 " --> pdb=" O SER h 95 " (cutoff:3.500A) Processing helix chain 'i' and resid 7 through 14 removed outlier: 3.657A pdb=" N LYS i 13 " --> pdb=" O GLY i 9 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG i 14 " --> pdb=" O SER i 10 " (cutoff:3.500A) Processing helix chain 'i' and resid 53 through 61 removed outlier: 3.624A pdb=" N LYS i 57 " --> pdb=" O SER i 53 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N HIS i 60 " --> pdb=" O ALA i 56 " (cutoff:3.500A) Processing helix chain 'i' and resid 67 through 72 removed outlier: 4.575A pdb=" N ASP i 72 " --> pdb=" O ARG i 68 " (cutoff:3.500A) Processing helix chain 'i' and resid 72 through 79 removed outlier: 3.737A pdb=" N ASN i 79 " --> pdb=" O ARG i 75 " (cutoff:3.500A) Processing helix chain 'j' and resid 7 through 17 removed outlier: 3.533A pdb=" N PHE j 11 " --> pdb=" O ASP j 7 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU j 12 " --> pdb=" O LEU j 8 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU j 13 " --> pdb=" O ARG j 9 " (cutoff:3.500A) Processing helix chain 'j' and resid 60 through 71 removed outlier: 3.947A pdb=" N GLY j 69 " --> pdb=" O GLN j 65 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER j 70 " --> pdb=" O LYS j 66 " (cutoff:3.500A) Processing helix chain 'k' and resid 6 through 19 removed outlier: 3.566A pdb=" N LYS k 18 " --> pdb=" O GLY k 14 " (cutoff:3.500A) Processing helix chain 'k' and resid 24 through 30 removed outlier: 4.393A pdb=" N ARG k 28 " --> pdb=" O PRO k 24 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N MET k 29 " --> pdb=" O PRO k 25 " (cutoff:3.500A) Processing helix chain 'l' and resid 79 through 91 removed outlier: 3.649A pdb=" N LEU l 84 " --> pdb=" O PRO l 80 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU l 85 " --> pdb=" O SER l 81 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N TYR l 89 " --> pdb=" O LEU l 85 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN l 90 " --> pdb=" O ALA l 86 " (cutoff:3.500A) Processing helix chain 'n' and resid 37 through 48 Processing helix chain 'o' and resid 8 through 13 removed outlier: 3.599A pdb=" N GLY o 12 " --> pdb=" O GLY o 9 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS o 13 " --> pdb=" O VAL o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 19 through 34 removed outlier: 3.785A pdb=" N ILE o 29 " --> pdb=" O GLN o 25 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN o 32 " --> pdb=" O LYS o 28 " (cutoff:3.500A) Processing helix chain 'o' and resid 73 through 91 removed outlier: 3.627A pdb=" N ALA o 84 " --> pdb=" O ARG o 80 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA o 90 " --> pdb=" O LEU o 86 " (cutoff:3.500A) Processing helix chain 'p' and resid 3 through 12 Processing helix chain 'p' and resid 76 through 80 Processing helix chain 'p' and resid 92 through 104 removed outlier: 3.580A pdb=" N VAL p 96 " --> pdb=" O GLU p 92 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA p 101 " --> pdb=" O MET p 97 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG p 103 " --> pdb=" O ALA p 99 " (cutoff:3.500A) Processing helix chain 'p' and resid 107 through 120 removed outlier: 4.185A pdb=" N ARG p 120 " --> pdb=" O LYS p 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 50 removed outlier: 6.069A pdb=" N VAL A 45 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N SER A 62 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103 removed outlier: 3.522A pdb=" N LEU A 102 " --> pdb=" O GLY A 164 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ILE A 136 " --> pdb=" O ARG A 149 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ARG A 149 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY A 138 " --> pdb=" O ARG A 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA5, first strand: chain 'B' and resid 273 through 274 removed outlier: 5.582A pdb=" N VAL B 219 " --> pdb=" O PRO B 334 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL B 78 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N MET B 53 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N VAL B 76 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS B 55 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLU B 74 " --> pdb=" O HIS B 55 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL B 57 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE B 72 " --> pdb=" O VAL B 57 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 279 through 280 removed outlier: 5.582A pdb=" N VAL B 219 " --> pdb=" O PRO B 334 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLU B 59 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU B 355 " --> pdb=" O GLU B 59 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 99 through 105 removed outlier: 7.021A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 156 " --> pdb=" O TYR B 92 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 99 through 105 removed outlier: 7.021A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 156 " --> pdb=" O TYR B 92 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N THR B 200 " --> pdb=" O CYS B 86 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 225 through 226 Processing sheet with id=AB1, first strand: chain 'C' and resid 21 through 23 removed outlier: 4.710A pdb=" N VAL C 153 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU C 152 " --> pdb=" O CYS C 251 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU C 209 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N THR C 254 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL C 211 " --> pdb=" O THR C 254 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR C 212 " --> pdb=" O CYS C 231 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 65 through 66 Processing sheet with id=AB3, first strand: chain 'D' and resid 72 through 79 removed outlier: 6.815A pdb=" N VAL D 64 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N THR D 77 " --> pdb=" O CYS D 62 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N CYS D 62 " --> pdb=" O THR D 77 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU D 79 " --> pdb=" O ILE D 60 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE D 60 " --> pdb=" O GLU D 79 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ARG D 59 " --> pdb=" O THR D 56 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL D 53 " --> pdb=" O ASP D 146 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 84 through 86 removed outlier: 3.618A pdb=" N ARG E 84 " --> pdb=" O VAL E 72 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS E 62 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 85 through 87 Processing sheet with id=AB6, first strand: chain 'F' and resid 219 through 220 removed outlier: 4.332A pdb=" N ASN F 123 " --> pdb=" O ARG F 98 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE F 144 " --> pdb=" O GLY F 244 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 175 through 176 removed outlier: 4.784A pdb=" N TYR F 163 " --> pdb=" O TRP F 217 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 83 through 84 Processing sheet with id=AB9, first strand: chain 'G' and resid 144 through 145 removed outlier: 3.547A pdb=" N LEU G 161 " --> pdb=" O ILE G 211 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL G 162 " --> pdb=" O CYS G 189 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL G 191 " --> pdb=" O VAL G 162 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE G 164 " --> pdb=" O VAL G 191 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 11 removed outlier: 6.539A pdb=" N VAL H 4 " --> pdb=" O TYR H 60 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 16 through 21 removed outlier: 3.735A pdb=" N THR H 26 " --> pdb=" O ASP H 19 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS H 21 " --> pdb=" O VAL H 24 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 131 through 135 removed outlier: 7.286A pdb=" N GLN H 88 " --> pdb=" O THR H 183 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N THR H 183 " --> pdb=" O GLN H 88 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS H 90 " --> pdb=" O SER H 181 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 101 through 104 removed outlier: 3.659A pdb=" N GLU H 112 " --> pdb=" O ASN H 103 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 36 through 37 removed outlier: 6.678A pdb=" N LEU I 52 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N SER I 137 " --> pdb=" O ALA I 50 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA I 50 " --> pdb=" O SER I 137 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ARG I 139 " --> pdb=" O GLY I 48 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N GLY I 48 " --> pdb=" O ARG I 139 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 58 through 61 removed outlier: 6.693A pdb=" N LEU I 97 " --> pdb=" O MET I 123 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LEU I 125 " --> pdb=" O HIS I 95 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N HIS I 95 " --> pdb=" O LEU I 125 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 190 through 191 Processing sheet with id=AC8, first strand: chain 'J' and resid 47 through 49 removed outlier: 3.606A pdb=" N ALA J 67 " --> pdb=" O SER J 49 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ILE J 15 " --> pdb=" O THR J 133 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR J 133 " --> pdb=" O ILE J 15 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS J 17 " --> pdb=" O GLN J 131 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N CYS J 23 " --> pdb=" O GLY J 125 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N GLY J 125 " --> pdb=" O CYS J 23 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 21 through 23 removed outlier: 6.555A pdb=" N LYS K 22 " --> pdb=" O LEU M 201 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'K' and resid 56 through 57 Processing sheet with id=AD2, first strand: chain 'K' and resid 122 through 124 Processing sheet with id=AD3, first strand: chain 'L' and resid 7 through 8 Processing sheet with id=AD4, first strand: chain 'L' and resid 50 through 52 removed outlier: 3.870A pdb=" N ASP L 30 " --> pdb=" O LEU L 38 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ASP L 40 " --> pdb=" O VAL L 28 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N VAL L 28 " --> pdb=" O ASP L 40 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG L 12 " --> pdb=" O VAL L 28 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LEU L 13 " --> pdb=" O THR L 60 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 37 through 38 removed outlier: 3.530A pdb=" N HIS M 37 " --> pdb=" O ARG M 63 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TYR M 130 " --> pdb=" O VAL M 122 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN M 118 " --> pdb=" O ILE M 134 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL M 136 " --> pdb=" O VAL M 116 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N VAL M 116 " --> pdb=" O VAL M 136 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 72 through 76 Processing sheet with id=AD7, first strand: chain 'N' and resid 108 through 110 Processing sheet with id=AD8, first strand: chain 'O' and resid 14 through 22 removed outlier: 4.273A pdb=" N ASP O 21 " --> pdb=" O CYS O 150 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N CYS O 150 " --> pdb=" O ASP O 21 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N HIS O 151 " --> pdb=" O VAL O 125 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL O 125 " --> pdb=" O HIS O 151 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLU O 153 " --> pdb=" O ILE O 123 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ILE O 123 " --> pdb=" O GLU O 153 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE O 155 " --> pdb=" O GLU O 121 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 64 through 65 Processing sheet with id=AE1, first strand: chain 'O' and resid 131 through 136 Processing sheet with id=AE2, first strand: chain 'P' and resid 62 through 63 removed outlier: 3.856A pdb=" N LEU P 102 " --> pdb=" O LEU P 81 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N GLY P 83 " --> pdb=" O LEU P 102 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N PHE P 104 " --> pdb=" O GLY P 83 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL P 85 " --> pdb=" O PHE P 104 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL P 99 " --> pdb=" O LEU P 120 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 62 through 63 removed outlier: 6.625A pdb=" N ILE P 78 " --> pdb=" O VAL P 136 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N LEU P 138 " --> pdb=" O ILE P 78 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL P 80 " --> pdb=" O LEU P 138 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 21 through 23 Processing sheet with id=AE5, first strand: chain 'R' and resid 34 through 38 removed outlier: 3.569A pdb=" N ALA R 67 " --> pdb=" O VAL R 17 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'R' and resid 94 through 103 removed outlier: 3.692A pdb=" N ASP R 103 " --> pdb=" O LYS R 80 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS R 80 " --> pdb=" O ASP R 103 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASN R 81 " --> pdb=" O ILE R 136 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA R 134 " --> pdb=" O GLY R 83 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG R 132 " --> pdb=" O TRP R 85 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ARG R 87 " --> pdb=" O ILE R 130 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ILE R 130 " --> pdb=" O ARG R 87 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'S' and resid 83 through 92 removed outlier: 3.826A pdb=" N ARG S 83 " --> pdb=" O VAL S 80 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLY S 73 " --> pdb=" O PHE S 65 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ASN S 77 " --> pdb=" O THR S 61 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N THR S 61 " --> pdb=" O ASN S 77 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG S 60 " --> pdb=" O ILE S 42 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'T' and resid 70 through 73 removed outlier: 3.715A pdb=" N VAL T 80 " --> pdb=" O PHE T 30 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP T 33 " --> pdb=" O TYR T 118 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU T 120 " --> pdb=" O ASP T 33 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'U' and resid 60 through 63 removed outlier: 6.578A pdb=" N LEU U 61 " --> pdb=" O ILE U 39 " (cutoff:3.500A) removed outlier: 8.984A pdb=" N GLY U 102 " --> pdb=" O LEU U 24 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASN U 26 " --> pdb=" O GLY U 102 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL U 104 " --> pdb=" O ASN U 26 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA U 101 " --> pdb=" O VAL U 81 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N MET U 77 " --> pdb=" O ALA U 105 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'U' and resid 87 through 88 removed outlier: 6.672A pdb=" N PHE U 94 " --> pdb=" O ARG V 27 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL V 29 " --> pdb=" O PHE U 94 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TYR U 96 " --> pdb=" O VAL V 29 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'W' and resid 87 through 90 removed outlier: 3.946A pdb=" N LEU W 143 " --> pdb=" O ARG W 139 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'X' and resid 31 through 33 Processing sheet with id=AF4, first strand: chain 'X' and resid 80 through 81 removed outlier: 3.905A pdb=" N LYS X 71 " --> pdb=" O HIS X 80 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARG X 65 " --> pdb=" O VAL X 57 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N GLU X 54 " --> pdb=" O THR X 106 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'X' and resid 85 through 87 Processing sheet with id=AF6, first strand: chain 'Y' and resid 68 through 75 removed outlier: 6.845A pdb=" N LYS Y 68 " --> pdb=" O GLU Y 46 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN Y 27 " --> pdb=" O LEU Y 41 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ALA Y 43 " --> pdb=" O VAL Y 25 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL Y 25 " --> pdb=" O ALA Y 43 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE Y 45 " --> pdb=" O GLY Y 23 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLY Y 23 " --> pdb=" O ILE Y 45 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG Y 9 " --> pdb=" O VAL Y 25 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N VAL Y 10 " --> pdb=" O THR Y 82 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR Y 82 " --> pdb=" O VAL Y 10 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Z' and resid 72 through 74 Processing sheet with id=AF8, first strand: chain 'Z' and resid 98 through 101 removed outlier: 3.660A pdb=" N ILE Z 122 " --> pdb=" O ALA Z 98 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL Z 121 " --> pdb=" O ALA Z 142 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL Z 144 " --> pdb=" O VAL Z 121 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL Z 123 " --> pdb=" O VAL Z 144 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'b' and resid 25 through 26 removed outlier: 3.726A pdb=" N LYS b 25 " --> pdb=" O ASP b 97 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP b 97 " --> pdb=" O LYS b 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'b' and resid 46 through 47 Processing sheet with id=AG2, first strand: chain 'c' and resid 17 through 23 removed outlier: 7.065A pdb=" N ARG c 58 " --> pdb=" O VAL c 101 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N HIS c 103 " --> pdb=" O ARG c 58 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'd' and resid 74 through 75 removed outlier: 6.007A pdb=" N PHE d 74 " --> pdb=" O ALA d 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'e' and resid 16 through 23 removed outlier: 5.594A pdb=" N VAL e 18 " --> pdb=" O GLN e 36 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLN e 36 " --> pdb=" O VAL e 18 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY e 20 " --> pdb=" O LEU e 34 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N CYS e 32 " --> pdb=" O LYS e 22 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N SER e 31 " --> pdb=" O PHE e 90 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N PHE e 90 " --> pdb=" O SER e 31 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG e 78 " --> pdb=" O ARG e 87 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LYS e 89 " --> pdb=" O ILE e 76 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ILE e 76 " --> pdb=" O LYS e 89 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N VAL e 57 " --> pdb=" O ARG e 102 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG e 102 " --> pdb=" O VAL e 57 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY e 101 " --> pdb=" O VAL e 18 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'f' and resid 21 through 24 Processing sheet with id=AG6, first strand: chain 'f' and resid 43 through 44 removed outlier: 4.053A pdb=" N ARG f 49 " --> pdb=" O CYS f 44 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'i' and resid 19 through 20 removed outlier: 3.534A pdb=" N THR i 36 " --> pdb=" O HIS i 31 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'j' and resid 53 through 58 removed outlier: 3.876A pdb=" N ARG j 22 " --> pdb=" O ARG j 48 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL j 23 " --> pdb=" O LYS j 77 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER j 79 " --> pdb=" O VAL j 23 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'l' and resid 102 through 103 Processing sheet with id=AH1, first strand: chain 'n' and resid 7 through 11 Processing sheet with id=AH2, first strand: chain 'n' and resid 26 through 27 removed outlier: 3.505A pdb=" N ILE n 68 " --> pdb=" O ILE n 85 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'o' and resid 47 through 51 removed outlier: 6.868A pdb=" N ILE o 54 " --> pdb=" O GLN o 50 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'p' and resid 18 through 21 Processing sheet with id=AH5, first strand: chain 'p' and resid 50 through 54 1604 hydrogen bonds defined for protein. 4575 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2264 hydrogen bonds 3790 hydrogen bond angles 0 basepair planarities 933 basepair parallelities 1779 stacking parallelities Total time for adding SS restraints: 171.92 Time building geometry restraints manager: 49.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 25507 1.34 - 1.47: 50804 1.47 - 1.60: 50846 1.60 - 1.73: 3158 1.73 - 1.86: 386 Bond restraints: 130701 Sorted by residual: bond pdb=" C ILE k 23 " pdb=" N PRO k 24 " ideal model delta sigma weight residual 1.331 1.390 -0.058 8.70e-03 1.32e+04 4.52e+01 bond pdb=" C ASN Y 124 " pdb=" N PRO Y 125 " ideal model delta sigma weight residual 1.332 1.387 -0.055 8.90e-03 1.26e+04 3.81e+01 bond pdb=" C ILE Z 119 " pdb=" N PRO Z 120 " ideal model delta sigma weight residual 1.331 1.391 -0.060 1.20e-02 6.94e+03 2.49e+01 bond pdb=" C HIS Z 49 " pdb=" N PRO Z 50 " ideal model delta sigma weight residual 1.329 1.388 -0.060 1.20e-02 6.94e+03 2.48e+01 bond pdb=" C ALA X 21 " pdb=" N PRO X 22 " ideal model delta sigma weight residual 1.330 1.390 -0.060 1.22e-02 6.72e+03 2.41e+01 ... (remaining 130696 not shown) Histogram of bond angle deviations from ideal: 98.56 - 106.62: 21098 106.62 - 114.68: 81132 114.68 - 122.75: 64887 122.75 - 130.81: 24087 130.81 - 138.88: 1108 Bond angle restraints: 192312 Sorted by residual: angle pdb=" N ASN d 123 " pdb=" CA ASN d 123 " pdb=" C ASN d 123 " ideal model delta sigma weight residual 111.28 122.91 -11.63 1.09e+00 8.42e-01 1.14e+02 angle pdb=" N THR G 92 " pdb=" CA THR G 92 " pdb=" C THR G 92 " ideal model delta sigma weight residual 114.31 100.67 13.64 1.29e+00 6.01e-01 1.12e+02 angle pdb=" N PHE p 17 " pdb=" CA PHE p 17 " pdb=" C PHE p 17 " ideal model delta sigma weight residual 111.28 122.45 -11.17 1.09e+00 8.42e-01 1.05e+02 angle pdb=" N LEU i 70 " pdb=" CA LEU i 70 " pdb=" C LEU i 70 " ideal model delta sigma weight residual 111.36 121.59 -10.23 1.09e+00 8.42e-01 8.80e+01 angle pdb=" N GLN O 20 " pdb=" CA GLN O 20 " pdb=" C GLN O 20 " ideal model delta sigma weight residual 111.14 121.07 -9.93 1.08e+00 8.57e-01 8.45e+01 ... (remaining 192307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 68524 35.94 - 71.88: 3008 71.88 - 107.82: 246 107.82 - 143.76: 19 143.76 - 179.69: 59 Dihedral angle restraints: 71856 sinusoidal: 53965 harmonic: 17891 Sorted by residual: dihedral pdb=" C5' G 11403 " pdb=" C4' G 11403 " pdb=" C3' G 11403 " pdb=" O3' G 11403 " ideal model delta sinusoidal sigma weight residual 147.00 78.28 68.72 1 8.00e+00 1.56e-02 9.56e+01 dihedral pdb=" C5' G 13477 " pdb=" C4' G 13477 " pdb=" C3' G 13477 " pdb=" O3' G 13477 " ideal model delta sinusoidal sigma weight residual 147.00 79.90 67.10 1 8.00e+00 1.56e-02 9.16e+01 dihedral pdb=" C5' A 1 802 " pdb=" C4' A 1 802 " pdb=" C3' A 1 802 " pdb=" O3' A 1 802 " ideal model delta sinusoidal sigma weight residual 147.00 81.29 65.71 1 8.00e+00 1.56e-02 8.83e+01 ... (remaining 71853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.132: 19881 0.132 - 0.265: 4149 0.265 - 0.397: 52 0.397 - 0.529: 22 0.529 - 0.661: 12 Chirality restraints: 24116 Sorted by residual: chirality pdb=" C3' A 11436 " pdb=" C4' A 11436 " pdb=" O3' A 11436 " pdb=" C2' A 11436 " both_signs ideal model delta sigma weight residual False -2.74 -2.08 -0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" C3' G 1 407 " pdb=" C4' G 1 407 " pdb=" O3' G 1 407 " pdb=" C2' G 1 407 " both_signs ideal model delta sigma weight residual False -2.74 -2.09 -0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" C3' A 12704 " pdb=" C4' A 12704 " pdb=" O3' A 12704 " pdb=" C2' A 12704 " both_signs ideal model delta sigma weight residual False -2.74 -2.12 -0.62 2.00e-01 2.50e+01 9.63e+00 ... (remaining 24113 not shown) Planarity restraints: 11934 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 255 " -0.066 5.00e-02 4.00e+02 1.00e-01 1.61e+01 pdb=" N PRO B 256 " 0.173 5.00e-02 4.00e+02 pdb=" CA PRO B 256 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 256 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A 11961 " -0.041 2.00e-02 2.50e+03 1.74e-02 8.37e+00 pdb=" N9 A 11961 " 0.036 2.00e-02 2.50e+03 pdb=" C8 A 11961 " 0.004 2.00e-02 2.50e+03 pdb=" N7 A 11961 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A 11961 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A 11961 " -0.009 2.00e-02 2.50e+03 pdb=" N6 A 11961 " -0.008 2.00e-02 2.50e+03 pdb=" N1 A 11961 " -0.005 2.00e-02 2.50e+03 pdb=" C2 A 11961 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A 11961 " 0.012 2.00e-02 2.50e+03 pdb=" C4 A 11961 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 11920 " -0.037 2.00e-02 2.50e+03 1.73e-02 8.23e+00 pdb=" N9 A 11920 " 0.042 2.00e-02 2.50e+03 pdb=" C8 A 11920 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A 11920 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A 11920 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A 11920 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A 11920 " -0.009 2.00e-02 2.50e+03 pdb=" N1 A 11920 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A 11920 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A 11920 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A 11920 " 0.004 2.00e-02 2.50e+03 ... (remaining 11931 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 16 1.99 - 2.72: 9141 2.72 - 3.44: 148013 3.44 - 4.17: 370193 4.17 - 4.90: 527105 Nonbonded interactions: 1054468 Sorted by model distance: nonbonded pdb=" CD2 LEU d 117 " pdb=" NH2 ARG p 54 " model vdw 1.261 3.540 nonbonded pdb=" OP2 A 4 95 " pdb=" NH1 ARG i 75 " model vdw 1.612 2.520 nonbonded pdb=" OP1 C 12899 " pdb=" O VAL Z 56 " model vdw 1.821 3.040 nonbonded pdb=" OP1 C 11039 " pdb=" NH2 ARG P 10 " model vdw 1.845 2.520 nonbonded pdb=" O ASN I 14 " pdb=" NH2 ARG I 128 " model vdw 1.866 2.520 ... (remaining 1054463 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 15.250 Check model and map are aligned: 1.390 Set scattering table: 0.820 Process input model: 380.210 Find NCS groups from input model: 2.460 Set up NCS constraints: 0.280 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: 0.010 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 405.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 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 : 0.006 0.063 130701 Z= 0.398 Angle : 1.070 15.386 192312 Z= 0.718 Chirality : 0.093 0.661 24116 Planarity : 0.004 0.100 11934 Dihedral : 17.433 179.694 60270 Min Nonbonded Distance : 1.261 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 1.54 % Allowed : 7.13 % Favored : 91.33 % Rotamer Outliers : 4.74 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.09), residues: 6041 helix: -2.49 (0.09), residues: 1909 sheet: -2.71 (0.16), residues: 786 loop : -2.16 (0.09), residues: 3346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12082 Ramachandran restraints generated. 6041 Oldfield, 0 Emsley, 6041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12082 Ramachandran restraints generated. 6041 Oldfield, 0 Emsley, 6041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2202 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 1950 time to evaluate : 6.365 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 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: 252 outliers final: 77 residues processed: 2100 average time/residue: 1.3118 time to fit residues: 4424.6175 Evaluate side-chains 1400 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 1323 time to evaluate : 6.331 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 77 outliers final: 1 residues processed: 77 average time/residue: 0.9336 time to fit residues: 138.8618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 789 optimal weight: 6.9990 chunk 708 optimal weight: 8.9990 chunk 393 optimal weight: 0.7980 chunk 242 optimal weight: 10.0000 chunk 478 optimal weight: 2.9990 chunk 378 optimal weight: 4.9990 chunk 732 optimal weight: 3.9990 chunk 283 optimal weight: 10.0000 chunk 445 optimal weight: 4.9990 chunk 545 optimal weight: 6.9990 chunk 849 optimal weight: 3.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS A 209 HIS B 55 HIS B 68 HIS ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 HIS B 260 GLN B 268 GLN B 317 ASN C 50 GLN C 318 GLN C 353 GLN D 130 HIS D 225 GLN D 247 HIS E 174 GLN E 185 ASN E 189 HIS F 130 ASN F 141 GLN F 156 GLN F 178 GLN F 251 ASN G 89 ASN G 99 GLN G 102 GLN G 124 GLN H 103 ASN I 59 GLN I 86 HIS I 133 GLN I 144 ASN I 185 GLN J 40 GLN J 44 GLN ** J 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 137 ASN J 141 HIS K 32 GLN M 37 HIS M 124 GLN O 20 GLN O 86 GLN O 124 GLN O 143 ASN O 151 HIS O 159 GLN P 45 ASN Q 74 HIS Q 120 HIS Q 129 ASN Q 133 ASN R 13 GLN S 58 HIS T 63 ASN W 48 HIS W 135 ASN W 161 ASN X 63 HIS X 99 HIS Y 78 HIS Z 60 HIS a 17 HIS b 77 ASN c 23 HIS c 64 ASN d 56 ASN d 91 ASN d 100 HIS ** d 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 93 ASN f 10 HIS ** f 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 112 GLN i 19 HIS j 65 GLN k 43 HIS l 87 GLN n 20 HIS n 23 HIS n 38 GLN n 47 GLN n 53 GLN p 48 GLN p 55 HIS p 59 ASN p 82 GLN p 123 ASN Total number of N/Q/H flips: 84 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 130701 Z= 0.338 Angle : 0.733 14.119 192312 Z= 0.379 Chirality : 0.044 0.359 24116 Planarity : 0.006 0.065 11934 Dihedral : 15.727 179.673 47125 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.63 % Allowed : 5.20 % Favored : 94.17 % Rotamer Outliers : 5.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.09), residues: 6041 helix: -0.86 (0.10), residues: 1959 sheet: -2.17 (0.15), residues: 868 loop : -1.80 (0.10), residues: 3214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12082 Ramachandran restraints generated. 6041 Oldfield, 0 Emsley, 6041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12082 Ramachandran restraints generated. 6041 Oldfield, 0 Emsley, 6041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1726 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 1458 time to evaluate : 6.361 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 outliers start: 268 outliers final: 156 residues processed: 1619 average time/residue: 1.1874 time to fit residues: 3145.1022 Evaluate side-chains 1452 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1296 time to evaluate : 5.681 Switching outliers to nearest non-outliers outliers start: 156 outliers final: 0 residues processed: 156 average time/residue: 0.8893 time to fit residues: 261.9396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 471 optimal weight: 10.0000 chunk 263 optimal weight: 8.9990 chunk 706 optimal weight: 0.6980 chunk 578 optimal weight: 2.9990 chunk 234 optimal weight: 8.9990 chunk 850 optimal weight: 4.9990 chunk 918 optimal weight: 0.0980 chunk 757 optimal weight: 0.6980 chunk 843 optimal weight: 1.9990 chunk 289 optimal weight: 10.0000 chunk 682 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 GLN E 88 GLN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN E 185 ASN G 72 GLN G 219 GLN I 133 GLN ** J 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 146 GLN L 62 GLN L 89 ASN L 90 GLN L 102 GLN N 265 GLN O 30 HIS O 34 GLN O 103 ASN ** O 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 127 ASN U 83 GLN a 42 ASN c 88 ASN d 100 HIS d 116 GLN ** f 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 65 GLN g 99 GLN j 65 GLN l 87 GLN n 47 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 130701 Z= 0.164 Angle : 0.584 14.617 192312 Z= 0.306 Chirality : 0.036 0.285 24116 Planarity : 0.005 0.067 11934 Dihedral : 15.319 179.713 47125 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.02 % Favored : 94.42 % Rotamer Outliers : 2.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.10), residues: 6041 helix: -0.02 (0.11), residues: 1979 sheet: -1.83 (0.15), residues: 908 loop : -1.51 (0.10), residues: 3154 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12082 Ramachandran restraints generated. 6041 Oldfield, 0 Emsley, 6041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12082 Ramachandran restraints generated. 6041 Oldfield, 0 Emsley, 6041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1534 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1396 time to evaluate : 6.351 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 outliers start: 138 outliers final: 50 residues processed: 1472 average time/residue: 1.3041 time to fit residues: 3176.0043 Evaluate side-chains 1310 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 1260 time to evaluate : 6.151 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.9684 time to fit residues: 96.5855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 840 optimal weight: 3.9990 chunk 639 optimal weight: 0.9980 chunk 441 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 405 optimal weight: 5.9990 chunk 571 optimal weight: 1.9990 chunk 853 optimal weight: 1.9990 chunk 903 optimal weight: 9.9990 chunk 446 optimal weight: 10.0000 chunk 809 optimal weight: 10.0000 chunk 243 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 ASN E 185 ASN F 233 HIS G 54 GLN G 72 GLN G 80 GLN I 73 ASN I 133 GLN J 108 GLN ** J 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 141 HIS K 39 GLN K 65 ASN K 109 ASN L 89 ASN L 90 GLN M 37 HIS ** O 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 HIS R 127 ASN U 76 HIS c 88 ASN e 8 GLN ** f 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 20 GLN g 65 GLN ** g 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 33 GLN j 65 GLN l 87 GLN n 53 GLN ** p 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 130701 Z= 0.290 Angle : 0.643 14.978 192312 Z= 0.331 Chirality : 0.039 0.351 24116 Planarity : 0.005 0.063 11934 Dihedral : 15.327 179.637 47125 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.79 % Favored : 93.64 % Rotamer Outliers : 3.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.10), residues: 6041 helix: 0.09 (0.11), residues: 1993 sheet: -1.61 (0.16), residues: 853 loop : -1.44 (0.10), residues: 3195 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12082 Ramachandran restraints generated. 6041 Oldfield, 0 Emsley, 6041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12082 Ramachandran restraints generated. 6041 Oldfield, 0 Emsley, 6041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1515 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1334 time to evaluate : 6.328 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 outliers start: 181 outliers final: 102 residues processed: 1418 average time/residue: 1.2391 time to fit residues: 2905.5734 Evaluate side-chains 1360 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1258 time to evaluate : 6.364 Switching outliers to nearest non-outliers outliers start: 102 outliers final: 0 residues processed: 102 average time/residue: 0.9598 time to fit residues: 186.1523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 752 optimal weight: 8.9990 chunk 513 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 672 optimal weight: 0.9990 chunk 372 optimal weight: 0.9990 chunk 771 optimal weight: 10.0000 chunk 624 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 461 optimal weight: 8.9990 chunk 811 optimal weight: 9.9990 chunk 228 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN E 185 ASN F 156 GLN G 72 GLN G 80 GLN I 73 ASN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 133 GLN J 110 HIS ** J 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 18 GLN K 149 ASN L 89 ASN L 90 GLN ** O 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 127 ASN W 161 ASN a 11 ASN ** b 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 116 GLN ** f 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 65 GLN l 87 GLN n 47 GLN p 15 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 130701 Z= 0.264 Angle : 0.621 14.166 192312 Z= 0.320 Chirality : 0.038 0.331 24116 Planarity : 0.005 0.059 11934 Dihedral : 15.265 179.971 47125 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.81 % Favored : 93.66 % Rotamer Outliers : 2.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.10), residues: 6041 helix: 0.22 (0.11), residues: 1992 sheet: -1.38 (0.17), residues: 842 loop : -1.41 (0.10), residues: 3207 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12082 Ramachandran restraints generated. 6041 Oldfield, 0 Emsley, 6041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12082 Ramachandran restraints generated. 6041 Oldfield, 0 Emsley, 6041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1430 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1297 time to evaluate : 6.557 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: 133 outliers final: 66 residues processed: 1370 average time/residue: 1.2590 time to fit residues: 2851.2982 Evaluate side-chains 1308 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 1242 time to evaluate : 6.358 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 0 residues processed: 66 average time/residue: 0.9611 time to fit residues: 124.9594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 304 optimal weight: 10.0000 chunk 813 optimal weight: 1.9990 chunk 178 optimal weight: 6.9990 chunk 530 optimal weight: 2.9990 chunk 223 optimal weight: 10.0000 chunk 904 optimal weight: 10.0000 chunk 750 optimal weight: 0.9990 chunk 418 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 299 optimal weight: 7.9990 chunk 474 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 GLN E 185 ASN G 72 GLN G 80 GLN I 73 ASN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 133 GLN ** J 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** O 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 127 ASN S 112 ASN ** b 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 88 ASN ** f 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 65 GLN l 87 GLN n 47 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 130701 Z= 0.289 Angle : 0.637 13.773 192312 Z= 0.326 Chirality : 0.039 0.294 24116 Planarity : 0.005 0.063 11934 Dihedral : 15.267 179.940 47125 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.24 % Favored : 93.23 % Rotamer Outliers : 2.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.10), residues: 6041 helix: 0.23 (0.11), residues: 1992 sheet: -1.25 (0.17), residues: 841 loop : -1.38 (0.10), residues: 3208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12082 Ramachandran restraints generated. 6041 Oldfield, 0 Emsley, 6041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12082 Ramachandran restraints generated. 6041 Oldfield, 0 Emsley, 6041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1446 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1309 time to evaluate : 6.448 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 outliers start: 137 outliers final: 91 residues processed: 1370 average time/residue: 1.2008 time to fit residues: 2705.4056 Evaluate side-chains 1349 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1258 time to evaluate : 6.379 Switching outliers to nearest non-outliers outliers start: 91 outliers final: 0 residues processed: 91 average time/residue: 0.8555 time to fit residues: 152.6783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 872 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 515 optimal weight: 0.2980 chunk 660 optimal weight: 1.9990 chunk 511 optimal weight: 1.9990 chunk 761 optimal weight: 0.9980 chunk 505 optimal weight: 7.9990 chunk 901 optimal weight: 3.9990 chunk 563 optimal weight: 5.9990 chunk 549 optimal weight: 1.9990 chunk 416 optimal weight: 0.2980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN C 338 ASN E 185 ASN F 156 GLN G 72 GLN G 80 GLN I 73 ASN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 133 GLN ** J 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 ASN L 90 GLN ** O 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 133 ASN R 127 ASN ** b 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 20 GLN ** g 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 65 GLN l 87 GLN n 53 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.075 130701 Z= 0.150 Angle : 0.575 13.077 192312 Z= 0.297 Chirality : 0.035 0.283 24116 Planarity : 0.005 0.067 11934 Dihedral : 15.150 179.984 47125 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.41 % Favored : 94.11 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.10), residues: 6041 helix: 0.46 (0.12), residues: 1999 sheet: -1.07 (0.17), residues: 841 loop : -1.31 (0.10), residues: 3201 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12082 Ramachandran restraints generated. 6041 Oldfield, 0 Emsley, 6041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12082 Ramachandran restraints generated. 6041 Oldfield, 0 Emsley, 6041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1369 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1300 time to evaluate : 6.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 40 residues processed: 1334 average time/residue: 1.2292 time to fit residues: 2694.5892 Evaluate side-chains 1282 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1242 time to evaluate : 5.853 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.9169 time to fit residues: 75.2560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 557 optimal weight: 9.9990 chunk 359 optimal weight: 10.0000 chunk 538 optimal weight: 8.9990 chunk 271 optimal weight: 6.9990 chunk 177 optimal weight: 8.9990 chunk 174 optimal weight: 7.9990 chunk 572 optimal weight: 0.7980 chunk 613 optimal weight: 0.1980 chunk 445 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 708 optimal weight: 5.9990 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 338 ASN C 353 GLN E 185 ASN G 72 GLN G 80 GLN ** G 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 133 GLN ** J 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 21 GLN R 127 ASN S 82 ASN Y 127 ASN Z 60 HIS ** b 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 88 ASN ** f 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 79 ASN l 87 GLN n 47 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.071 130701 Z= 0.351 Angle : 0.677 13.360 192312 Z= 0.344 Chirality : 0.040 0.290 24116 Planarity : 0.006 0.063 11934 Dihedral : 15.283 179.767 47125 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.74 % Favored : 92.75 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.10), residues: 6041 helix: 0.28 (0.12), residues: 1995 sheet: -1.19 (0.17), residues: 858 loop : -1.42 (0.10), residues: 3188 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12082 Ramachandran restraints generated. 6041 Oldfield, 0 Emsley, 6041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12082 Ramachandran restraints generated. 6041 Oldfield, 0 Emsley, 6041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1365 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1267 time to evaluate : 6.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 98 outliers final: 64 residues processed: 1315 average time/residue: 1.2377 time to fit residues: 2674.0298 Evaluate side-chains 1298 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 1234 time to evaluate : 6.403 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 0 residues processed: 64 average time/residue: 0.8960 time to fit residues: 115.1895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 819 optimal weight: 1.9990 chunk 863 optimal weight: 0.3980 chunk 787 optimal weight: 7.9990 chunk 839 optimal weight: 2.9990 chunk 505 optimal weight: 4.9990 chunk 365 optimal weight: 0.8980 chunk 659 optimal weight: 4.9990 chunk 257 optimal weight: 10.0000 chunk 758 optimal weight: 5.9990 chunk 794 optimal weight: 0.4980 chunk 836 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN C 338 ASN C 353 GLN E 185 ASN F 130 ASN F 156 GLN G 72 GLN G 80 GLN G 225 GLN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 133 GLN ** J 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 149 ASN L 90 GLN Q 133 ASN R 127 ASN R 148 GLN V 49 GLN ** f 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 99 GLN ** k 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 87 GLN n 9 ASN n 47 GLN p 9 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 130701 Z= 0.157 Angle : 0.566 12.670 192312 Z= 0.292 Chirality : 0.034 0.270 24116 Planarity : 0.004 0.058 11934 Dihedral : 15.030 179.986 47125 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.66 % Favored : 93.79 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.10), residues: 6041 helix: 0.56 (0.12), residues: 1995 sheet: -1.00 (0.17), residues: 862 loop : -1.29 (0.10), residues: 3184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12082 Ramachandran restraints generated. 6041 Oldfield, 0 Emsley, 6041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12082 Ramachandran restraints generated. 6041 Oldfield, 0 Emsley, 6041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1326 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 1285 time to evaluate : 6.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 24 residues processed: 1303 average time/residue: 1.3160 time to fit residues: 2839.0253 Evaluate side-chains 1255 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1231 time to evaluate : 6.457 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 1.0694 time to fit residues: 55.8323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 551 optimal weight: 5.9990 chunk 888 optimal weight: 0.9980 chunk 542 optimal weight: 0.8980 chunk 421 optimal weight: 8.9990 chunk 617 optimal weight: 3.9990 chunk 931 optimal weight: 7.9990 chunk 857 optimal weight: 5.9990 chunk 741 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 572 optimal weight: 5.9990 chunk 454 optimal weight: 6.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 ASN C 338 ASN D 198 HIS E 185 ASN G 72 GLN G 80 GLN I 133 GLN ** J 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 127 ASN ** b 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 87 GLN p 9 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 130701 Z= 0.334 Angle : 0.665 15.247 192312 Z= 0.338 Chirality : 0.039 0.288 24116 Planarity : 0.005 0.059 11934 Dihedral : 15.190 179.893 47125 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.74 % Favored : 92.70 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.10), residues: 6041 helix: 0.33 (0.12), residues: 2002 sheet: -1.12 (0.17), residues: 868 loop : -1.40 (0.10), residues: 3171 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12082 Ramachandran restraints generated. 6041 Oldfield, 0 Emsley, 6041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12082 Ramachandran restraints generated. 6041 Oldfield, 0 Emsley, 6041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1294 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1257 time to evaluate : 6.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 27 residues processed: 1268 average time/residue: 1.3018 time to fit residues: 2711.8004 Evaluate side-chains 1261 residues out of total 5327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 1234 time to evaluate : 6.347 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.9238 time to fit residues: 54.5488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 935 random chunks: chunk 589 optimal weight: 1.9990 chunk 790 optimal weight: 8.9990 chunk 227 optimal weight: 20.0000 chunk 683 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 206 optimal weight: 10.0000 chunk 742 optimal weight: 8.9990 chunk 310 optimal weight: 10.0000 chunk 762 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 HIS ** B 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN E 185 ASN ** F 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 GLN G 225 GLN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 133 GLN ** J 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** M 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 50 ASN d 123 ASN ** g 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 87 GLN n 47 GLN n 53 GLN p 9 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.136702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.109403 restraints weight = 167978.307| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 0.95 r_work: 0.2980 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.106 130701 Z= 0.532 Angle : 0.833 15.202 192312 Z= 0.417 Chirality : 0.048 0.381 24116 Planarity : 0.007 0.089 11934 Dihedral : 15.700 179.772 47125 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.68 % Favored : 91.76 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.10), residues: 6041 helix: -0.20 (0.11), residues: 2001 sheet: -1.33 (0.17), residues: 876 loop : -1.70 (0.10), residues: 3164 =============================================================================== Job complete usr+sys time: 40049.48 seconds wall clock time: 695 minutes 36.62 seconds (41736.62 seconds total)