Starting phenix.real_space_refine on Fri Apr 12 05:30:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bhp_12189/04_2024/7bhp_12189.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bhp_12189/04_2024/7bhp_12189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bhp_12189/04_2024/7bhp_12189.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bhp_12189/04_2024/7bhp_12189.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bhp_12189/04_2024/7bhp_12189.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bhp_12189/04_2024/7bhp_12189.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 3953 5.49 5 Mg 41 5.21 5 S 237 5.16 5 C 70674 2.51 5 N 25680 2.21 5 O 36223 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "LA ARG 28": "NH1" <-> "NH2" Residue "LA ASP 33": "OD1" <-> "OD2" Residue "LA PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA GLU 36": "OE1" <-> "OE2" Residue "LA TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA ARG 68": "NH1" <-> "NH2" Residue "LA PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA GLU 118": "OE1" <-> "OE2" Residue "LA ARG 198": "NH1" <-> "NH2" Residue "LA ARG 245": "NH1" <-> "NH2" Residue "LB ARG 10": "NH1" <-> "NH2" Residue "LB PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB GLU 74": "OE1" <-> "OE2" Residue "LB TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB ARG 97": "NH1" <-> "NH2" Residue "LB GLU 113": "OE1" <-> "OE2" Residue "LB PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB GLU 182": "OE1" <-> "OE2" Residue "LB ASP 195": "OD1" <-> "OD2" Residue "LB ARG 198": "NH1" <-> "NH2" Residue "LB ASP 218": "OD1" <-> "OD2" Residue "LB TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB ARG 268": "NH1" <-> "NH2" Residue "LB TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB ASP 295": "OD1" <-> "OD2" Residue "LB TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB ASP 311": "OD1" <-> "OD2" Residue "LB GLU 325": "OE1" <-> "OE2" Residue "LB ARG 358": "NH1" <-> "NH2" Residue "LB ARG 378": "NH1" <-> "NH2" Residue "LC ARG 49": "NH1" <-> "NH2" Residue "LC TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC ARG 71": "NH1" <-> "NH2" Residue "LC ARG 78": "NH1" <-> "NH2" Residue "LC ARG 100": "NH1" <-> "NH2" Residue "LC ARG 110": "NH1" <-> "NH2" Residue "LC GLU 146": "OE1" <-> "OE2" Residue "LC ARG 204": "NH1" <-> "NH2" Residue "LC ARG 205": "NH1" <-> "NH2" Residue "LC PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC PHE 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC ARG 306": "NH1" <-> "NH2" Residue "LC ARG 311": "NH1" <-> "NH2" Residue "LC ARG 323": "NH1" <-> "NH2" Residue "LC TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC ASP 352": "OD1" <-> "OD2" Residue "LD PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD ARG 15": "NH1" <-> "NH2" Residue "LD ARG 23": "NH1" <-> "NH2" Residue "LD TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD ARG 33": "NH1" <-> "NH2" Residue "LD ARG 58": "NH1" <-> "NH2" Residue "LD TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD ARG 108": "NH1" <-> "NH2" Residue "LD TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD ARG 179": "NH1" <-> "NH2" Residue "LD ASP 184": "OD1" <-> "OD2" Residue "LD GLU 186": "OE1" <-> "OE2" Residue "LD TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD GLU 260": "OE1" <-> "OE2" Residue "LD ARG 265": "NH1" <-> "NH2" Residue "LE TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LE ARG 156": "NH1" <-> "NH2" Residue "LE ARG 161": "NH1" <-> "NH2" Residue "LE ARG 188": "NH1" <-> "NH2" Residue "LE TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LE TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LE GLU 241": "OE1" <-> "OE2" Residue "LE ASP 254": "OD1" <-> "OD2" Residue "LF GLU 27": "OE1" <-> "OE2" Residue "LF ARG 43": "NH1" <-> "NH2" Residue "LF ARG 46": "NH1" <-> "NH2" Residue "LF ARG 94": "NH1" <-> "NH2" Residue "LF TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LF ARG 200": "NH1" <-> "NH2" Residue "LF ASP 232": "OD1" <-> "OD2" Residue "LF ARG 245": "NH1" <-> "NH2" Residue "LG PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG ARG 73": "NH1" <-> "NH2" Residue "LG ARG 89": "NH1" <-> "NH2" Residue "LG ARG 113": "NH1" <-> "NH2" Residue "LG GLU 148": "OE1" <-> "OE2" Residue "LG ARG 189": "NH1" <-> "NH2" Residue "LG TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG ARG 234": "NH1" <-> "NH2" Residue "LH ARG 23": "NH1" <-> "NH2" Residue "LH ARG 89": "NH1" <-> "NH2" Residue "LH ARG 93": "NH1" <-> "NH2" Residue "LH TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LH PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LH TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LI ARG 4": "NH1" <-> "NH2" Residue "LI ARG 7": "NH1" <-> "NH2" Residue "LI ARG 24": "NH1" <-> "NH2" Residue "LI PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LI ASP 35": "OD1" <-> "OD2" Residue "LI GLU 45": "OE1" <-> "OE2" Residue "LI ASP 55": "OD1" <-> "OD2" Residue "LI GLU 66": "OE1" <-> "OE2" Residue "LI ARG 69": "NH1" <-> "NH2" Residue "LI ARG 98": "NH1" <-> "NH2" Residue "LI ARG 116": "NH1" <-> "NH2" Residue "LI ARG 153": "NH1" <-> "NH2" Residue "LI ARG 162": "NH1" <-> "NH2" Residue "LI ASP 179": "OD1" <-> "OD2" Residue "LI ARG 210": "NH1" <-> "NH2" Residue "LJ ARG 35": "NH1" <-> "NH2" Residue "LJ ARG 63": "NH1" <-> "NH2" Residue "LJ GLU 93": "OE1" <-> "OE2" Residue "LJ ARG 95": "NH1" <-> "NH2" Residue "LJ PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LJ PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LJ ARG 146": "NH1" <-> "NH2" Residue "LJ GLU 161": "OE1" <-> "OE2" Residue "LL ARG 21": "NH1" <-> "NH2" Residue "LL ARG 31": "NH1" <-> "NH2" Residue "LL ARG 44": "NH1" <-> "NH2" Residue "LL ARG 65": "NH1" <-> "NH2" Residue "LL PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LL ARG 102": "NH1" <-> "NH2" Residue "LL ARG 116": "NH1" <-> "NH2" Residue "LL GLU 119": "OE1" <-> "OE2" Residue "LL ASP 138": "OD1" <-> "OD2" Residue "LL GLU 143": "OE1" <-> "OE2" Residue "LL ARG 158": "NH1" <-> "NH2" Residue "LM TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LM ASP 32": "OD1" <-> "OD2" Residue "LM ASP 59": "OD1" <-> "OD2" Residue "LM ARG 98": "NH1" <-> "NH2" Residue "LM ASP 106": "OD1" <-> "OD2" Residue "LM ARG 109": "NH1" <-> "NH2" Residue "LM ARG 119": "NH1" <-> "NH2" Residue "LM ARG 121": "NH1" <-> "NH2" Residue "LN ARG 20": "NH1" <-> "NH2" Residue "LN ARG 50": "NH1" <-> "NH2" Residue "LN TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN ARG 65": "NH1" <-> "NH2" Residue "LN ARG 67": "NH1" <-> "NH2" Residue "LN ARG 96": "NH1" <-> "NH2" Residue "LN GLU 104": "OE1" <-> "OE2" Residue "LN TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN ARG 169": "NH1" <-> "NH2" Residue "LN ARG 189": "NH1" <-> "NH2" Residue "LN ARG 194": "NH1" <-> "NH2" Residue "LO ARG 37": "NH1" <-> "NH2" Residue "LO ARG 78": "NH1" <-> "NH2" Residue "LO ARG 128": "NH1" <-> "NH2" Residue "LO ARG 140": "NH1" <-> "NH2" Residue "LO TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LP ARG 3": "NH1" <-> "NH2" Residue "LP ARG 30": "NH1" <-> "NH2" Residue "LP ARG 61": "NH1" <-> "NH2" Residue "LP ARG 62": "NH1" <-> "NH2" Residue "LP PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LP TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LQ ARG 14": "NH1" <-> "NH2" Residue "LQ PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LQ ARG 37": "NH1" <-> "NH2" Residue "LQ ARG 55": "NH1" <-> "NH2" Residue "LQ ARG 91": "NH1" <-> "NH2" Residue "LQ ASP 124": "OD1" <-> "OD2" Residue "LQ GLU 147": "OE1" <-> "OE2" Residue "LQ TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LQ ARG 180": "NH1" <-> "NH2" Residue "LQ ARG 181": "NH1" <-> "NH2" Residue "LQ TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LR ARG 38": "NH1" <-> "NH2" Residue "LR ARG 52": "NH1" <-> "NH2" Residue "LR ARG 74": "NH1" <-> "NH2" Residue "LR GLU 91": "OE1" <-> "OE2" Residue "LR ARG 117": "NH1" <-> "NH2" Residue "LR TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LR PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LR ARG 151": "NH1" <-> "NH2" Residue "LS ARG 31": "NH1" <-> "NH2" Residue "LS ARG 43": "NH1" <-> "NH2" Residue "LS GLU 69": "OE1" <-> "OE2" Residue "LS PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS ARG 83": "NH1" <-> "NH2" Residue "LS ASP 85": "OD1" <-> "OD2" Residue "LS TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS ARG 111": "NH1" <-> "NH2" Residue "LS ARG 118": "NH1" <-> "NH2" Residue "LS PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LT ARG 8": "NH1" <-> "NH2" Residue "LT TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LT ARG 17": "NH1" <-> "NH2" Residue "LT TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LT ARG 130": "NH1" <-> "NH2" Residue "LT ARG 136": "NH1" <-> "NH2" Residue "LT PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LT GLU 147": "OE1" <-> "OE2" Residue "LT PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LU GLU 30": "OE1" <-> "OE2" Residue "LU PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LU GLU 45": "OE1" <-> "OE2" Residue "LU ARG 46": "NH1" <-> "NH2" Residue "LU TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LU PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LW PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LW TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LX ARG 53": "NH1" <-> "NH2" Residue "LX ARG 139": "NH1" <-> "NH2" Residue "LY ARG 27": "NH1" <-> "NH2" Residue "LY ARG 87": "NH1" <-> "NH2" Residue "LZ PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LZ TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LZ TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LZ ARG 65": "NH1" <-> "NH2" Residue "LZ ARG 84": "NH1" <-> "NH2" Residue "LZ TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LZ ASP 88": "OD1" <-> "OD2" Residue "LZ PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LZ GLU 119": "OE1" <-> "OE2" Residue "La ARG 9": "NH1" <-> "NH2" Residue "La ARG 21": "NH1" <-> "NH2" Residue "La PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "La ARG 65": "NH1" <-> "NH2" Residue "La PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "La PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "La ARG 131": "NH1" <-> "NH2" Residue "La GLU 134": "OE1" <-> "OE2" Residue "Lb ARG 14": "NH1" <-> "NH2" Residue "Lb ARG 18": "NH1" <-> "NH2" Residue "Lb ARG 28": "NH1" <-> "NH2" Residue "Lc TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lc ARG 39": "NH1" <-> "NH2" Residue "Lc GLU 61": "OE1" <-> "OE2" Residue "Lc TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lc TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ld GLU 19": "OE1" <-> "OE2" Residue "Ld ARG 90": "NH1" <-> "NH2" Residue "Ld GLU 94": "OE1" <-> "OE2" Residue "Ld ASP 97": "OD1" <-> "OD2" Residue "Ld PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Le PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Le ARG 39": "NH1" <-> "NH2" Residue "Le PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Le GLU 86": "OE1" <-> "OE2" Residue "Le TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Le GLU 113": "OE1" <-> "OE2" Residue "Le ARG 128": "NH1" <-> "NH2" Residue "Lf ARG 36": "NH1" <-> "NH2" Residue "Lf TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lf ARG 89": "NH1" <-> "NH2" Residue "Lg TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lg TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lg ARG 60": "NH1" <-> "NH2" Residue "Lg GLU 98": "OE1" <-> "OE2" Residue "Lh ARG 7": "NH1" <-> "NH2" Residue "Lh GLU 27": "OE1" <-> "OE2" Residue "Lh ARG 56": "NH1" <-> "NH2" Residue "Lh ASP 82": "OD1" <-> "OD2" Residue "Lh ARG 94": "NH1" <-> "NH2" Residue "Li ARG 25": "NH1" <-> "NH2" Residue "Li ARG 45": "NH1" <-> "NH2" Residue "Li GLU 54": "OE1" <-> "OE2" Residue "Li GLU 59": "OE1" <-> "OE2" Residue "Li ARG 68": "NH1" <-> "NH2" Residue "Li ARG 76": "NH1" <-> "NH2" Residue "Li ARG 85": "NH1" <-> "NH2" Residue "Li ARG 98": "NH1" <-> "NH2" Residue "Lj ARG 20": "NH1" <-> "NH2" Residue "Lj ARG 45": "NH1" <-> "NH2" Residue "Lj ARG 55": "NH1" <-> "NH2" Residue "Lj ARG 56": "NH1" <-> "NH2" Residue "Lj ARG 72": "NH1" <-> "NH2" Residue "Lj PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lj ARG 79": "NH1" <-> "NH2" Residue "Lk ARG 3": "NH1" <-> "NH2" Residue "Lk PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lk ASP 19": "OD1" <-> "OD2" Residue "Lk ASP 30": "OD1" <-> "OD2" Residue "Lk PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lk ARG 40": "NH1" <-> "NH2" Residue "Lk ASP 49": "OD1" <-> "OD2" Residue "Ll PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ll ARG 21": "NH1" <-> "NH2" Residue "Ll ARG 28": "NH1" <-> "NH2" Residue "Lm TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lm ARG 97": "NH1" <-> "NH2" Residue "Lm ARG 106": "NH1" <-> "NH2" Residue "Lm ARG 111": "NH1" <-> "NH2" Residue "Lo ARG 40": "NH1" <-> "NH2" Residue "Lo TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lo PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lp ARG 17": "NH1" <-> "NH2" Residue "Lp ARG 49": "NH1" <-> "NH2" Residue "Lr ARG 35": "NH1" <-> "NH2" Residue "Lr ARG 39": "NH1" <-> "NH2" Residue "Lr ASP 56": "OD1" <-> "OD2" Residue "Lr ARG 71": "NH1" <-> "NH2" Residue "Lr TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lr ARG 112": "NH1" <-> "NH2" Residue "Lr ARG 113": "NH1" <-> "NH2" Residue "A TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 67": "OE1" <-> "OE2" Residue "A PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A ARG 281": "NH1" <-> "NH2" Residue "A TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A GLU 348": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 136812 Number of models: 1 Model: "" Number of chains: 56 Chain: "L5" Number of atoms: 78119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3644, 78119 Classifications: {'RNA': 3644} Modifications used: {'5*END': 1, 'rna2p_pur': 362, 'rna2p_pyr': 238, 'rna3p_pur': 1628, 'rna3p_pyr': 1416} Link IDs: {'rna2p': 599, 'rna3p': 3044} Chain breaks: 17 Chain: "L7" Number of atoms: 2558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2558 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 55, 'rna3p_pyr': 52} Link IDs: {'rna2p': 12, 'rna3p': 107} Chain: "L8" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3314 Classifications: {'RNA': 156} Modifications used: {'5*END': 1, 'rna2p_pur': 13, 'rna2p_pyr': 14, 'rna3p_pur': 63, 'rna3p_pyr': 66} Link IDs: {'rna2p': 27, 'rna3p': 128} Chain: "LA" Number of atoms: 1887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1887 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 232} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "LB" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3183 Classifications: {'peptide': 395} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 379} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "LC" Number of atoms: 2855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2855 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 340} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "LD" Number of atoms: 2354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2354 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 280} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "LE" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1777 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 205} Chain breaks: 2 Chain: "LF" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "LG" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1780 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 206} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "LH" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1518 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "LI" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1643 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 192} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "LJ" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1294 Classifications: {'peptide': 161} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 155} Chain breaks: 1 Chain: "LL" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1612 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 14, 'TRANS': 184} Chain: "LM" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1067 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain: "LN" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1701 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain: "LO" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1625 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 188} Chain: "LP" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1242 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "LQ" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1513 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain: "LR" Number of atoms: 1264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1264 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain: "LS" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1453 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 163} Chain: "LT" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1284 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 9, 'TRANS': 147} Chain: "LU" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 821 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 98} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "LW" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 350 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 2, 'TRANS': 39} Chain breaks: 1 Chain: "LX" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 946 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 108} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "LY" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1102 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "LZ" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1074 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain breaks: 1 Chain: "La" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1162 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "Lb" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 559 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "Lc" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 737 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain breaks: 1 Chain: "Ld" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 888 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "Le" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1043 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "Lf" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 870 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "Lg" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 821 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "Lh" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 995 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "Li" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 803 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "Lj" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 705 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "Lk" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "Ll" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 444 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Lm" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 429 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "Lo" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 862 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "Lp" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 558 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "Lr" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 980 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "A" Number of atoms: 2352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2352 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 308} Chain breaks: 10 Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 9, 'ASN:plan1': 3, 'HIS:plan': 2, 'GLU:plan': 11, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 122 Chain: "B" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 774 Classifications: {'RNA': 36} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 18, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 34} Chain breaks: 2 Chain: "L5" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Unusual residues: {' MG': 33} Classifications: {'undetermined': 33} Link IDs: {None: 32} Chain: "L7" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L8" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "Lj" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Ll" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Lm" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lo" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lp" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L5" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "L7" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "LI" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0MJS SG CYSLj 19 94.268 90.010 145.924 1.00 78.79 S ATOM A0MKK SG CYSLj 22 93.942 91.704 142.663 1.00 78.10 S ATOM A0MN3 SG CYSLj 34 93.720 93.798 145.945 1.00 70.44 S ATOM A0MNM SG CYSLj 37 90.965 91.993 144.970 1.00 75.84 S ATOM A0NW4 SG CYSLm 96 160.453 184.398 150.941 1.00100.53 S ATOM A0NZC SG CYSLm 110 163.375 183.723 148.075 1.00 99.01 S ATOM A0O0K SG CYSLm 115 161.644 182.863 147.487 1.00 96.09 S ATOM A0O62 SG CYSLo 12 51.828 173.891 122.386 1.00111.76 S ATOM A0OJR SG CYSLo 72 49.846 175.722 125.345 1.00116.24 S ATOM A0OKS SG CYSLo 77 47.682 174.088 123.803 1.00120.34 S ATOM A0P0G SG CYSLp 42 85.713 94.691 214.446 1.00106.93 S ATOM A0P3U SG CYSLp 57 86.399 94.855 211.232 1.00101.44 S ATOM A0P4A SG CYSLp 60 83.598 93.796 211.047 1.00109.18 S Time building chain proxies: 52.88, per 1000 atoms: 0.39 Number of scatterers: 136812 At special positions: 0 Unit cell: (231.34, 266.6, 256.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 237 16.00 P 3953 15.00 Mg 41 11.99 O 36223 8.00 N 25680 7.00 C 70674 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 63.48 Conformation dependent library (CDL) restraints added in 7.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNLj 101 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 37 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 34 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 19 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 22 " pdb=" ZNLm 201 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 96 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 115 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 110 " pdb=" ZNLo 201 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 77 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 72 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 12 " pdb=" ZNLp 101 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 60 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 57 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 42 " Number of angles added : 6 12630 Ramachandran restraints generated. 6315 Oldfield, 0 Emsley, 6315 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12006 Finding SS restraints... Secondary structure from input PDB file: 226 helices and 73 sheets defined 36.5% alpha, 13.3% beta 1140 base pairs and 1860 stacking pairs defined. Time for finding SS restraints: 49.64 Creating SS restraints... Processing helix chain 'LA' and resid 33 through 38 Processing helix chain 'LA' and resid 103 through 107 Processing helix chain 'LA' and resid 141 through 144 Processing helix chain 'LA' and resid 181 through 191 removed outlier: 3.595A pdb=" N ALALA 191 " --> pdb=" O HISLA 187 " (cutoff:3.500A) Processing helix chain 'LA' and resid 200 through 204 Processing helix chain 'LB' and resid 111 through 118 removed outlier: 3.599A pdb=" N ARGLB 117 " --> pdb=" O GLULB 113 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHELB 118 " --> pdb=" O CYSLB 114 " (cutoff:3.500A) Processing helix chain 'LB' and resid 132 through 137 removed outlier: 4.256A pdb=" N LYSLB 136 " --> pdb=" O LYSLB 132 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TRPLB 137 " --> pdb=" O TYRLB 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'LB' and resid 132 through 137' Processing helix chain 'LB' and resid 139 through 157 removed outlier: 4.053A pdb=" N LYSLB 148 " --> pdb=" O LYSLB 144 " (cutoff:3.500A) Processing helix chain 'LB' and resid 189 through 201 Processing helix chain 'LB' and resid 207 through 211 Processing helix chain 'LB' and resid 230 through 235 Processing helix chain 'LB' and resid 299 through 303 Processing helix chain 'LB' and resid 381 through 388 removed outlier: 3.952A pdb=" N LYSLB 385 " --> pdb=" O THRLB 381 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYSLB 386 " --> pdb=" O METLB 382 " (cutoff:3.500A) Processing helix chain 'LC' and resid 25 through 30 Processing helix chain 'LC' and resid 33 through 45 Processing helix chain 'LC' and resid 116 through 133 removed outlier: 3.762A pdb=" N LYSLC 120 " --> pdb=" O ASNLC 116 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARGLC 121 " --> pdb=" O THRLC 117 " (cutoff:3.500A) Processing helix chain 'LC' and resid 133 through 139 removed outlier: 3.533A pdb=" N VALLC 137 " --> pdb=" O LEULC 133 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N METLC 138 " --> pdb=" O PROLC 134 " (cutoff:3.500A) Processing helix chain 'LC' and resid 155 through 161 removed outlier: 3.907A pdb=" N VALLC 158 " --> pdb=" O GLULC 155 " (cutoff:3.500A) Processing helix chain 'LC' and resid 163 through 174 removed outlier: 3.560A pdb=" N LEULC 169 " --> pdb=" O LYSLC 165 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEULC 170 " --> pdb=" O GLULC 166 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEULC 171 " --> pdb=" O ALALC 167 " (cutoff:3.500A) Processing helix chain 'LC' and resid 176 through 184 Processing helix chain 'LC' and resid 191 through 198 removed outlier: 3.767A pdb=" N GLYLC 194 " --> pdb=" O ALALC 191 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYSLC 195 " --> pdb=" O GLYLC 192 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N METLC 196 " --> pdb=" O LYSLC 193 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASNLC 198 " --> pdb=" O LYSLC 195 " (cutoff:3.500A) Processing helix chain 'LC' and resid 216 through 221 Processing helix chain 'LC' and resid 236 through 241 Processing helix chain 'LC' and resid 254 through 259 Processing helix chain 'LC' and resid 259 through 265 removed outlier: 3.545A pdb=" N TYRLC 264 " --> pdb=" O LEULC 260 " (cutoff:3.500A) Processing helix chain 'LC' and resid 288 through 294 Processing helix chain 'LC' and resid 295 through 301 removed outlier: 3.830A pdb=" N ALALC 301 " --> pdb=" O GLULC 297 " (cutoff:3.500A) Processing helix chain 'LC' and resid 321 through 329 removed outlier: 3.878A pdb=" N METLC 325 " --> pdb=" O ASNLC 321 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYSLC 327 " --> pdb=" O ARGLC 323 " (cutoff:3.500A) Processing helix chain 'LC' and resid 330 through 358 removed outlier: 4.399A pdb=" N THRLC 334 " --> pdb=" O PROLC 330 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEULC 349 " --> pdb=" O ARGLC 345 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARGLC 350 " --> pdb=" O ASNLC 346 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VALLC 351 " --> pdb=" O HISLC 347 " (cutoff:3.500A) Processing helix chain 'LD' and resid 11 through 16 Processing helix chain 'LD' and resid 20 through 26 Processing helix chain 'LD' and resid 29 through 38 removed outlier: 4.002A pdb=" N ARGLD 35 " --> pdb=" O TYRLD 31 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEULD 36 " --> pdb=" O ALALD 32 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILELD 38 " --> pdb=" O LYSLD 34 " (cutoff:3.500A) Processing helix chain 'LD' and resid 94 through 112 removed outlier: 3.503A pdb=" N TYRLD 99 " --> pdb=" O TYRLD 95 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N CYSLD 100 " --> pdb=" O ALALD 96 " (cutoff:3.500A) Processing helix chain 'LD' and resid 157 through 171 removed outlier: 4.171A pdb=" N ASPLD 168 " --> pdb=" O LYSLD 164 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEULD 171 " --> pdb=" O VALLD 167 " (cutoff:3.500A) Processing helix chain 'LD' and resid 193 through 200 Processing helix chain 'LD' and resid 201 through 210 removed outlier: 3.514A pdb=" N ARGLD 209 " --> pdb=" O ALALD 205 " (cutoff:3.500A) Processing helix chain 'LD' and resid 216 through 223 Processing helix chain 'LD' and resid 223 through 228 Processing helix chain 'LD' and resid 234 through 248 removed outlier: 4.069A pdb=" N LYSLD 241 " --> pdb=" O GLULD 237 " (cutoff:3.500A) Processing helix chain 'LD' and resid 272 through 291 Processing helix chain 'LE' and resid 58 through 66 Processing helix chain 'LE' and resid 132 through 136 Processing helix chain 'LE' and resid 190 through 192 No H-bonds generated for 'chain 'LE' and resid 190 through 192' Processing helix chain 'LE' and resid 211 through 215 Processing helix chain 'LE' and resid 243 through 263 removed outlier: 3.511A pdb=" N GLNLE 250 " --> pdb=" O ARGLE 246 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYSLE 251 " --> pdb=" O LYSLE 247 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALALE 252 " --> pdb=" O ILELE 248 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLNLE 256 " --> pdb=" O ALALE 252 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILELE 257 " --> pdb=" O VALLE 253 " (cutoff:3.500A) Proline residue: LE 259 - end of helix Processing helix chain 'LE' and resid 266 through 273 removed outlier: 3.702A pdb=" N SERLE 273 " --> pdb=" O GLYLE 269 " (cutoff:3.500A) Processing helix chain 'LF' and resid 25 through 79 removed outlier: 3.540A pdb=" N LYSLF 48 " --> pdb=" O LYSLF 44 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARGLF 62 " --> pdb=" O HISLF 58 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLULF 68 " --> pdb=" O METLF 64 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILELF 69 " --> pdb=" O TYRLF 65 " (cutoff:3.500A) Processing helix chain 'LF' and resid 102 through 112 removed outlier: 3.578A pdb=" N VALLF 108 " --> pdb=" O LYSLF 104 " (cutoff:3.500A) Processing helix chain 'LF' and resid 126 through 134 Processing helix chain 'LF' and resid 136 through 138 No H-bonds generated for 'chain 'LF' and resid 136 through 138' Processing helix chain 'LF' and resid 146 through 157 Processing helix chain 'LF' and resid 171 through 180 removed outlier: 3.960A pdb=" N ILELF 175 " --> pdb=" O ASPLF 171 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SERLF 178 " --> pdb=" O LEULF 174 " (cutoff:3.500A) Processing helix chain 'LF' and resid 186 through 196 removed outlier: 3.578A pdb=" N ILELF 194 " --> pdb=" O LEULF 190 " (cutoff:3.500A) Processing helix chain 'LF' and resid 200 through 208 removed outlier: 3.577A pdb=" N ALALF 204 " --> pdb=" O ARGLF 200 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEULF 208 " --> pdb=" O ALALF 204 " (cutoff:3.500A) Processing helix chain 'LF' and resid 226 through 230 Processing helix chain 'LF' and resid 239 through 248 Processing helix chain 'LG' and resid 58 through 71 Processing helix chain 'LG' and resid 77 through 85 removed outlier: 5.041A pdb=" N PHELG 83 " --> pdb=" O ALALG 79 " (cutoff:3.500A) Processing helix chain 'LG' and resid 88 through 100 removed outlier: 3.641A pdb=" N ALALG 92 " --> pdb=" O ASPLG 88 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THRLG 93 " --> pdb=" O ARGLG 89 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLNLG 94 " --> pdb=" O GLNLG 90 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEULG 95 " --> pdb=" O THRLG 91 " (cutoff:3.500A) Processing helix chain 'LG' and resid 106 through 119 Processing helix chain 'LG' and resid 139 through 149 removed outlier: 4.729A pdb=" N THRLG 145 " --> pdb=" O ASNLG 141 " (cutoff:3.500A) Processing helix chain 'LG' and resid 163 through 167 Processing helix chain 'LG' and resid 169 through 177 Processing helix chain 'LG' and resid 186 through 194 Processing helix chain 'LG' and resid 210 through 224 removed outlier: 4.436A pdb=" N ALALG 214 " --> pdb=" O GLULG 210 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THRLG 224 " --> pdb=" O GLULG 220 " (cutoff:3.500A) Processing helix chain 'LG' and resid 229 through 234 Processing helix chain 'LG' and resid 243 through 256 Processing helix chain 'LH' and resid 65 through 68 removed outlier: 3.731A pdb=" N ALALH 68 " --> pdb=" O LYSLH 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'LH' and resid 65 through 68' Processing helix chain 'LH' and resid 69 through 86 removed outlier: 3.697A pdb=" N LYSLH 82 " --> pdb=" O GLNLH 78 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VALLH 84 " --> pdb=" O METLH 80 " (cutoff:3.500A) Processing helix chain 'LH' and resid 107 through 109 No H-bonds generated for 'chain 'LH' and resid 107 through 109' Processing helix chain 'LH' and resid 150 through 164 Processing helix chain 'LI' and resid 5 through 9 Processing helix chain 'LI' and resid 62 through 77 removed outlier: 3.597A pdb=" N CYSLI 71 " --> pdb=" O ALALI 67 " (cutoff:3.500A) Processing helix chain 'LI' and resid 145 through 157 removed outlier: 3.698A pdb=" N ILELI 149 " --> pdb=" O GLULI 145 " (cutoff:3.500A) Processing helix chain 'LI' and resid 177 through 187 removed outlier: 3.718A pdb=" N GLULI 182 " --> pdb=" O ALALI 178 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ASPLI 183 " --> pdb=" O ASPLI 179 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALALI 186 " --> pdb=" O GLULI 182 " (cutoff:3.500A) Processing helix chain 'LI' and resid 206 through 212 removed outlier: 3.611A pdb=" N VALLI 211 " --> pdb=" O ASPLI 207 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 30 through 45 Processing helix chain 'LJ' and resid 57 through 61 Processing helix chain 'LJ' and resid 78 through 90 removed outlier: 3.733A pdb=" N ILELJ 82 " --> pdb=" O LYSLJ 78 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 95 through 99 Processing helix chain 'LJ' and resid 158 through 171 Processing helix chain 'LL' and resid 27 through 46 Processing helix chain 'LL' and resid 77 through 85 Processing helix chain 'LL' and resid 90 through 95 removed outlier: 3.854A pdb=" N GLYLL 95 " --> pdb=" O ARGLL 92 " (cutoff:3.500A) Processing helix chain 'LL' and resid 106 through 124 Processing helix chain 'LL' and resid 140 through 146 removed outlier: 3.898A pdb=" N LEULL 144 " --> pdb=" O SERLL 140 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYSLL 145 " --> pdb=" O ALALL 141 " (cutoff:3.500A) Processing helix chain 'LL' and resid 170 through 176 removed outlier: 4.076A pdb=" N LYSLL 174 " --> pdb=" O THRLL 170 " (cutoff:3.500A) Processing helix chain 'LL' and resid 177 through 200 removed outlier: 5.376A pdb=" N GLYLL 193 " --> pdb=" O ALALL 189 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ILELL 194 " --> pdb=" O ARGLL 190 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALALL 196 " --> pdb=" O PHELL 192 " (cutoff:3.500A) Processing helix chain 'LM' and resid 69 through 79 removed outlier: 3.681A pdb=" N VALLM 73 " --> pdb=" O HISLM 69 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLNLM 75 " --> pdb=" O LYSLM 71 " (cutoff:3.500A) Processing helix chain 'LM' and resid 81 through 86 Processing helix chain 'LM' and resid 89 through 95 removed outlier: 3.740A pdb=" N ILELM 95 " --> pdb=" O TRPLM 91 " (cutoff:3.500A) Processing helix chain 'LM' and resid 97 through 103 removed outlier: 3.673A pdb=" N ALALM 102 " --> pdb=" O ARGLM 98 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYSLM 103 " --> pdb=" O GLULM 99 " (cutoff:3.500A) Processing helix chain 'LM' and resid 105 through 129 removed outlier: 4.243A pdb=" N METLM 118 " --> pdb=" O LYSLM 114 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARGLM 121 " --> pdb=" O LYSLM 117 " (cutoff:3.500A) Processing helix chain 'LN' and resid 3 through 9 removed outlier: 3.769A pdb=" N GLULN 9 " --> pdb=" O LYSLN 5 " (cutoff:3.500A) Processing helix chain 'LN' and resid 10 through 13 Processing helix chain 'LN' and resid 16 through 32 removed outlier: 3.652A pdb=" N GLNLN 32 " --> pdb=" O TRPLN 28 " (cutoff:3.500A) Processing helix chain 'LN' and resid 44 through 51 Processing helix chain 'LN' and resid 75 through 79 removed outlier: 3.637A pdb=" N GLYLN 78 " --> pdb=" O VALLN 75 " (cutoff:3.500A) Processing helix chain 'LN' and resid 83 through 87 Processing helix chain 'LN' and resid 97 through 111 removed outlier: 3.787A pdb=" N GLULN 103 " --> pdb=" O GLNLN 99 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLULN 104 " --> pdb=" O SERLN 100 " (cutoff:3.500A) Processing helix chain 'LN' and resid 139 through 144 Processing helix chain 'LN' and resid 145 through 149 removed outlier: 3.517A pdb=" N THRLN 148 " --> pdb=" O ASNLN 145 " (cutoff:3.500A) Processing helix chain 'LN' and resid 153 through 157 Processing helix chain 'LN' and resid 165 through 172 Processing helix chain 'LN' and resid 177 through 181 removed outlier: 3.974A pdb=" N HISLN 181 " --> pdb=" O HISLN 178 " (cutoff:3.500A) Processing helix chain 'LN' and resid 187 through 195 Processing helix chain 'LO' and resid 16 through 29 removed outlier: 3.532A pdb=" N GLNLO 26 " --> pdb=" O ILELO 22 " (cutoff:3.500A) Processing helix chain 'LO' and resid 46 through 59 removed outlier: 3.563A pdb=" N PHELO 57 " --> pdb=" O LYSLO 53 " (cutoff:3.500A) Processing helix chain 'LO' and resid 75 through 87 Processing helix chain 'LO' and resid 94 through 100 removed outlier: 3.653A pdb=" N ASPLO 100 " --> pdb=" O GLNLO 96 " (cutoff:3.500A) Processing helix chain 'LO' and resid 120 through 123 Processing helix chain 'LO' and resid 124 through 129 Processing helix chain 'LO' and resid 138 through 145 removed outlier: 3.526A pdb=" N GLULO 144 " --> pdb=" O ARGLO 140 " (cutoff:3.500A) Processing helix chain 'LO' and resid 149 through 198 removed outlier: 3.986A pdb=" N THRLO 153 " --> pdb=" O TYRLO 149 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALALO 154 " --> pdb=" O GLNLO 150 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYSLO 163 " --> pdb=" O LYSLO 159 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HISLO 167 " --> pdb=" O LYSLO 163 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARGLO 178 " --> pdb=" O LEULO 174 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LYSLO 183 " --> pdb=" O LYSLO 179 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASNLO 184 " --> pdb=" O GLNLO 180 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LYSLO 187 " --> pdb=" O LYSLO 183 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LYSLO 188 " --> pdb=" O ASNLO 184 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILELO 189 " --> pdb=" O VALLO 185 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LYSLO 191 " --> pdb=" O LYSLO 187 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N TYRLO 192 " --> pdb=" O LYSLO 188 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLULO 194 " --> pdb=" O ASPLO 190 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VALLO 195 " --> pdb=" O LYSLO 191 " (cutoff:3.500A) Processing helix chain 'LP' and resid 10 through 14 removed outlier: 3.940A pdb=" N SERLP 14 " --> pdb=" O PROLP 11 " (cutoff:3.500A) Processing helix chain 'LP' and resid 25 through 37 Processing helix chain 'LP' and resid 40 through 53 removed outlier: 3.910A pdb=" N THRLP 52 " --> pdb=" O LEULP 48 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEULP 53 " --> pdb=" O LYSLP 49 " (cutoff:3.500A) Processing helix chain 'LP' and resid 73 through 77 Processing helix chain 'LP' and resid 85 through 106 removed outlier: 4.044A pdb=" N PHELP 90 " --> pdb=" O LYSLP 86 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEULP 91 " --> pdb=" O SERLP 87 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALALP 102 " --> pdb=" O ALALP 98 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEULP 104 " --> pdb=" O SERLP 100 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 22 through 39 Processing helix chain 'LQ' and resid 41 through 52 removed outlier: 3.767A pdb=" N GLNLQ 45 " --> pdb=" O SERLQ 41 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 62 through 69 Processing helix chain 'LQ' and resid 106 through 116 Processing helix chain 'LQ' and resid 124 through 130 removed outlier: 3.623A pdb=" N LEULQ 128 " --> pdb=" O ASPLQ 124 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 146 through 152 removed outlier: 3.664A pdb=" N TYRLQ 149 " --> pdb=" O ARGLQ 146 " (cutoff:3.500A) Processing helix chain 'LR' and resid 4 through 16 removed outlier: 3.766A pdb=" N ARGLR 9 " --> pdb=" O ARGLR 5 " (cutoff:3.500A) Processing helix chain 'LR' and resid 18 through 22 Processing helix chain 'LR' and resid 28 through 33 Processing helix chain 'LR' and resid 40 through 48 Processing helix chain 'LR' and resid 60 through 72 Processing helix chain 'LR' and resid 77 through 81 Processing helix chain 'LR' and resid 84 through 89 Processing helix chain 'LR' and resid 90 through 103 removed outlier: 3.533A pdb=" N ILELR 101 " --> pdb=" O ARGLR 97 " (cutoff:3.500A) Processing helix chain 'LR' and resid 103 through 112 Processing helix chain 'LR' and resid 116 through 129 removed outlier: 3.575A pdb=" N LYSLR 126 " --> pdb=" O SERLR 122 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYSLR 128 " --> pdb=" O TYRLR 124 " (cutoff:3.500A) Processing helix chain 'LR' and resid 134 through 151 Processing helix chain 'LS' and resid 36 through 50 removed outlier: 3.566A pdb=" N SERLS 42 " --> pdb=" O VALLS 38 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLNLS 50 " --> pdb=" O TYRLS 46 " (cutoff:3.500A) Processing helix chain 'LS' and resid 55 through 57 No H-bonds generated for 'chain 'LS' and resid 55 through 57' Processing helix chain 'LS' and resid 101 through 117 removed outlier: 3.605A pdb=" N GLNLS 108 " --> pdb=" O GLYLS 104 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N CYSLS 109 " --> pdb=" O ALALS 105 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYRLS 110 " --> pdb=" O VALLS 106 " (cutoff:3.500A) Processing helix chain 'LS' and resid 139 through 144 removed outlier: 3.627A pdb=" N LYSLS 143 " --> pdb=" O ARGLS 139 " (cutoff:3.500A) Processing helix chain 'LT' and resid 11 through 16 removed outlier: 3.570A pdb=" N SERLT 16 " --> pdb=" O ARGLT 12 " (cutoff:3.500A) Processing helix chain 'LT' and resid 27 through 32 Processing helix chain 'LT' and resid 99 through 123 removed outlier: 3.649A pdb=" N ASPLT 103 " --> pdb=" O SERLT 99 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SERLT 104 " --> pdb=" O LYSLT 100 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHELT 105 " --> pdb=" O SERLT 101 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYSLT 110 " --> pdb=" O LEULT 106 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLNLT 114 " --> pdb=" O LYSLT 110 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLULT 121 " --> pdb=" O LYSLT 117 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYSLT 122 " --> pdb=" O GLULT 118 " (cutoff:3.500A) Processing helix chain 'LU' and resid 35 through 46 removed outlier: 3.642A pdb=" N GLULU 45 " --> pdb=" O GLNLU 41 " (cutoff:3.500A) Processing helix chain 'LU' and resid 48 through 52 Processing helix chain 'LU' and resid 55 through 60 removed outlier: 3.750A pdb=" N VALLU 60 " --> pdb=" O LEULU 56 " (cutoff:3.500A) Processing helix chain 'LU' and resid 79 through 94 removed outlier: 3.847A pdb=" N LEULU 83 " --> pdb=" O SERLU 79 " (cutoff:3.500A) Processing helix chain 'LW' and resid 34 through 42 Processing helix chain 'LW' and resid 45 through 49 removed outlier: 3.593A pdb=" N GLNLW 48 " --> pdb=" O ASNLW 45 " (cutoff:3.500A) Processing helix chain 'LW' and resid 53 through 60 Processing helix chain 'LX' and resid 72 through 76 Processing helix chain 'LX' and resid 83 through 92 removed outlier: 3.636A pdb=" N LYSLX 88 " --> pdb=" O GLULX 84 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYSLX 89 " --> pdb=" O SERLX 85 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILELX 90 " --> pdb=" O ALALX 86 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLULX 91 " --> pdb=" O METLX 87 " (cutoff:3.500A) Processing helix chain 'LX' and resid 107 through 117 removed outlier: 3.836A pdb=" N LYSLX 114 " --> pdb=" O LYSLX 110 " (cutoff:3.500A) Processing helix chain 'LX' and resid 146 through 154 Processing helix chain 'LY' and resid 10 through 20 Processing helix chain 'LY' and resid 60 through 64 removed outlier: 4.369A pdb=" N GLYLY 64 " --> pdb=" O HISLY 61 " (cutoff:3.500A) Processing helix chain 'LY' and resid 100 through 102 No H-bonds generated for 'chain 'LY' and resid 100 through 102' Processing helix chain 'LY' and resid 112 through 131 removed outlier: 3.823A pdb=" N ILELY 118 " --> pdb=" O ASPLY 114 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEULY 119 " --> pdb=" O ARGLY 115 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLULY 120 " --> pdb=" O LYSLY 116 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SERLY 125 " --> pdb=" O ARGLY 121 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLYLY 129 " --> pdb=" O SERLY 125 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYSLY 130 " --> pdb=" O ARGLY 126 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 58 through 63 removed outlier: 3.793A pdb=" N ALALZ 63 " --> pdb=" O LYSLZ 59 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 103 through 124 removed outlier: 3.727A pdb=" N GLULZ 120 " --> pdb=" O VALLZ 116 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARGLZ 121 " --> pdb=" O LYSLZ 117 " (cutoff:3.500A) Processing helix chain 'La' and resid 7 through 11 Processing helix chain 'La' and resid 41 through 49 removed outlier: 3.611A pdb=" N LYSLa 47 " --> pdb=" O ILELa 43 " (cutoff:3.500A) Processing helix chain 'La' and resid 64 through 69 removed outlier: 4.098A pdb=" N SERLa 68 " --> pdb=" O LYSLa 64 " (cutoff:3.500A) Processing helix chain 'La' and resid 75 through 81 removed outlier: 3.915A pdb=" N TRPLa 79 " --> pdb=" O ASPLa 76 " (cutoff:3.500A) Processing helix chain 'La' and resid 83 through 91 removed outlier: 3.714A pdb=" N ARGLa 87 " --> pdb=" O SERLa 83 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASNLa 89 " --> pdb=" O GLNLa 85 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALALa 91 " --> pdb=" O ARGLa 87 " (cutoff:3.500A) Processing helix chain 'La' and resid 104 through 107 Processing helix chain 'La' and resid 130 through 141 Processing helix chain 'Lb' and resid 11 through 18 removed outlier: 3.554A pdb=" N ARGLb 18 " --> pdb=" O ARGLb 14 " (cutoff:3.500A) Processing helix chain 'Lb' and resid 36 through 49 removed outlier: 3.913A pdb=" N ASNLb 42 " --> pdb=" O LYSLb 38 " (cutoff:3.500A) Processing helix chain 'Lb' and resid 53 through 69 removed outlier: 4.217A pdb=" N ALALb 59 " --> pdb=" O LYSLb 55 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASNLb 60 " --> pdb=" O LYSLb 56 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N METLb 65 " --> pdb=" O ASNLb 61 " (cutoff:3.500A) Processing helix chain 'Lc' and resid 17 through 25 removed outlier: 4.164A pdb=" N VALLc 21 " --> pdb=" O ARGLc 17 " (cutoff:3.500A) Processing helix chain 'Lc' and resid 31 through 40 Processing helix chain 'Lc' and resid 53 through 68 removed outlier: 3.645A pdb=" N SERLc 58 " --> pdb=" O ALALc 54 " (cutoff:3.500A) Processing helix chain 'Lc' and resid 77 through 85 Processing helix chain 'Ld' and resid 30 through 32 No H-bonds generated for 'chain 'Ld' and resid 30 through 32' Processing helix chain 'Ld' and resid 37 through 40 Processing helix chain 'Ld' and resid 41 through 57 removed outlier: 3.620A pdb=" N ARGLd 50 " --> pdb=" O LEULd 46 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYSLd 51 " --> pdb=" O LYSLd 47 " (cutoff:3.500A) Processing helix chain 'Ld' and resid 65 through 73 removed outlier: 3.669A pdb=" N ASNLd 69 " --> pdb=" O ASPLd 65 " (cutoff:3.500A) Processing helix chain 'Le' and resid 43 through 48 removed outlier: 3.530A pdb=" N ARGLe 47 " --> pdb=" O ASNLe 43 " (cutoff:3.500A) Processing helix chain 'Le' and resid 57 through 61 removed outlier: 3.633A pdb=" N TYRLe 60 " --> pdb=" O ASNLe 57 " (cutoff:3.500A) Processing helix chain 'Le' and resid 81 through 86 removed outlier: 3.579A pdb=" N LEULe 85 " --> pdb=" O ASNLe 81 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLULe 86 " --> pdb=" O VALLe 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'Le' and resid 81 through 86' Processing helix chain 'Le' and resid 87 through 91 removed outlier: 3.895A pdb=" N METLe 90 " --> pdb=" O VALLe 87 " (cutoff:3.500A) Processing helix chain 'Le' and resid 104 through 118 removed outlier: 3.837A pdb=" N LYSLe 109 " --> pdb=" O SERLe 105 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ALALe 110 " --> pdb=" O LYSLe 106 " (cutoff:3.500A) Processing helix chain 'Lf' and resid 35 through 44 removed outlier: 4.689A pdb=" N GLULf 40 " --> pdb=" O ASPLf 37 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHELf 41 " --> pdb=" O GLULf 38 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLYLf 44 " --> pdb=" O PHELf 41 " (cutoff:3.500A) Processing helix chain 'Lg' and resid 60 through 66 removed outlier: 3.683A pdb=" N LEULg 64 " --> pdb=" O PROLg 61 " (cutoff:3.500A) Processing helix chain 'Lg' and resid 68 through 73 Processing helix chain 'Lg' and resid 83 through 104 removed outlier: 3.908A pdb=" N LYSLg 92 " --> pdb=" O ARGLg 88 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 5 through 10 removed outlier: 3.604A pdb=" N LEULh 9 " --> pdb=" O LYSLh 5 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 13 through 37 removed outlier: 3.549A pdb=" N LEULh 17 " --> pdb=" O LYSLh 13 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEULh 18 " --> pdb=" O LYSLh 14 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASPLh 23 " --> pdb=" O LYSLh 19 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N SERLh 29 " --> pdb=" O LYSLh 25 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THRLh 37 " --> pdb=" O VALLh 33 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 40 through 45 Processing helix chain 'Lh' and resid 47 through 52 Processing helix chain 'Lh' and resid 52 through 73 removed outlier: 3.919A pdb=" N VALLh 60 " --> pdb=" O ARGLh 56 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 96 through 101 Processing helix chain 'Lh' and resid 104 through 112 removed outlier: 3.968A pdb=" N LYSLh 110 " --> pdb=" O LYSLh 106 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLULh 111 " --> pdb=" O GLNLh 107 " (cutoff:3.500A) Processing helix chain 'Li' and resid 9 through 13 removed outlier: 4.434A pdb=" N ASNLi 12 " --> pdb=" O VALLi 9 " (cutoff:3.500A) Processing helix chain 'Li' and resid 25 through 30 Processing helix chain 'Li' and resid 34 through 40 Processing helix chain 'Li' and resid 40 through 49 removed outlier: 3.661A pdb=" N GLULi 46 " --> pdb=" O ASPLi 42 " (cutoff:3.500A) Processing helix chain 'Li' and resid 51 through 63 removed outlier: 3.658A pdb=" N ARGLi 55 " --> pdb=" O ALALi 51 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEULi 60 " --> pdb=" O ARGLi 56 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VALLi 63 " --> pdb=" O GLULi 59 " (cutoff:3.500A) Processing helix chain 'Li' and resid 65 through 78 removed outlier: 3.783A pdb=" N LYSLi 75 " --> pdb=" O LYSLi 71 " (cutoff:3.500A) Processing helix chain 'Li' and resid 79 through 99 removed outlier: 4.299A pdb=" N VALLi 93 " --> pdb=" O GLULi 89 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 6 through 11 removed outlier: 3.551A pdb=" N ARGLj 11 " --> pdb=" O PHELj 8 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 52 through 56 Processing helix chain 'Lj' and resid 66 through 75 removed outlier: 3.992A pdb=" N ARGLj 72 " --> pdb=" O LYSLj 68 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARGLj 75 " --> pdb=" O TYRLj 71 " (cutoff:3.500A) Processing helix chain 'Lk' and resid 7 through 16 Processing helix chain 'Lk' and resid 51 through 58 removed outlier: 3.830A pdb=" N LYSLk 55 " --> pdb=" O GLULk 51 " (cutoff:3.500A) Processing helix chain 'Ll' and resid 6 through 19 removed outlier: 4.526A pdb=" N LYSLl 15 " --> pdb=" O ARGLl 11 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYSLl 16 " --> pdb=" O PHELl 12 " (cutoff:3.500A) Processing helix chain 'Ll' and resid 24 through 28 Processing helix chain 'Lm' and resid 79 through 91 removed outlier: 4.539A pdb=" N LEULm 85 " --> pdb=" O SERLm 81 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TYRLm 89 " --> pdb=" O LEULm 85 " (cutoff:3.500A) Processing helix chain 'Lo' and resid 38 through 43 removed outlier: 3.729A pdb=" N ARGLo 43 " --> pdb=" O ARGLo 39 " (cutoff:3.500A) Processing helix chain 'Lp' and resid 8 through 15 removed outlier: 3.501A pdb=" N VALLp 11 " --> pdb=" O VALLp 8 " (cutoff:3.500A) Processing helix chain 'Lp' and resid 20 through 34 removed outlier: 4.222A pdb=" N LYSLp 27 " --> pdb=" O ARGLp 23 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LYSLp 28 " --> pdb=" O LYSLp 24 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILELp 29 " --> pdb=" O METLp 25 " (cutoff:3.500A) Processing helix chain 'Lr' and resid 3 through 11 removed outlier: 3.698A pdb=" N METLr 8 " --> pdb=" O HISLr 4 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VALLr 9 " --> pdb=" O LEULr 5 " (cutoff:3.500A) Processing helix chain 'Lr' and resid 72 through 76 removed outlier: 3.527A pdb=" N SERLr 76 " --> pdb=" O PROLr 73 " (cutoff:3.500A) Processing helix chain 'Lr' and resid 85 through 96 Processing helix chain 'Lr' and resid 97 through 101 removed outlier: 3.540A pdb=" N LYSLr 101 " --> pdb=" O ARGLr 98 " (cutoff:3.500A) Processing helix chain 'Lr' and resid 108 through 122 Processing helix chain 'A' and resid 14 through 39 removed outlier: 4.222A pdb=" N LYS A 20 " --> pdb=" O LEU A 16 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR A 21 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE A 27 " --> pdb=" O MET A 23 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 61 removed outlier: 3.714A pdb=" N ASP A 53 " --> pdb=" O CYS A 49 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ALA A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLU A 59 " --> pdb=" O MET A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 157 removed outlier: 3.602A pdb=" N ASP A 141 " --> pdb=" O GLY A 137 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N HIS A 147 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA A 153 " --> pdb=" O CYS A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 176 removed outlier: 3.569A pdb=" N THR A 167 " --> pdb=" O ASN A 163 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA A 169 " --> pdb=" O GLN A 165 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASN A 171 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LYS A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 213 removed outlier: 3.670A pdb=" N HIS A 213 " --> pdb=" O GLN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 274 Processing helix chain 'A' and resid 286 through 297 removed outlier: 3.795A pdb=" N MET A 291 " --> pdb=" O LYS A 287 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU A 295 " --> pdb=" O MET A 291 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N CYS A 296 " --> pdb=" O GLY A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 353 through 359 removed outlier: 4.333A pdb=" N LEU A 357 " --> pdb=" O GLU A 353 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'LA' and resid 72 through 77 Processing sheet with id=AA2, first strand: chain 'LA' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'LA' and resid 112 through 113 removed outlier: 5.663A pdb=" N VALLA 136 " --> pdb=" O LYSLA 149 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LYSLA 149 " --> pdb=" O VALLA 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'LA' and resid 224 through 225 Processing sheet with id=AA5, first strand: chain 'LB' and resid 276 through 282 removed outlier: 4.985A pdb=" N THRLB 278 " --> pdb=" O GLYLB 221 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N GLYLB 221 " --> pdb=" O THRLB 278 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ILELB 280 " --> pdb=" O VALLB 219 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N VALLB 219 " --> pdb=" O ILELB 280 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N VALLB 222 " --> pdb=" O VALLB 344 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VALLB 344 " --> pdb=" O VALLB 222 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N LYSLB 50 " --> pdb=" O GLULB 80 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLULB 80 " --> pdb=" O LYSLB 50 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLYLB 52 " --> pdb=" O ILELB 78 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THRLB 77 " --> pdb=" O LEULB 333 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYSLB 286 " --> pdb=" O METLB 332 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'LB' and resid 276 through 282 removed outlier: 4.985A pdb=" N THRLB 278 " --> pdb=" O GLYLB 221 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N GLYLB 221 " --> pdb=" O THRLB 278 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ILELB 280 " --> pdb=" O VALLB 219 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N VALLB 219 " --> pdb=" O ILELB 280 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N VALLB 222 " --> pdb=" O VALLB 344 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VALLB 344 " --> pdb=" O VALLB 222 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N HISLB 55 " --> pdb=" O ASPLB 369 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLULB 59 " --> pdb=" O LEULB 365 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEULB 365 " --> pdb=" O GLULB 59 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'LB' and resid 98 through 106 removed outlier: 6.664A pdb=" N GLYLB 91 " --> pdb=" O PHELB 102 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N THRLB 104 " --> pdb=" O ILELB 89 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILELB 89 " --> pdb=" O THRLB 104 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N PHELB 106 " --> pdb=" O VALLB 87 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N VALLB 87 " --> pdb=" O PHELB 106 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N VALLB 86 " --> pdb=" O HISLB 165 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N HISLB 165 " --> pdb=" O VALLB 86 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLYLB 88 " --> pdb=" O ILELB 163 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VALLB 90 " --> pdb=" O ARGLB 161 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ARGLB 161 " --> pdb=" O VALLB 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'LB' and resid 98 through 106 removed outlier: 6.664A pdb=" N GLYLB 91 " --> pdb=" O PHELB 102 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N THRLB 104 " --> pdb=" O ILELB 89 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILELB 89 " --> pdb=" O THRLB 104 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N PHELB 106 " --> pdb=" O VALLB 87 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N VALLB 87 " --> pdb=" O PHELB 106 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'LB' and resid 225 through 229 Processing sheet with id=AB1, first strand: chain 'LC' and resid 7 through 11 removed outlier: 5.018A pdb=" N LYSLC 20 " --> pdb=" O VALLC 10 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'LC' and resid 64 through 65 Processing sheet with id=AB3, first strand: chain 'LC' and resid 152 through 154 removed outlier: 4.471A pdb=" N LEULC 152 " --> pdb=" O CYSLC 250 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYRLC 211 " --> pdb=" O LEULC 230 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'LD' and resid 71 through 78 removed outlier: 6.732A pdb=" N ILELD 64 " --> pdb=" O VALLD 75 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ALALD 77 " --> pdb=" O CYSLD 62 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N CYSLD 62 " --> pdb=" O ALALD 77 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VALLD 53 " --> pdb=" O ASPLD 147 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'LD' and resid 183 through 184 Processing sheet with id=AB6, first strand: chain 'LE' and resid 49 through 51 removed outlier: 7.013A pdb=" N ILELE 54 " --> pdb=" O LEULE 50 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'LE' and resid 187 through 189 removed outlier: 7.361A pdb=" N LEULE 174 " --> pdb=" O LEULE 165 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEULE 165 " --> pdb=" O LEULE 174 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THRLE 148 " --> pdb=" O PHELE 164 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N ILELE 149 " --> pdb=" O THRLE 197 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'LF' and resid 81 through 83 Processing sheet with id=AB9, first strand: chain 'LF' and resid 211 through 212 removed outlier: 3.916A pdb=" N ASNLF 119 " --> pdb=" O ARGLF 94 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLYLF 143 " --> pdb=" O PHELF 91 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILELF 140 " --> pdb=" O GLYLF 234 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'LF' and resid 159 through 162 Processing sheet with id=AC2, first strand: chain 'LG' and resid 75 through 76 removed outlier: 3.622A pdb=" N GLYLG 238 " --> pdb=" O VALLG 76 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'LG' and resid 181 through 184 Processing sheet with id=AC4, first strand: chain 'LH' and resid 3 through 10 removed outlier: 6.973A pdb=" N ILELH 4 " --> pdb=" O TRPLH 61 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASPLH 58 " --> pdb=" O GLULH 44 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLULH 44 " --> pdb=" O ASPLH 58 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'LH' and resid 17 through 21 removed outlier: 4.047A pdb=" N THRLH 24 " --> pdb=" O LYSLH 21 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'LH' and resid 132 through 136 removed outlier: 3.629A pdb=" N SERLH 135 " --> pdb=" O ILELH 145 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ARGLH 93 " --> pdb=" O VALLH 181 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N VALLH 181 " --> pdb=" O ARGLH 93 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VALLH 95 " --> pdb=" O ILELH 179 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ILELH 179 " --> pdb=" O VALLH 95 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'LH' and resid 103 through 106 removed outlier: 3.598A pdb=" N LEULH 111 " --> pdb=" O GLNLH 106 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARGLH 124 " --> pdb=" O ILELH 114 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'LI' and resid 35 through 37 removed outlier: 7.039A pdb=" N METLI 52 " --> pdb=" O ILELI 135 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N SERLI 137 " --> pdb=" O GLYLI 50 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N GLYLI 50 " --> pdb=" O SERLI 137 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLYLI 49 " --> pdb=" O SERLI 168 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SERLI 168 " --> pdb=" O GLYLI 49 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYSLI 164 " --> pdb=" O VALLI 53 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'LI' and resid 58 through 61 removed outlier: 6.021A pdb=" N ILELI 99 " --> pdb=" O PROLI 122 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'LJ' and resid 49 through 52 removed outlier: 7.020A pdb=" N VALLJ 133 " --> pdb=" O ARGLJ 18 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LEULJ 20 " --> pdb=" O TYRLJ 131 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N TYRLJ 131 " --> pdb=" O LEULJ 20 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LEULJ 22 " --> pdb=" O ASPLJ 129 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ASPLJ 129 " --> pdb=" O LEULJ 22 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'LL' and resid 22 through 23 removed outlier: 3.672A pdb=" N ALALL 23 " --> pdb=" O LEULN 198 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'LL' and resid 58 through 60 Processing sheet with id=AD4, first strand: chain 'LL' and resid 125 through 126 Processing sheet with id=AD5, first strand: chain 'LL' and resid 167 through 168 Processing sheet with id=AD6, first strand: chain 'LM' and resid 6 through 8 Processing sheet with id=AD7, first strand: chain 'LM' and resid 48 through 51 removed outlier: 7.862A pdb=" N ARGLM 35 " --> pdb=" O VALLM 30 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N VALLM 30 " --> pdb=" O ARGLM 35 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEULM 37 " --> pdb=" O VALLM 28 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALALM 13 " --> pdb=" O VALLM 25 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ARGLM 11 " --> pdb=" O ILELM 27 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N VALLM 12 " --> pdb=" O THRLM 58 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THRLM 58 " --> pdb=" O VALLM 12 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'LN' and resid 36 through 39 removed outlier: 4.343A pdb=" N ILELN 61 " --> pdb=" O ALALN 39 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYRLN 127 " --> pdb=" O GLYLN 122 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLYLN 122 " --> pdb=" O TYRLN 127 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N PHELN 129 " --> pdb=" O TRPLN 120 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N TRPLN 120 " --> pdb=" O PHELN 129 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N GLULN 131 " --> pdb=" O SERLN 118 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SERLN 118 " --> pdb=" O GLULN 131 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILELN 133 " --> pdb=" O LEULN 116 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'LO' and resid 7 through 10 removed outlier: 6.598A pdb=" N LEULO 7 " --> pdb=" O VALLO 34 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N VALLO 36 " --> pdb=" O LEULO 7 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEULO 9 " --> pdb=" O VALLO 36 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYSLO 103 " --> pdb=" O VALLO 33 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'LO' and resid 14 through 15 removed outlier: 5.029A pdb=" N HISLO 14 " --> pdb=" O ASNLO 42 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N SERLO 44 " --> pdb=" O HISLO 14 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'LP' and resid 16 through 22 removed outlier: 4.775A pdb=" N ASNLP 21 " --> pdb=" O CYSLP 144 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N CYSLP 144 " --> pdb=" O ASNLP 21 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N THRLP 151 " --> pdb=" O ILELP 114 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ILELP 114 " --> pdb=" O THRLP 151 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'LP' and resid 58 through 59 Processing sheet with id=AE4, first strand: chain 'LP' and resid 128 through 131 removed outlier: 3.621A pdb=" N ARGLP 135 " --> pdb=" O ARGLP 131 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'LQ' and resid 119 through 121 removed outlier: 6.296A pdb=" N ALALQ 80 " --> pdb=" O CYSLQ 101 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'LQ' and resid 85 through 86 Processing sheet with id=AE7, first strand: chain 'LS' and resid 28 through 33 removed outlier: 6.847A pdb=" N ARGLS 15 " --> pdb=" O ILELS 61 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ILELS 61 " --> pdb=" O ARGLS 15 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'LS' and resid 90 through 99 removed outlier: 3.534A pdb=" N TYRLS 97 " --> pdb=" O PHELS 78 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ASNLS 77 " --> pdb=" O GLULS 131 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N GLULS 131 " --> pdb=" O ASNLS 77 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLYLS 79 " --> pdb=" O VALLS 129 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N VALLS 129 " --> pdb=" O GLYLS 79 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'LT' and resid 85 through 92 removed outlier: 3.522A pdb=" N VALLT 76 " --> pdb=" O LYSLT 87 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASNLT 66 " --> pdb=" O GLYLT 73 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VALLT 75 " --> pdb=" O VALLT 64 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N VALLT 64 " --> pdb=" O VALLT 75 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N ASNLT 77 " --> pdb=" O GLYLT 62 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N GLYLT 62 " --> pdb=" O ASNLT 77 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYSLT 97 " --> pdb=" O ASPLT 41 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'LU' and resid 62 through 65 removed outlier: 3.650A pdb=" N THRLU 73 " --> pdb=" O THRLU 62 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N TYRLU 110 " --> pdb=" O LYSLU 20 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N THRLU 22 " --> pdb=" O TYRLU 110 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N LEULU 112 " --> pdb=" O THRLU 22 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASPLU 24 " --> pdb=" O LEULU 112 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'LX' and resid 77 through 80 removed outlier: 3.827A pdb=" N PHELX 79 " --> pdb=" O ILELX 99 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LYSLX 135 " --> pdb=" O THRLX 126 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N THRLX 126 " --> pdb=" O LYSLX 135 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYRLX 137 " --> pdb=" O VALLX 124 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VALLX 124 " --> pdb=" O TYRLX 137 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ARGLX 139 " --> pdb=" O ALALX 122 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'LY' and resid 31 through 33 Processing sheet with id=AF4, first strand: chain 'LY' and resid 54 through 57 removed outlier: 6.473A pdb=" N GLULY 54 " --> pdb=" O THRLY 107 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'LY' and resid 70 through 74 removed outlier: 6.655A pdb=" N TYRLY 81 " --> pdb=" O VALLY 71 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VALLY 73 " --> pdb=" O VALLY 79 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VALLY 79 " --> pdb=" O VALLY 73 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'LY' and resid 86 through 88 Processing sheet with id=AF7, first strand: chain 'LZ' and resid 69 through 76 removed outlier: 6.505A pdb=" N LYSLZ 69 " --> pdb=" O ASPLZ 47 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYSLZ 73 " --> pdb=" O VALLZ 43 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LYSLZ 22 " --> pdb=" O ILELZ 46 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'La' and resid 72 through 73 removed outlier: 3.613A pdb=" N VALLa 111 " --> pdb=" O PHELa 128 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'La' and resid 100 through 102 Processing sheet with id=AG1, first strand: chain 'Lc' and resid 27 through 29 Processing sheet with id=AG2, first strand: chain 'Ld' and resid 22 through 28 Processing sheet with id=AG3, first strand: chain 'Ld' and resid 22 through 28 removed outlier: 4.059A pdb=" N ARGLd 85 " --> pdb=" O VALLd 109 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Le' and resid 78 through 79 Processing sheet with id=AG5, first strand: chain 'Lf' and resid 7 through 14 removed outlier: 6.073A pdb=" N PHELf 11 " --> pdb=" O LYSLf 29 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYSLf 29 " --> pdb=" O PHELf 11 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLYLf 13 " --> pdb=" O LEULf 27 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARGLf 76 " --> pdb=" O ARGLf 85 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYSLf 87 " --> pdb=" O VALLf 74 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N VALLf 74 " --> pdb=" O LYSLf 87 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VALLf 50 " --> pdb=" O ARGLf 100 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARGLf 100 " --> pdb=" O VALLf 50 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Lf' and resid 57 through 59 removed outlier: 3.740A pdb=" N ASNLf 65 " --> pdb=" O THRLf 57 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N THRLf 59 " --> pdb=" O LYSLf 63 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LYSLf 63 " --> pdb=" O THRLf 59 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Lg' and resid 20 through 25 removed outlier: 3.668A pdb=" N ARGLg 29 " --> pdb=" O THRLg 25 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Lj' and resid 16 through 17 Processing sheet with id=AG9, first strand: chain 'Lk' and resid 3 through 4 removed outlier: 6.628A pdb=" N ARGLk 3 " --> pdb=" O THRLk 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'Lk' and resid 46 through 47 removed outlier: 3.701A pdb=" N ILELk 47 " --> pdb=" O VALLk 32 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SERLk 22 " --> pdb=" O ARGLk 37 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VALLk 23 " --> pdb=" O LYSLk 67 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LEULk 69 " --> pdb=" O VALLk 23 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ILELk 25 " --> pdb=" O LEULk 69 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Lm' and resid 102 through 103 Processing sheet with id=AH3, first strand: chain 'Lo' and resid 8 through 12 Processing sheet with id=AH4, first strand: chain 'Lo' and resid 24 through 25 Processing sheet with id=AH5, first strand: chain 'Lp' and resid 47 through 49 Processing sheet with id=AH6, first strand: chain 'Lr' and resid 49 through 53 removed outlier: 3.777A pdb=" N ILELr 64 " --> pdb=" O VALLr 78 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'A' and resid 72 through 73 Processing sheet with id=AH8, first strand: chain 'A' and resid 105 through 110 Processing sheet with id=AH9, first strand: chain 'A' and resid 223 through 225 removed outlier: 3.527A pdb=" N MET A 331 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'A' and resid 278 through 279 1709 hydrogen bonds defined for protein. 4677 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2883 hydrogen bonds 4514 hydrogen bond angles 0 basepair planarities 1140 basepair parallelities 1860 stacking parallelities Total time for adding SS restraints: 297.61 Time building geometry restraints manager: 68.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 21364 1.33 - 1.45: 58868 1.45 - 1.57: 59264 1.57 - 1.69: 7885 1.69 - 1.82: 377 Bond restraints: 147758 Sorted by residual: bond pdb=" C GLNLM 33 " pdb=" N ASNLM 34 " ideal model delta sigma weight residual 1.332 1.253 0.079 1.40e-02 5.10e+03 3.19e+01 bond pdb=" CA ARGLA 245 " pdb=" C ARGLA 245 " ideal model delta sigma weight residual 1.523 1.485 0.038 1.34e-02 5.57e+03 7.97e+00 bond pdb=" CA ASNLG 141 " pdb=" C ASNLG 141 " ideal model delta sigma weight residual 1.522 1.473 0.049 1.72e-02 3.38e+03 7.96e+00 bond pdb=" CA ARGLh 112 " pdb=" C ARGLh 112 " ideal model delta sigma weight residual 1.523 1.484 0.039 1.41e-02 5.03e+03 7.69e+00 bond pdb=" CG1 ILELa 43 " pdb=" CD1 ILELa 43 " ideal model delta sigma weight residual 1.513 1.421 0.092 3.90e-02 6.57e+02 5.56e+00 ... (remaining 147753 not shown) Histogram of bond angle deviations from ideal: 91.31 - 100.50: 166 100.50 - 109.69: 59726 109.69 - 118.88: 83077 118.88 - 128.07: 68989 128.07 - 137.26: 6729 Bond angle restraints: 218687 Sorted by residual: angle pdb=" CA LYSLh 25 " pdb=" CB LYSLh 25 " pdb=" CG LYSLh 25 " ideal model delta sigma weight residual 114.10 129.12 -15.02 2.00e+00 2.50e-01 5.64e+01 angle pdb=" CA ARGLl 11 " pdb=" CB ARGLl 11 " pdb=" CG ARGLl 11 " ideal model delta sigma weight residual 114.10 127.16 -13.06 2.00e+00 2.50e-01 4.27e+01 angle pdb=" C GLNLM 33 " pdb=" N ASNLM 34 " pdb=" CA ASNLM 34 " ideal model delta sigma weight residual 121.54 109.55 11.99 1.91e+00 2.74e-01 3.94e+01 angle pdb=" N ASPLI 55 " pdb=" CA ASPLI 55 " pdb=" C ASPLI 55 " ideal model delta sigma weight residual 114.56 106.97 7.59 1.27e+00 6.20e-01 3.57e+01 angle pdb=" CA METLF 132 " pdb=" CB METLF 132 " pdb=" CG METLF 132 " ideal model delta sigma weight residual 114.10 125.81 -11.71 2.00e+00 2.50e-01 3.43e+01 ... (remaining 218682 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 83587 35.99 - 71.98: 10715 71.98 - 107.97: 1417 107.97 - 143.96: 37 143.96 - 179.95: 23 Dihedral angle restraints: 95779 sinusoidal: 77170 harmonic: 18609 Sorted by residual: dihedral pdb=" O4' CL51703 " pdb=" C1' CL51703 " pdb=" N1 CL51703 " pdb=" C2 CL51703 " ideal model delta sinusoidal sigma weight residual -160.00 -0.25 -159.75 1 1.50e+01 4.44e-03 8.27e+01 dihedral pdb=" O4' UL8 111 " pdb=" C1' UL8 111 " pdb=" N1 UL8 111 " pdb=" C2 UL8 111 " ideal model delta sinusoidal sigma weight residual 200.00 41.88 158.12 1 1.50e+01 4.44e-03 8.23e+01 dihedral pdb=" CA TYRLj 39 " pdb=" C TYRLj 39 " pdb=" N PROLj 40 " pdb=" CA PROLj 40 " ideal model delta harmonic sigma weight residual 180.00 134.75 45.25 0 5.00e+00 4.00e-02 8.19e+01 ... (remaining 95776 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 23517 0.058 - 0.115: 3372 0.115 - 0.173: 425 0.173 - 0.231: 55 0.231 - 0.288: 13 Chirality restraints: 27382 Sorted by residual: chirality pdb=" CG LEULQ 28 " pdb=" CB LEULQ 28 " pdb=" CD1 LEULQ 28 " pdb=" CD2 LEULQ 28 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" C3' UL5 914 " pdb=" C4' UL5 914 " pdb=" O3' UL5 914 " pdb=" C2' UL5 914 " both_signs ideal model delta sigma weight residual False -2.74 -2.47 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB ILELa 43 " pdb=" CA ILELa 43 " pdb=" CG1 ILELa 43 " pdb=" CG2 ILELa 43 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 27379 not shown) Planarity restraints: 12914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILELO 108 " 0.094 5.00e-02 4.00e+02 1.41e-01 3.16e+01 pdb=" N PROLO 109 " -0.243 5.00e-02 4.00e+02 pdb=" CA PROLO 109 " 0.076 5.00e-02 4.00e+02 pdb=" CD PROLO 109 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' CL5 131 " -0.007 2.00e-02 2.50e+03 3.53e-02 2.80e+01 pdb=" N1 CL5 131 " -0.005 2.00e-02 2.50e+03 pdb=" C2 CL5 131 " 0.088 2.00e-02 2.50e+03 pdb=" O2 CL5 131 " -0.052 2.00e-02 2.50e+03 pdb=" N3 CL5 131 " -0.004 2.00e-02 2.50e+03 pdb=" C4 CL5 131 " 0.012 2.00e-02 2.50e+03 pdb=" N4 CL5 131 " -0.016 2.00e-02 2.50e+03 pdb=" C5 CL5 131 " -0.013 2.00e-02 2.50e+03 pdb=" C6 CL5 131 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYRLj 39 " 0.081 5.00e-02 4.00e+02 1.22e-01 2.40e+01 pdb=" N PROLj 40 " -0.212 5.00e-02 4.00e+02 pdb=" CA PROLj 40 " 0.066 5.00e-02 4.00e+02 pdb=" CD PROLj 40 " 0.065 5.00e-02 4.00e+02 ... (remaining 12911 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 1545 2.45 - 3.06: 90713 3.06 - 3.67: 267007 3.67 - 4.29: 379617 4.29 - 4.90: 523771 Nonbonded interactions: 1262653 Sorted by model distance: nonbonded pdb=" OP1 CL5 112 " pdb="MG MGL55103 " model vdw 1.837 2.170 nonbonded pdb=" OP1 GL51633 " pdb="MG MGL55117 " model vdw 1.847 2.170 nonbonded pdb=" OP2 AL52423 " pdb="MG MGL55120 " model vdw 1.848 2.170 nonbonded pdb=" O4' AL5 410 " pdb="MG MGL55111 " model vdw 1.868 2.170 nonbonded pdb=" OP1 CL54561 " pdb="MG MGL55127 " model vdw 1.869 2.170 ... (remaining 1262648 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: 13.950 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: 0.130 Extract box with map and model: 44.890 Check model and map are aligned: 1.570 Set scattering table: 0.980 Process input model: 587.630 Find NCS groups from input model: 2.710 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 654.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 147758 Z= 0.400 Angle : 0.769 16.287 218687 Z= 0.400 Chirality : 0.042 0.288 27382 Planarity : 0.005 0.141 12914 Dihedral : 24.377 179.951 83773 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 21.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.89 % Favored : 89.04 % Rotamer: Outliers : 0.02 % Allowed : 0.58 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.05 % Twisted Proline : 0.73 % Twisted General : 0.07 % 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: -2.98 (0.10), residues: 6315 helix: -1.61 (0.11), residues: 1952 sheet: -2.12 (0.16), residues: 901 loop : -2.17 (0.10), residues: 3462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.003 TRPLb 16 HIS 0.013 0.002 HISLE 43 PHE 0.028 0.002 PHELa 69 TYR 0.042 0.002 TYRLZ 18 ARG 0.051 0.001 ARGLZ 84 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12630 Ramachandran restraints generated. 6315 Oldfield, 0 Emsley, 6315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12630 Ramachandran restraints generated. 6315 Oldfield, 0 Emsley, 6315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 984 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 983 time to evaluate : 7.011 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: LA 132 ASN cc_start: 0.7978 (m110) cc_final: 0.7659 (m110) REVERT: LA 133 TYR cc_start: 0.8413 (p90) cc_final: 0.7964 (p90) REVERT: LA 160 SER cc_start: 0.9251 (t) cc_final: 0.8971 (p) REVERT: LB 66 LYS cc_start: 0.7341 (pttt) cc_final: 0.6607 (mptt) REVERT: LC 1 MET cc_start: 0.4967 (mtp) cc_final: 0.4375 (tmm) REVERT: LC 267 TRP cc_start: 0.8415 (m-10) cc_final: 0.8048 (m-10) REVERT: LD 239 MET cc_start: 0.8581 (ppp) cc_final: 0.8183 (ppp) REVERT: LD 271 MET cc_start: 0.7888 (pmm) cc_final: 0.7564 (pmm) REVERT: LE 115 TYR cc_start: 0.8804 (t80) cc_final: 0.8293 (t80) REVERT: LF 110 GLN cc_start: 0.8774 (mp-120) cc_final: 0.8521 (mp10) REVERT: LF 186 CYS cc_start: 0.7331 (m) cc_final: 0.6488 (m) REVERT: LF 189 ASP cc_start: 0.7633 (m-30) cc_final: 0.6506 (m-30) REVERT: LH 74 CYS cc_start: 0.8223 (m) cc_final: 0.7760 (m) REVERT: LI 52 MET cc_start: 0.7689 (ttm) cc_final: 0.7379 (ttm) REVERT: LI 142 LEU cc_start: 0.8159 (mm) cc_final: 0.7949 (mm) REVERT: LI 183 ASP cc_start: 0.8073 (p0) cc_final: 0.7782 (p0) REVERT: LM 44 GLN cc_start: 0.8249 (mm-40) cc_final: 0.8033 (mm-40) REVERT: LS 54 MET cc_start: 0.7101 (mmm) cc_final: 0.6901 (mmt) REVERT: LT 30 TYR cc_start: 0.7871 (m-80) cc_final: 0.7568 (m-80) REVERT: LT 57 TYR cc_start: 0.8613 (m-80) cc_final: 0.8369 (m-80) REVERT: LZ 49 TYR cc_start: 0.8255 (m-80) cc_final: 0.7983 (m-80) REVERT: Lc 22 MET cc_start: 0.8924 (mmp) cc_final: 0.8691 (mmp) REVERT: Lc 27 TYR cc_start: 0.7988 (p90) cc_final: 0.7553 (p90) REVERT: Lc 81 LEU cc_start: 0.9280 (tp) cc_final: 0.8957 (tp) REVERT: Lc 90 ARG cc_start: 0.8911 (mpp80) cc_final: 0.8592 (mpp80) REVERT: Ld 93 ASN cc_start: 0.7020 (t0) cc_final: 0.6338 (t0) REVERT: Lg 13 TYR cc_start: 0.8779 (m-80) cc_final: 0.8262 (m-80) REVERT: Lk 10 ASP cc_start: 0.8478 (p0) cc_final: 0.8170 (p0) REVERT: Lk 12 LEU cc_start: 0.9165 (tp) cc_final: 0.8813 (tp) REVERT: Lm 92 ASP cc_start: 0.7809 (p0) cc_final: 0.7570 (p0) REVERT: Lr 25 TYR cc_start: 0.8526 (m-80) cc_final: 0.8195 (m-80) REVERT: A 88 HIS cc_start: 0.8006 (m170) cc_final: 0.7782 (m170) REVERT: A 255 TYR cc_start: 0.8540 (t80) cc_final: 0.8088 (t80) outliers start: 1 outliers final: 0 residues processed: 984 average time/residue: 1.3443 time to fit residues: 2403.0076 Evaluate side-chains 782 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 782 time to evaluate : 6.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1019 random chunks: chunk 860 optimal weight: 10.0000 chunk 772 optimal weight: 7.9990 chunk 428 optimal weight: 0.9990 chunk 263 optimal weight: 10.0000 chunk 520 optimal weight: 9.9990 chunk 412 optimal weight: 5.9990 chunk 798 optimal weight: 10.0000 chunk 309 optimal weight: 10.0000 chunk 485 optimal weight: 8.9990 chunk 594 optimal weight: 9.9990 chunk 925 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** LC 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 38 ASN ** LG 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 85 GLN ** LG 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LG 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 159 HIS LG 240 ASN LH 162 GLN LH 163 GLN ** LI 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LL 115 GLN LL 188 ASN LM 56 GLN ** LP 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 145 HIS LS 125 GLN ** LT 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LZ 78 ASN LZ 132 GLN La 25 HIS ** La 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lc 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lc 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Le 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lf 78 HIS Lg 3 GLN ** Lh 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Li 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ll 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.0717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 147758 Z= 0.370 Angle : 0.726 14.519 218687 Z= 0.367 Chirality : 0.040 0.333 27382 Planarity : 0.006 0.105 12914 Dihedral : 25.382 179.758 70126 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 22.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.21 % Favored : 89.72 % Rotamer: Outliers : 1.91 % Allowed : 12.12 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.05 % Twisted Proline : 0.73 % Twisted General : 0.05 % 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: -2.73 (0.10), residues: 6315 helix: -1.22 (0.11), residues: 2045 sheet: -2.02 (0.17), residues: 885 loop : -2.15 (0.10), residues: 3385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRPLb 16 HIS 0.008 0.001 HISLH 76 PHE 0.022 0.002 PHELa 69 TYR 0.032 0.002 TYRLZ 18 ARG 0.010 0.001 ARGLl 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12630 Ramachandran restraints generated. 6315 Oldfield, 0 Emsley, 6315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12630 Ramachandran restraints generated. 6315 Oldfield, 0 Emsley, 6315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 982 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 877 time to evaluate : 6.865 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: LA 132 ASN cc_start: 0.7919 (m110) cc_final: 0.7571 (m110) REVERT: LA 133 TYR cc_start: 0.8428 (p90) cc_final: 0.7943 (p90) REVERT: LA 160 SER cc_start: 0.9198 (t) cc_final: 0.8933 (p) REVERT: LB 66 LYS cc_start: 0.7202 (pttt) cc_final: 0.6510 (mptt) REVERT: LC 1 MET cc_start: 0.4841 (mtp) cc_final: 0.4411 (tmm) REVERT: LD 239 MET cc_start: 0.8574 (ppp) cc_final: 0.8275 (ppp) REVERT: LD 271 MET cc_start: 0.7942 (pmm) cc_final: 0.7622 (pmm) REVERT: LE 115 TYR cc_start: 0.8801 (t80) cc_final: 0.8308 (t80) REVERT: LF 152 GLU cc_start: 0.8177 (pp20) cc_final: 0.7883 (pp20) REVERT: LF 186 CYS cc_start: 0.7461 (m) cc_final: 0.6256 (m) REVERT: LF 189 ASP cc_start: 0.7345 (m-30) cc_final: 0.6465 (m-30) REVERT: LH 58 ASP cc_start: 0.7865 (p0) cc_final: 0.6947 (p0) REVERT: LI 87 MET cc_start: 0.6617 (tmm) cc_final: 0.6233 (tmm) REVERT: LI 115 MET cc_start: 0.6960 (ppp) cc_final: 0.6632 (ppp) REVERT: LI 179 ASP cc_start: 0.8499 (p0) cc_final: 0.8217 (p0) REVERT: LL 115 GLN cc_start: 0.8299 (mm110) cc_final: 0.7966 (mm-40) REVERT: LM 44 GLN cc_start: 0.8284 (mm-40) cc_final: 0.8060 (mm-40) REVERT: LN 46 ASP cc_start: 0.7910 (p0) cc_final: 0.7687 (p0) REVERT: LN 53 TYR cc_start: 0.8688 (t80) cc_final: 0.8461 (t80) REVERT: LO 47 PHE cc_start: 0.8225 (t80) cc_final: 0.7932 (t80) REVERT: LQ 147 GLU cc_start: 0.8515 (pm20) cc_final: 0.8096 (pm20) REVERT: LT 30 TYR cc_start: 0.8113 (m-80) cc_final: 0.7664 (m-80) REVERT: LT 31 MET cc_start: 0.7710 (ptm) cc_final: 0.7399 (tmm) REVERT: LT 57 TYR cc_start: 0.8602 (m-80) cc_final: 0.8387 (m-80) REVERT: LT 65 TYR cc_start: 0.8229 (p90) cc_final: 0.7832 (p90) REVERT: LW 58 LYS cc_start: 0.8084 (ptpp) cc_final: 0.7804 (ptpp) REVERT: LY 62 TYR cc_start: 0.8017 (m-80) cc_final: 0.7595 (m-10) REVERT: Ld 93 ASN cc_start: 0.6874 (t0) cc_final: 0.6128 (t0) REVERT: Lf 104 MET cc_start: 0.8365 (mmm) cc_final: 0.8103 (mmm) REVERT: Lh 30 GLN cc_start: 0.8973 (mm-40) cc_final: 0.8616 (mp10) REVERT: Lk 6 GLU cc_start: 0.8476 (pm20) cc_final: 0.8046 (mp0) REVERT: Lk 12 LEU cc_start: 0.9236 (tp) cc_final: 0.8968 (tp) REVERT: Lr 25 TYR cc_start: 0.8570 (m-80) cc_final: 0.8313 (m-80) REVERT: A 207 ASP cc_start: 0.8314 (p0) cc_final: 0.7988 (p0) REVERT: A 255 TYR cc_start: 0.8550 (t80) cc_final: 0.8109 (t80) outliers start: 105 outliers final: 75 residues processed: 915 average time/residue: 1.1486 time to fit residues: 1887.0591 Evaluate side-chains 854 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 779 time to evaluate : 6.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LA residue 47 ASP Chi-restraints excluded: chain LB residue 336 CYS Chi-restraints excluded: chain LF residue 83 VAL Chi-restraints excluded: chain LF residue 105 VAL Chi-restraints excluded: chain LF residue 108 VAL Chi-restraints excluded: chain LF residue 121 THR Chi-restraints excluded: chain LF residue 170 THR Chi-restraints excluded: chain LG residue 38 ASN Chi-restraints excluded: chain LG residue 44 ASP Chi-restraints excluded: chain LG residue 149 ASN Chi-restraints excluded: chain LG residue 204 PHE Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LH residue 183 GLU Chi-restraints excluded: chain LI residue 144 ASN Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 101 ASP Chi-restraints excluded: chain LJ residue 132 VAL Chi-restraints excluded: chain LM residue 83 ASN Chi-restraints excluded: chain LN residue 27 CYS Chi-restraints excluded: chain LN residue 135 ILE Chi-restraints excluded: chain LN residue 147 ASP Chi-restraints excluded: chain LN residue 151 ILE Chi-restraints excluded: chain LO residue 67 SER Chi-restraints excluded: chain LO residue 153 THR Chi-restraints excluded: chain LO residue 190 ASP Chi-restraints excluded: chain LP residue 29 THR Chi-restraints excluded: chain LP residue 32 THR Chi-restraints excluded: chain LP residue 67 VAL Chi-restraints excluded: chain LP residue 114 ILE Chi-restraints excluded: chain LP residue 117 ILE Chi-restraints excluded: chain LP residue 146 ILE Chi-restraints excluded: chain LQ residue 10 ASP Chi-restraints excluded: chain LQ residue 134 CYS Chi-restraints excluded: chain LR residue 47 ASP Chi-restraints excluded: chain LR residue 57 VAL Chi-restraints excluded: chain LR residue 115 ILE Chi-restraints excluded: chain LS residue 64 CYS Chi-restraints excluded: chain LT residue 33 ILE Chi-restraints excluded: chain LT residue 68 THR Chi-restraints excluded: chain LU residue 26 THR Chi-restraints excluded: chain LX residue 120 ASP Chi-restraints excluded: chain LX residue 128 ILE Chi-restraints excluded: chain LZ residue 47 ASP Chi-restraints excluded: chain La residue 34 ASN Chi-restraints excluded: chain La residue 76 ASP Chi-restraints excluded: chain La residue 78 LEU Chi-restraints excluded: chain La residue 95 THR Chi-restraints excluded: chain La residue 144 CYS Chi-restraints excluded: chain Lc residue 13 SER Chi-restraints excluded: chain Lc residue 45 LEU Chi-restraints excluded: chain Ld residue 65 ASP Chi-restraints excluded: chain Ld residue 116 ASN Chi-restraints excluded: chain Ld residue 119 THR Chi-restraints excluded: chain Le residue 91 CYS Chi-restraints excluded: chain Le residue 122 VAL Chi-restraints excluded: chain Lf residue 25 THR Chi-restraints excluded: chain Lf residue 27 LEU Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lf residue 47 CYS Chi-restraints excluded: chain Lf residue 84 VAL Chi-restraints excluded: chain Lh residue 8 ASP Chi-restraints excluded: chain Lh residue 23 ASP Chi-restraints excluded: chain Li residue 47 VAL Chi-restraints excluded: chain Li residue 88 GLU Chi-restraints excluded: chain Lj residue 17 THR Chi-restraints excluded: chain Lj residue 18 LEU Chi-restraints excluded: chain Lj residue 24 SER Chi-restraints excluded: chain Lk residue 46 VAL Chi-restraints excluded: chain Ll residue 6 THR Chi-restraints excluded: chain Ll residue 29 MET Chi-restraints excluded: chain Lm residue 103 LEU Chi-restraints excluded: chain Lo residue 24 THR Chi-restraints excluded: chain Lp residue 72 ASN Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain A residue 252 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1019 random chunks: chunk 514 optimal weight: 20.0000 chunk 287 optimal weight: 10.0000 chunk 770 optimal weight: 10.0000 chunk 630 optimal weight: 7.9990 chunk 255 optimal weight: 10.0000 chunk 927 optimal weight: 4.9990 chunk 1001 optimal weight: 0.0570 chunk 825 optimal weight: 8.9990 chunk 919 optimal weight: 0.8980 chunk 316 optimal weight: 10.0000 chunk 743 optimal weight: 3.9990 overall best weight: 3.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LA 83 HIS ** LC 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 226 HIS LG 81 ASN ** LG 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LG 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 240 ASN ** LI 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LI 166 HIS ** LJ 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LJ 110 GLN ** LL 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LL 188 ASN ** LP 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 97 ASN LS 125 GLN ** LT 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LT 95 HIS ** La 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lb 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lc 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Le 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lg 3 GLN ** Lh 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ll 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lr 12 ASN Lr 30 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 147758 Z= 0.238 Angle : 0.641 13.345 218687 Z= 0.324 Chirality : 0.036 0.356 27382 Planarity : 0.005 0.091 12914 Dihedral : 25.236 179.998 70126 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.52 % Favored : 91.43 % Rotamer: Outliers : 2.68 % Allowed : 15.93 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.05 % Twisted Proline : 0.73 % Twisted General : 0.07 % 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: -2.43 (0.10), residues: 6315 helix: -0.96 (0.11), residues: 2049 sheet: -1.80 (0.17), residues: 880 loop : -1.99 (0.11), residues: 3386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRPLb 16 HIS 0.011 0.001 HISLI 166 PHE 0.027 0.002 PHELM 64 TYR 0.028 0.002 TYRLZ 18 ARG 0.009 0.000 ARGLb 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12630 Ramachandran restraints generated. 6315 Oldfield, 0 Emsley, 6315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12630 Ramachandran restraints generated. 6315 Oldfield, 0 Emsley, 6315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1068 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 921 time to evaluate : 7.067 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: LA 132 ASN cc_start: 0.7818 (m110) cc_final: 0.7475 (m110) REVERT: LA 133 TYR cc_start: 0.8383 (p90) cc_final: 0.7906 (p90) REVERT: LA 160 SER cc_start: 0.9141 (t) cc_final: 0.8901 (p) REVERT: LB 66 LYS cc_start: 0.7121 (pttt) cc_final: 0.6497 (mptt) REVERT: LC 1 MET cc_start: 0.4661 (mtp) cc_final: 0.4322 (tmm) REVERT: LD 271 MET cc_start: 0.7765 (pmm) cc_final: 0.7501 (pmm) REVERT: LE 115 TYR cc_start: 0.8799 (t80) cc_final: 0.8412 (t80) REVERT: LE 245 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8306 (tm-30) REVERT: LF 154 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8975 (mp) REVERT: LF 189 ASP cc_start: 0.7247 (m-30) cc_final: 0.6493 (m-30) REVERT: LG 204 PHE cc_start: 0.7898 (OUTLIER) cc_final: 0.7083 (m-80) REVERT: LH 74 CYS cc_start: 0.8377 (m) cc_final: 0.8106 (m) REVERT: LI 56 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7519 (tm-30) REVERT: LI 87 MET cc_start: 0.6600 (tmm) cc_final: 0.6134 (tmm) REVERT: LI 115 MET cc_start: 0.6869 (ppp) cc_final: 0.6191 (ppp) REVERT: LI 183 ASP cc_start: 0.8272 (p0) cc_final: 0.7992 (p0) REVERT: LJ 12 MET cc_start: 0.7520 (ppp) cc_final: 0.6795 (ppp) REVERT: LJ 155 HIS cc_start: 0.7566 (OUTLIER) cc_final: 0.6668 (m170) REVERT: LL 18 TRP cc_start: 0.8491 (p-90) cc_final: 0.8275 (p-90) REVERT: LL 115 GLN cc_start: 0.8481 (mm110) cc_final: 0.8150 (mm-40) REVERT: LL 155 MET cc_start: 0.7377 (mpp) cc_final: 0.7172 (mpp) REVERT: LM 44 GLN cc_start: 0.8294 (mm-40) cc_final: 0.8044 (mm-40) REVERT: LM 113 MET cc_start: 0.8687 (tpt) cc_final: 0.8370 (tpt) REVERT: LN 46 ASP cc_start: 0.7954 (p0) cc_final: 0.7745 (p0) REVERT: LO 47 PHE cc_start: 0.8124 (t80) cc_final: 0.7865 (t80) REVERT: LQ 147 GLU cc_start: 0.8636 (pm20) cc_final: 0.8172 (pm20) REVERT: LR 102 LEU cc_start: 0.9114 (pp) cc_final: 0.8865 (pp) REVERT: LS 99 ASP cc_start: 0.6656 (m-30) cc_final: 0.6332 (m-30) REVERT: LT 57 TYR cc_start: 0.8520 (m-80) cc_final: 0.8285 (m-80) REVERT: LW 40 PHE cc_start: 0.8923 (t80) cc_final: 0.8689 (t80) REVERT: LX 155 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.7624 (tt) REVERT: LZ 119 GLU cc_start: 0.8290 (pp20) cc_final: 0.8078 (tm-30) REVERT: Ld 93 ASN cc_start: 0.6694 (t0) cc_final: 0.5947 (t0) REVERT: Lf 104 MET cc_start: 0.8319 (mmm) cc_final: 0.8114 (mmm) REVERT: Li 7 MET cc_start: 0.8043 (pmm) cc_final: 0.7714 (pmm) REVERT: Lk 6 GLU cc_start: 0.8475 (pm20) cc_final: 0.8089 (mp0) REVERT: Lk 12 LEU cc_start: 0.9228 (tp) cc_final: 0.8963 (tp) REVERT: Lr 25 TYR cc_start: 0.8557 (m-80) cc_final: 0.8086 (m-80) REVERT: A 157 VAL cc_start: 0.6993 (OUTLIER) cc_final: 0.6678 (t) REVERT: A 255 TYR cc_start: 0.8544 (t80) cc_final: 0.8089 (t80) REVERT: A 331 MET cc_start: 0.5592 (mtt) cc_final: 0.5373 (mtt) outliers start: 147 outliers final: 102 residues processed: 988 average time/residue: 1.1818 time to fit residues: 2105.4555 Evaluate side-chains 933 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 826 time to evaluate : 6.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LA residue 138 SER Chi-restraints excluded: chain LB residue 329 ASP Chi-restraints excluded: chain LC residue 111 TRP Chi-restraints excluded: chain LC residue 116 ASN Chi-restraints excluded: chain LD residue 51 MET Chi-restraints excluded: chain LD residue 55 VAL Chi-restraints excluded: chain LD residue 100 CYS Chi-restraints excluded: chain LD residue 155 THR Chi-restraints excluded: chain LE residue 202 ASP Chi-restraints excluded: chain LF residue 83 VAL Chi-restraints excluded: chain LF residue 105 VAL Chi-restraints excluded: chain LF residue 108 VAL Chi-restraints excluded: chain LF residue 121 THR Chi-restraints excluded: chain LF residue 154 ILE Chi-restraints excluded: chain LF residue 170 THR Chi-restraints excluded: chain LG residue 204 PHE Chi-restraints excluded: chain LG residue 231 ASP Chi-restraints excluded: chain LH residue 95 VAL Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LH residue 183 GLU Chi-restraints excluded: chain LI residue 26 VAL Chi-restraints excluded: chain LI residue 135 ILE Chi-restraints excluded: chain LI residue 142 LEU Chi-restraints excluded: chain LI residue 144 ASN Chi-restraints excluded: chain LI residue 150 GLU Chi-restraints excluded: chain LI residue 166 HIS Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 132 VAL Chi-restraints excluded: chain LJ residue 155 HIS Chi-restraints excluded: chain LL residue 168 VAL Chi-restraints excluded: chain LL residue 175 ASN Chi-restraints excluded: chain LL residue 194 ILE Chi-restraints excluded: chain LM residue 43 THR Chi-restraints excluded: chain LM residue 83 ASN Chi-restraints excluded: chain LN residue 80 THR Chi-restraints excluded: chain LN residue 135 ILE Chi-restraints excluded: chain LN residue 147 ASP Chi-restraints excluded: chain LN residue 151 ILE Chi-restraints excluded: chain LO residue 8 VAL Chi-restraints excluded: chain LO residue 34 VAL Chi-restraints excluded: chain LO residue 153 THR Chi-restraints excluded: chain LO residue 167 HIS Chi-restraints excluded: chain LO residue 190 ASP Chi-restraints excluded: chain LP residue 15 CYS Chi-restraints excluded: chain LP residue 29 THR Chi-restraints excluded: chain LP residue 32 THR Chi-restraints excluded: chain LP residue 67 VAL Chi-restraints excluded: chain LP residue 70 CYS Chi-restraints excluded: chain LP residue 103 GLU Chi-restraints excluded: chain LP residue 114 ILE Chi-restraints excluded: chain LP residue 117 ILE Chi-restraints excluded: chain LP residue 146 ILE Chi-restraints excluded: chain LQ residue 10 ASP Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LQ residue 134 CYS Chi-restraints excluded: chain LR residue 47 ASP Chi-restraints excluded: chain LR residue 57 VAL Chi-restraints excluded: chain LR residue 115 ILE Chi-restraints excluded: chain LS residue 7 LEU Chi-restraints excluded: chain LS residue 112 ASP Chi-restraints excluded: chain LS residue 129 VAL Chi-restraints excluded: chain LT residue 150 LEU Chi-restraints excluded: chain LW residue 44 ARG Chi-restraints excluded: chain LX residue 76 ILE Chi-restraints excluded: chain LX residue 90 ILE Chi-restraints excluded: chain LX residue 128 ILE Chi-restraints excluded: chain LX residue 155 ILE Chi-restraints excluded: chain LY residue 109 LEU Chi-restraints excluded: chain LZ residue 47 ASP Chi-restraints excluded: chain LZ residue 81 MET Chi-restraints excluded: chain La residue 76 ASP Chi-restraints excluded: chain La residue 95 THR Chi-restraints excluded: chain La residue 144 CYS Chi-restraints excluded: chain Lc residue 45 LEU Chi-restraints excluded: chain Ld residue 65 ASP Chi-restraints excluded: chain Ld residue 107 THR Chi-restraints excluded: chain Ld residue 116 ASN Chi-restraints excluded: chain Le residue 91 CYS Chi-restraints excluded: chain Le residue 122 VAL Chi-restraints excluded: chain Lf residue 10 ILE Chi-restraints excluded: chain Lf residue 25 THR Chi-restraints excluded: chain Lf residue 27 LEU Chi-restraints excluded: chain Lf residue 47 CYS Chi-restraints excluded: chain Lf residue 84 VAL Chi-restraints excluded: chain Lf residue 97 ILE Chi-restraints excluded: chain Lg residue 11 LEU Chi-restraints excluded: chain Lh residue 8 ASP Chi-restraints excluded: chain Lh residue 23 ASP Chi-restraints excluded: chain Li residue 47 VAL Chi-restraints excluded: chain Li residue 61 LEU Chi-restraints excluded: chain Li residue 88 GLU Chi-restraints excluded: chain Lj residue 18 LEU Chi-restraints excluded: chain Lj residue 24 SER Chi-restraints excluded: chain Lk residue 32 VAL Chi-restraints excluded: chain Lk residue 46 VAL Chi-restraints excluded: chain Ll residue 6 THR Chi-restraints excluded: chain Ll residue 29 MET Chi-restraints excluded: chain Lm residue 103 LEU Chi-restraints excluded: chain Lo residue 10 THR Chi-restraints excluded: chain Lo residue 24 THR Chi-restraints excluded: chain Lp residue 45 THR Chi-restraints excluded: chain Lp residue 72 ASN Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 323 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1019 random chunks: chunk 915 optimal weight: 6.9990 chunk 696 optimal weight: 8.9990 chunk 481 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 442 optimal weight: 9.9990 chunk 622 optimal weight: 9.9990 chunk 930 optimal weight: 9.9990 chunk 984 optimal weight: 0.0270 chunk 486 optimal weight: 0.9990 chunk 881 optimal weight: 2.9990 chunk 265 optimal weight: 10.0000 overall best weight: 3.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** LC 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 187 GLN ** LD 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 38 ASN ** LG 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LG 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LI 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LI 166 HIS ** LJ 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LL 188 ASN LN 156 HIS ** LO 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LO 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 125 GLN LS 144 GLN ** LT 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** La 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lb 19 ASN ** Lc 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Le 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lf 20 ASN ** Lh 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ll 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lm 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Lr 12 ASN Lr 30 ASN ** A 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 147758 Z= 0.241 Angle : 0.630 12.007 218687 Z= 0.318 Chirality : 0.036 0.352 27382 Planarity : 0.005 0.084 12914 Dihedral : 25.137 179.602 70126 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.66 % Favored : 91.29 % Rotamer: Outliers : 3.52 % Allowed : 18.11 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.05 % Twisted Proline : 0.73 % Twisted General : 0.03 % 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: -2.25 (0.10), residues: 6315 helix: -0.80 (0.11), residues: 2047 sheet: -1.76 (0.17), residues: 877 loop : -1.86 (0.11), residues: 3391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPLb 16 HIS 0.010 0.001 HIS A 88 PHE 0.027 0.002 PHELa 69 TYR 0.028 0.002 TYRLQ 186 ARG 0.009 0.000 ARGLb 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12630 Ramachandran restraints generated. 6315 Oldfield, 0 Emsley, 6315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12630 Ramachandran restraints generated. 6315 Oldfield, 0 Emsley, 6315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1076 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 883 time to evaluate : 6.920 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 revert: symmetry clash REVERT: LA 132 ASN cc_start: 0.7831 (m110) cc_final: 0.7533 (m110) REVERT: LA 133 TYR cc_start: 0.8368 (p90) cc_final: 0.7901 (p90) REVERT: LA 160 SER cc_start: 0.9127 (t) cc_final: 0.8868 (p) REVERT: LB 66 LYS cc_start: 0.7125 (pttt) cc_final: 0.6510 (mptt) REVERT: LC 85 HIS cc_start: 0.7806 (OUTLIER) cc_final: 0.7571 (t-170) REVERT: LC 138 MET cc_start: 0.8350 (mmt) cc_final: 0.8037 (mmt) REVERT: LD 271 MET cc_start: 0.7715 (pmm) cc_final: 0.7497 (ptp) REVERT: LE 62 MET cc_start: 0.9097 (mmm) cc_final: 0.8526 (mmm) REVERT: LE 115 TYR cc_start: 0.8801 (t80) cc_final: 0.8500 (t80) REVERT: LF 247 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7463 (mpp) REVERT: LG 204 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.7103 (m-80) REVERT: LH 74 CYS cc_start: 0.8396 (m) cc_final: 0.8120 (m) REVERT: LI 87 MET cc_start: 0.6638 (tmm) cc_final: 0.6278 (tmm) REVERT: LI 115 MET cc_start: 0.6981 (ppp) cc_final: 0.6182 (ppp) REVERT: LJ 12 MET cc_start: 0.7525 (ppp) cc_final: 0.6851 (ppp) REVERT: LJ 155 HIS cc_start: 0.7109 (OUTLIER) cc_final: 0.6860 (m170) REVERT: LM 44 GLN cc_start: 0.8353 (mm-40) cc_final: 0.8035 (mm-40) REVERT: LN 46 ASP cc_start: 0.7966 (p0) cc_final: 0.7695 (p0) REVERT: LO 47 PHE cc_start: 0.8146 (t80) cc_final: 0.7809 (t80) REVERT: LR 140 GLU cc_start: 0.8488 (pp20) cc_final: 0.8256 (pp20) REVERT: LW 40 PHE cc_start: 0.8910 (t80) cc_final: 0.8690 (t80) REVERT: LX 155 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7620 (tt) REVERT: LZ 119 GLU cc_start: 0.8324 (pp20) cc_final: 0.8057 (tm-30) REVERT: Ld 93 ASN cc_start: 0.6798 (t0) cc_final: 0.5990 (t0) REVERT: Lf 104 MET cc_start: 0.8313 (mmm) cc_final: 0.8096 (mmm) REVERT: Li 7 MET cc_start: 0.8000 (pmm) cc_final: 0.7645 (pmm) REVERT: Lk 6 GLU cc_start: 0.8517 (pm20) cc_final: 0.7905 (mp0) REVERT: Lk 12 LEU cc_start: 0.9249 (tp) cc_final: 0.8932 (tp) REVERT: A 157 VAL cc_start: 0.6903 (OUTLIER) cc_final: 0.6581 (t) REVERT: A 331 MET cc_start: 0.5713 (mtt) cc_final: 0.5505 (mtt) outliers start: 193 outliers final: 139 residues processed: 987 average time/residue: 1.1181 time to fit residues: 1990.6572 Evaluate side-chains 959 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 814 time to evaluate : 6.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LA residue 45 VAL Chi-restraints excluded: chain LA residue 62 VAL Chi-restraints excluded: chain LA residue 73 THR Chi-restraints excluded: chain LA residue 138 SER Chi-restraints excluded: chain LA residue 165 VAL Chi-restraints excluded: chain LB residue 90 VAL Chi-restraints excluded: chain LB residue 105 VAL Chi-restraints excluded: chain LB residue 147 GLU Chi-restraints excluded: chain LB residue 329 ASP Chi-restraints excluded: chain LB residue 336 CYS Chi-restraints excluded: chain LC residue 85 HIS Chi-restraints excluded: chain LC residue 111 TRP Chi-restraints excluded: chain LC residue 116 ASN Chi-restraints excluded: chain LD residue 55 VAL Chi-restraints excluded: chain LD residue 100 CYS Chi-restraints excluded: chain LD residue 110 LEU Chi-restraints excluded: chain LD residue 155 THR Chi-restraints excluded: chain LE residue 202 ASP Chi-restraints excluded: chain LF residue 83 VAL Chi-restraints excluded: chain LF residue 105 VAL Chi-restraints excluded: chain LF residue 121 THR Chi-restraints excluded: chain LF residue 170 THR Chi-restraints excluded: chain LF residue 175 ILE Chi-restraints excluded: chain LF residue 186 CYS Chi-restraints excluded: chain LF residue 247 MET Chi-restraints excluded: chain LG residue 38 ASN Chi-restraints excluded: chain LG residue 63 LEU Chi-restraints excluded: chain LG residue 149 ASN Chi-restraints excluded: chain LG residue 204 PHE Chi-restraints excluded: chain LG residue 231 ASP Chi-restraints excluded: chain LH residue 95 VAL Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LH residue 183 GLU Chi-restraints excluded: chain LI residue 26 VAL Chi-restraints excluded: chain LI residue 53 VAL Chi-restraints excluded: chain LI residue 135 ILE Chi-restraints excluded: chain LI residue 142 LEU Chi-restraints excluded: chain LI residue 144 ASN Chi-restraints excluded: chain LI residue 150 GLU Chi-restraints excluded: chain LI residue 166 HIS Chi-restraints excluded: chain LI residue 207 ASP Chi-restraints excluded: chain LI residue 213 HIS Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 101 ASP Chi-restraints excluded: chain LJ residue 104 ASN Chi-restraints excluded: chain LJ residue 132 VAL Chi-restraints excluded: chain LJ residue 155 HIS Chi-restraints excluded: chain LL residue 175 ASN Chi-restraints excluded: chain LL residue 194 ILE Chi-restraints excluded: chain LM residue 15 VAL Chi-restraints excluded: chain LM residue 43 THR Chi-restraints excluded: chain LM residue 61 ILE Chi-restraints excluded: chain LM residue 83 ASN Chi-restraints excluded: chain LM residue 96 GLU Chi-restraints excluded: chain LM residue 113 MET Chi-restraints excluded: chain LN residue 80 THR Chi-restraints excluded: chain LN residue 123 GLU Chi-restraints excluded: chain LN residue 135 ILE Chi-restraints excluded: chain LN residue 147 ASP Chi-restraints excluded: chain LN residue 151 ILE Chi-restraints excluded: chain LO residue 8 VAL Chi-restraints excluded: chain LO residue 34 VAL Chi-restraints excluded: chain LO residue 67 SER Chi-restraints excluded: chain LO residue 106 ASP Chi-restraints excluded: chain LO residue 153 THR Chi-restraints excluded: chain LO residue 167 HIS Chi-restraints excluded: chain LO residue 190 ASP Chi-restraints excluded: chain LP residue 15 CYS Chi-restraints excluded: chain LP residue 29 THR Chi-restraints excluded: chain LP residue 32 THR Chi-restraints excluded: chain LP residue 67 VAL Chi-restraints excluded: chain LP residue 70 CYS Chi-restraints excluded: chain LP residue 103 GLU Chi-restraints excluded: chain LP residue 114 ILE Chi-restraints excluded: chain LP residue 117 ILE Chi-restraints excluded: chain LQ residue 10 ASP Chi-restraints excluded: chain LQ residue 39 THR Chi-restraints excluded: chain LQ residue 134 CYS Chi-restraints excluded: chain LR residue 47 ASP Chi-restraints excluded: chain LR residue 57 VAL Chi-restraints excluded: chain LR residue 115 ILE Chi-restraints excluded: chain LS residue 62 VAL Chi-restraints excluded: chain LS residue 112 ASP Chi-restraints excluded: chain LS residue 129 VAL Chi-restraints excluded: chain LS residue 154 LEU Chi-restraints excluded: chain LT residue 33 ILE Chi-restraints excluded: chain LT residue 89 ILE Chi-restraints excluded: chain LT residue 103 ASP Chi-restraints excluded: chain LT residue 109 VAL Chi-restraints excluded: chain LT residue 150 LEU Chi-restraints excluded: chain LU residue 29 VAL Chi-restraints excluded: chain LW residue 44 ARG Chi-restraints excluded: chain LX residue 54 LEU Chi-restraints excluded: chain LX residue 76 ILE Chi-restraints excluded: chain LX residue 90 ILE Chi-restraints excluded: chain LX residue 128 ILE Chi-restraints excluded: chain LX residue 155 ILE Chi-restraints excluded: chain LY residue 109 LEU Chi-restraints excluded: chain LZ residue 47 ASP Chi-restraints excluded: chain LZ residue 68 ILE Chi-restraints excluded: chain LZ residue 81 MET Chi-restraints excluded: chain LZ residue 106 LEU Chi-restraints excluded: chain La residue 76 ASP Chi-restraints excluded: chain La residue 78 LEU Chi-restraints excluded: chain La residue 95 THR Chi-restraints excluded: chain Ld residue 49 ILE Chi-restraints excluded: chain Ld residue 59 THR Chi-restraints excluded: chain Ld residue 65 ASP Chi-restraints excluded: chain Ld residue 107 THR Chi-restraints excluded: chain Ld residue 116 ASN Chi-restraints excluded: chain Ld residue 119 THR Chi-restraints excluded: chain Le residue 76 LYS Chi-restraints excluded: chain Le residue 91 CYS Chi-restraints excluded: chain Le residue 122 VAL Chi-restraints excluded: chain Lf residue 25 THR Chi-restraints excluded: chain Lf residue 27 LEU Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lf residue 84 VAL Chi-restraints excluded: chain Lf residue 97 ILE Chi-restraints excluded: chain Lg residue 11 LEU Chi-restraints excluded: chain Lh residue 8 ASP Chi-restraints excluded: chain Lh residue 23 ASP Chi-restraints excluded: chain Lh residue 104 THR Chi-restraints excluded: chain Li residue 47 VAL Chi-restraints excluded: chain Li residue 61 LEU Chi-restraints excluded: chain Li residue 88 GLU Chi-restraints excluded: chain Lj residue 24 SER Chi-restraints excluded: chain Lk residue 32 VAL Chi-restraints excluded: chain Lk residue 46 VAL Chi-restraints excluded: chain Ll residue 6 THR Chi-restraints excluded: chain Lm residue 103 LEU Chi-restraints excluded: chain Lm residue 108 VAL Chi-restraints excluded: chain Lm residue 127 VAL Chi-restraints excluded: chain Lo residue 10 THR Chi-restraints excluded: chain Lo residue 24 THR Chi-restraints excluded: chain Lp residue 16 THR Chi-restraints excluded: chain Lp residue 72 ASN Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 323 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1019 random chunks: chunk 820 optimal weight: 8.9990 chunk 559 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 733 optimal weight: 0.7980 chunk 406 optimal weight: 3.9990 chunk 840 optimal weight: 10.0000 chunk 680 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 502 optimal weight: 30.0000 chunk 884 optimal weight: 20.0000 chunk 248 optimal weight: 10.0000 overall best weight: 4.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** LC 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LD 191 ASN ** LD 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 239 GLN LG 85 GLN ** LG 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LG 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LI 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LI 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 33 GLN ** LO 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LW 48 GLN ** La 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** La 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lc 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Le 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lf 20 ASN Lf 91 ASN ** Lh 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ll 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lm 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Lr 12 ASN ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 147758 Z= 0.291 Angle : 0.651 16.234 218687 Z= 0.328 Chirality : 0.037 0.337 27382 Planarity : 0.005 0.083 12914 Dihedral : 25.104 179.963 70126 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.99 % Favored : 90.97 % Rotamer: Outliers : 4.01 % Allowed : 19.37 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.05 % Twisted Proline : 0.73 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.10), residues: 6315 helix: -0.71 (0.11), residues: 2030 sheet: -1.75 (0.17), residues: 874 loop : -1.84 (0.11), residues: 3411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPLb 16 HIS 0.010 0.001 HISLI 166 PHE 0.031 0.002 PHELa 69 TYR 0.031 0.002 TYRLW 11 ARG 0.005 0.000 ARGLQ 108 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12630 Ramachandran restraints generated. 6315 Oldfield, 0 Emsley, 6315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12630 Ramachandran restraints generated. 6315 Oldfield, 0 Emsley, 6315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1073 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 853 time to evaluate : 7.025 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: LA 132 ASN cc_start: 0.7839 (m110) cc_final: 0.7533 (m110) REVERT: LA 133 TYR cc_start: 0.8396 (p90) cc_final: 0.7916 (p90) REVERT: LA 160 SER cc_start: 0.9166 (t) cc_final: 0.8911 (p) REVERT: LB 66 LYS cc_start: 0.7162 (pttt) cc_final: 0.6550 (mptt) REVERT: LC 85 HIS cc_start: 0.7851 (OUTLIER) cc_final: 0.7648 (t-170) REVERT: LC 138 MET cc_start: 0.8337 (mmt) cc_final: 0.8130 (mmt) REVERT: LC 145 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7992 (mm-30) REVERT: LE 62 MET cc_start: 0.9075 (mmm) cc_final: 0.8567 (mmm) REVERT: LE 115 TYR cc_start: 0.8827 (t80) cc_final: 0.8507 (t80) REVERT: LF 152 GLU cc_start: 0.8122 (pp20) cc_final: 0.7791 (pp20) REVERT: LG 204 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7084 (m-80) REVERT: LH 44 GLU cc_start: 0.6854 (mp0) cc_final: 0.6118 (mp0) REVERT: LH 58 ASP cc_start: 0.7713 (p0) cc_final: 0.6832 (p0) REVERT: LH 74 CYS cc_start: 0.8415 (m) cc_final: 0.8137 (m) REVERT: LJ 12 MET cc_start: 0.7611 (ppp) cc_final: 0.6886 (ppp) REVERT: LJ 155 HIS cc_start: 0.7226 (OUTLIER) cc_final: 0.6920 (m170) REVERT: LM 44 GLN cc_start: 0.8394 (mm-40) cc_final: 0.7969 (mm-40) REVERT: LN 46 ASP cc_start: 0.7985 (p0) cc_final: 0.7739 (p0) REVERT: LO 47 PHE cc_start: 0.8164 (t80) cc_final: 0.7956 (t80) REVERT: LQ 186 TYR cc_start: 0.8713 (p90) cc_final: 0.8481 (p90) REVERT: LR 140 GLU cc_start: 0.8584 (pp20) cc_final: 0.8300 (pp20) REVERT: LW 13 ILE cc_start: 0.6393 (OUTLIER) cc_final: 0.6023 (pt) REVERT: LZ 119 GLU cc_start: 0.8363 (pp20) cc_final: 0.8067 (tm-30) REVERT: Lc 90 ARG cc_start: 0.8742 (mpp80) cc_final: 0.8378 (mpp80) REVERT: Ld 93 ASN cc_start: 0.6825 (t0) cc_final: 0.6012 (t0) REVERT: Li 7 MET cc_start: 0.8037 (pmm) cc_final: 0.7663 (pmm) REVERT: Lk 12 LEU cc_start: 0.9247 (tp) cc_final: 0.8924 (tp) REVERT: Lo 82 MET cc_start: 0.4929 (ptt) cc_final: 0.4614 (ptt) REVERT: Lr 25 TYR cc_start: 0.8410 (m-80) cc_final: 0.8082 (m-80) REVERT: A 157 VAL cc_start: 0.6917 (OUTLIER) cc_final: 0.6593 (t) outliers start: 220 outliers final: 163 residues processed: 984 average time/residue: 1.0999 time to fit residues: 1949.2373 Evaluate side-chains 971 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 803 time to evaluate : 6.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LA residue 45 VAL Chi-restraints excluded: chain LA residue 62 VAL Chi-restraints excluded: chain LA residue 138 SER Chi-restraints excluded: chain LA residue 157 VAL Chi-restraints excluded: chain LA residue 165 VAL Chi-restraints excluded: chain LA residue 169 VAL Chi-restraints excluded: chain LB residue 90 VAL Chi-restraints excluded: chain LB residue 105 VAL Chi-restraints excluded: chain LB residue 147 GLU Chi-restraints excluded: chain LB residue 329 ASP Chi-restraints excluded: chain LB residue 336 CYS Chi-restraints excluded: chain LC residue 24 LEU Chi-restraints excluded: chain LC residue 85 HIS Chi-restraints excluded: chain LC residue 111 TRP Chi-restraints excluded: chain LC residue 116 ASN Chi-restraints excluded: chain LC residue 334 THR Chi-restraints excluded: chain LD residue 28 THR Chi-restraints excluded: chain LD residue 55 VAL Chi-restraints excluded: chain LD residue 100 CYS Chi-restraints excluded: chain LD residue 110 LEU Chi-restraints excluded: chain LD residue 115 MET Chi-restraints excluded: chain LD residue 155 THR Chi-restraints excluded: chain LD residue 171 LEU Chi-restraints excluded: chain LE residue 49 VAL Chi-restraints excluded: chain LE residue 202 ASP Chi-restraints excluded: chain LE residue 212 LEU Chi-restraints excluded: chain LE residue 258 LEU Chi-restraints excluded: chain LF residue 83 VAL Chi-restraints excluded: chain LF residue 105 VAL Chi-restraints excluded: chain LF residue 121 THR Chi-restraints excluded: chain LF residue 170 THR Chi-restraints excluded: chain LF residue 175 ILE Chi-restraints excluded: chain LF residue 186 CYS Chi-restraints excluded: chain LF residue 228 VAL Chi-restraints excluded: chain LG residue 33 GLU Chi-restraints excluded: chain LG residue 63 LEU Chi-restraints excluded: chain LG residue 149 ASN Chi-restraints excluded: chain LG residue 160 ASP Chi-restraints excluded: chain LG residue 204 PHE Chi-restraints excluded: chain LG residue 231 ASP Chi-restraints excluded: chain LH residue 95 VAL Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LH residue 183 GLU Chi-restraints excluded: chain LI residue 26 VAL Chi-restraints excluded: chain LI residue 53 VAL Chi-restraints excluded: chain LI residue 113 THR Chi-restraints excluded: chain LI residue 135 ILE Chi-restraints excluded: chain LI residue 142 LEU Chi-restraints excluded: chain LI residue 144 ASN Chi-restraints excluded: chain LI residue 150 GLU Chi-restraints excluded: chain LI residue 207 ASP Chi-restraints excluded: chain LI residue 213 HIS Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 101 ASP Chi-restraints excluded: chain LJ residue 104 ASN Chi-restraints excluded: chain LJ residue 132 VAL Chi-restraints excluded: chain LJ residue 155 HIS Chi-restraints excluded: chain LL residue 168 VAL Chi-restraints excluded: chain LL residue 175 ASN Chi-restraints excluded: chain LL residue 194 ILE Chi-restraints excluded: chain LM residue 15 VAL Chi-restraints excluded: chain LM residue 43 THR Chi-restraints excluded: chain LM residue 83 ASN Chi-restraints excluded: chain LM residue 96 GLU Chi-restraints excluded: chain LM residue 113 MET Chi-restraints excluded: chain LM residue 127 VAL Chi-restraints excluded: chain LN residue 27 CYS Chi-restraints excluded: chain LN residue 80 THR Chi-restraints excluded: chain LN residue 135 ILE Chi-restraints excluded: chain LN residue 147 ASP Chi-restraints excluded: chain LN residue 151 ILE Chi-restraints excluded: chain LN residue 174 LEU Chi-restraints excluded: chain LO residue 8 VAL Chi-restraints excluded: chain LO residue 34 VAL Chi-restraints excluded: chain LO residue 67 SER Chi-restraints excluded: chain LO residue 106 ASP Chi-restraints excluded: chain LO residue 132 THR Chi-restraints excluded: chain LO residue 153 THR Chi-restraints excluded: chain LO residue 167 HIS Chi-restraints excluded: chain LO residue 190 ASP Chi-restraints excluded: chain LP residue 15 CYS Chi-restraints excluded: chain LP residue 29 THR Chi-restraints excluded: chain LP residue 32 THR Chi-restraints excluded: chain LP residue 67 VAL Chi-restraints excluded: chain LP residue 70 CYS Chi-restraints excluded: chain LP residue 103 GLU Chi-restraints excluded: chain LP residue 114 ILE Chi-restraints excluded: chain LQ residue 5 ILE Chi-restraints excluded: chain LQ residue 10 ASP Chi-restraints excluded: chain LQ residue 39 THR Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LQ residue 134 CYS Chi-restraints excluded: chain LR residue 10 LEU Chi-restraints excluded: chain LR residue 47 ASP Chi-restraints excluded: chain LR residue 57 VAL Chi-restraints excluded: chain LR residue 115 ILE Chi-restraints excluded: chain LS residue 62 VAL Chi-restraints excluded: chain LS residue 112 ASP Chi-restraints excluded: chain LS residue 129 VAL Chi-restraints excluded: chain LS residue 154 LEU Chi-restraints excluded: chain LT residue 33 ILE Chi-restraints excluded: chain LT residue 89 ILE Chi-restraints excluded: chain LT residue 103 ASP Chi-restraints excluded: chain LT residue 109 VAL Chi-restraints excluded: chain LT residue 150 LEU Chi-restraints excluded: chain LU residue 40 GLU Chi-restraints excluded: chain LU residue 62 THR Chi-restraints excluded: chain LW residue 13 ILE Chi-restraints excluded: chain LW residue 44 ARG Chi-restraints excluded: chain LX residue 54 LEU Chi-restraints excluded: chain LX residue 76 ILE Chi-restraints excluded: chain LX residue 90 ILE Chi-restraints excluded: chain LX residue 128 ILE Chi-restraints excluded: chain LX residue 144 TYR Chi-restraints excluded: chain LY residue 109 LEU Chi-restraints excluded: chain LZ residue 47 ASP Chi-restraints excluded: chain LZ residue 68 ILE Chi-restraints excluded: chain LZ residue 81 MET Chi-restraints excluded: chain LZ residue 106 LEU Chi-restraints excluded: chain LZ residue 132 GLN Chi-restraints excluded: chain LZ residue 136 PHE Chi-restraints excluded: chain La residue 76 ASP Chi-restraints excluded: chain La residue 78 LEU Chi-restraints excluded: chain La residue 95 THR Chi-restraints excluded: chain Lc residue 13 SER Chi-restraints excluded: chain Lc residue 20 LEU Chi-restraints excluded: chain Ld residue 59 THR Chi-restraints excluded: chain Ld residue 65 ASP Chi-restraints excluded: chain Ld residue 107 THR Chi-restraints excluded: chain Ld residue 116 ASN Chi-restraints excluded: chain Ld residue 119 THR Chi-restraints excluded: chain Le residue 91 CYS Chi-restraints excluded: chain Le residue 122 VAL Chi-restraints excluded: chain Lf residue 25 THR Chi-restraints excluded: chain Lf residue 27 LEU Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lf residue 84 VAL Chi-restraints excluded: chain Lf residue 97 ILE Chi-restraints excluded: chain Lg residue 11 LEU Chi-restraints excluded: chain Lh residue 8 ASP Chi-restraints excluded: chain Lh residue 23 ASP Chi-restraints excluded: chain Li residue 47 VAL Chi-restraints excluded: chain Li residue 61 LEU Chi-restraints excluded: chain Li residue 88 GLU Chi-restraints excluded: chain Lj residue 24 SER Chi-restraints excluded: chain Lk residue 32 VAL Chi-restraints excluded: chain Lk residue 36 VAL Chi-restraints excluded: chain Lk residue 46 VAL Chi-restraints excluded: chain Lk residue 47 ILE Chi-restraints excluded: chain Ll residue 6 THR Chi-restraints excluded: chain Lm residue 103 LEU Chi-restraints excluded: chain Lm residue 108 VAL Chi-restraints excluded: chain Lm residue 127 VAL Chi-restraints excluded: chain Lo residue 10 THR Chi-restraints excluded: chain Lo residue 24 THR Chi-restraints excluded: chain Lo residue 76 ASN Chi-restraints excluded: chain Lp residue 16 THR Chi-restraints excluded: chain Lp residue 72 ASN Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 323 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1019 random chunks: chunk 331 optimal weight: 10.0000 chunk 887 optimal weight: 3.9990 chunk 194 optimal weight: 20.0000 chunk 578 optimal weight: 9.9990 chunk 243 optimal weight: 10.0000 chunk 985 optimal weight: 20.0000 chunk 818 optimal weight: 8.9990 chunk 456 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 326 optimal weight: 10.0000 chunk 517 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** LC 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LG 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LG 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LG 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LI 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LI 166 HIS ** LJ 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LL 19 GLN ** LO 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 56 GLN ** LP 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** La 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** La 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lb 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lc 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lc 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lc 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lc 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Le 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lf 20 ASN ** Lh 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lj 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ll 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lm 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Lr 83 ASN ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 147758 Z= 0.410 Angle : 0.733 14.921 218687 Z= 0.367 Chirality : 0.040 0.312 27382 Planarity : 0.006 0.116 12914 Dihedral : 25.160 179.588 70126 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 24.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.37 % Favored : 89.60 % Rotamer: Outliers : 4.61 % Allowed : 20.92 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.05 % Twisted Proline : 0.73 % Twisted General : 0.07 % 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: -2.34 (0.10), residues: 6315 helix: -0.83 (0.11), residues: 2029 sheet: -1.84 (0.17), residues: 879 loop : -1.93 (0.11), residues: 3407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPLb 16 HIS 0.015 0.002 HISLI 166 PHE 0.029 0.002 PHELa 69 TYR 0.027 0.002 TYRLZ 18 ARG 0.013 0.001 ARGLj 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12630 Ramachandran restraints generated. 6315 Oldfield, 0 Emsley, 6315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12630 Ramachandran restraints generated. 6315 Oldfield, 0 Emsley, 6315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1066 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 813 time to evaluate : 6.378 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: LA 132 ASN cc_start: 0.7893 (m110) cc_final: 0.7507 (m110) REVERT: LA 133 TYR cc_start: 0.8491 (p90) cc_final: 0.8106 (p90) REVERT: LA 160 SER cc_start: 0.9275 (t) cc_final: 0.9010 (p) REVERT: LB 66 LYS cc_start: 0.7175 (pttt) cc_final: 0.6576 (mptt) REVERT: LC 65 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7401 (tm-30) REVERT: LC 138 MET cc_start: 0.8391 (mmt) cc_final: 0.8156 (mmt) REVERT: LC 145 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8012 (mm-30) REVERT: LD 158 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8067 (mmtp) REVERT: LE 62 MET cc_start: 0.9068 (mmm) cc_final: 0.8787 (tpp) REVERT: LE 115 TYR cc_start: 0.8904 (t80) cc_final: 0.8516 (t80) REVERT: LF 57 TYR cc_start: 0.8416 (m-10) cc_final: 0.8216 (m-80) REVERT: LF 152 GLU cc_start: 0.8205 (pp20) cc_final: 0.7903 (pp20) REVERT: LG 204 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.7119 (m-80) REVERT: LH 44 GLU cc_start: 0.6830 (mp0) cc_final: 0.6335 (mp0) REVERT: LH 58 ASP cc_start: 0.7745 (p0) cc_final: 0.7164 (p0) REVERT: LH 74 CYS cc_start: 0.8406 (m) cc_final: 0.8117 (m) REVERT: LI 87 MET cc_start: 0.6515 (tmm) cc_final: 0.6288 (tmm) REVERT: LJ 101 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.7821 (p0) REVERT: LJ 111 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.6493 (tm-30) REVERT: LL 115 GLN cc_start: 0.8784 (mm110) cc_final: 0.8513 (mm110) REVERT: LM 44 GLN cc_start: 0.8361 (mm-40) cc_final: 0.7910 (mm-40) REVERT: LN 46 ASP cc_start: 0.8058 (p0) cc_final: 0.7810 (p0) REVERT: LO 192 TYR cc_start: 0.7681 (m-80) cc_final: 0.7337 (m-10) REVERT: LZ 119 GLU cc_start: 0.8390 (pp20) cc_final: 0.8042 (tm-30) REVERT: La 108 TYR cc_start: 0.8285 (m-80) cc_final: 0.8066 (m-80) REVERT: Lc 61 GLU cc_start: 0.8845 (tp30) cc_final: 0.8543 (tp30) REVERT: Ld 93 ASN cc_start: 0.6858 (t0) cc_final: 0.6073 (t0) REVERT: Li 7 MET cc_start: 0.8089 (pmm) cc_final: 0.7708 (pmm) REVERT: Lk 12 LEU cc_start: 0.9272 (tp) cc_final: 0.8968 (tp) REVERT: Ll 29 MET cc_start: 0.8520 (pmm) cc_final: 0.8054 (pmm) REVERT: Lo 82 MET cc_start: 0.5257 (ptt) cc_final: 0.4876 (ptt) REVERT: Lr 82 ILE cc_start: 0.9010 (mm) cc_final: 0.8723 (mm) REVERT: A 157 VAL cc_start: 0.6947 (OUTLIER) cc_final: 0.6637 (t) outliers start: 253 outliers final: 195 residues processed: 976 average time/residue: 1.1603 time to fit residues: 2054.1708 Evaluate side-chains 975 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 775 time to evaluate : 6.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LA residue 45 VAL Chi-restraints excluded: chain LA residue 47 ASP Chi-restraints excluded: chain LA residue 62 VAL Chi-restraints excluded: chain LA residue 138 SER Chi-restraints excluded: chain LA residue 157 VAL Chi-restraints excluded: chain LA residue 165 VAL Chi-restraints excluded: chain LA residue 169 VAL Chi-restraints excluded: chain LA residue 224 THR Chi-restraints excluded: chain LB residue 73 VAL Chi-restraints excluded: chain LB residue 90 VAL Chi-restraints excluded: chain LB residue 105 VAL Chi-restraints excluded: chain LB residue 147 GLU Chi-restraints excluded: chain LB residue 222 VAL Chi-restraints excluded: chain LB residue 329 ASP Chi-restraints excluded: chain LB residue 336 CYS Chi-restraints excluded: chain LC residue 24 LEU Chi-restraints excluded: chain LC residue 111 TRP Chi-restraints excluded: chain LC residue 116 ASN Chi-restraints excluded: chain LC residue 128 LEU Chi-restraints excluded: chain LC residue 334 THR Chi-restraints excluded: chain LD residue 28 THR Chi-restraints excluded: chain LD residue 55 VAL Chi-restraints excluded: chain LD residue 100 CYS Chi-restraints excluded: chain LD residue 110 LEU Chi-restraints excluded: chain LD residue 155 THR Chi-restraints excluded: chain LD residue 158 LYS Chi-restraints excluded: chain LD residue 171 LEU Chi-restraints excluded: chain LD residue 185 SER Chi-restraints excluded: chain LD residue 203 ASN Chi-restraints excluded: chain LE residue 49 VAL Chi-restraints excluded: chain LE residue 202 ASP Chi-restraints excluded: chain LE residue 212 LEU Chi-restraints excluded: chain LE residue 258 LEU Chi-restraints excluded: chain LF residue 83 VAL Chi-restraints excluded: chain LF residue 105 VAL Chi-restraints excluded: chain LF residue 121 THR Chi-restraints excluded: chain LF residue 170 THR Chi-restraints excluded: chain LF residue 175 ILE Chi-restraints excluded: chain LF residue 186 CYS Chi-restraints excluded: chain LF residue 228 VAL Chi-restraints excluded: chain LG residue 33 GLU Chi-restraints excluded: chain LG residue 63 LEU Chi-restraints excluded: chain LG residue 149 ASN Chi-restraints excluded: chain LG residue 160 ASP Chi-restraints excluded: chain LG residue 204 PHE Chi-restraints excluded: chain LG residue 231 ASP Chi-restraints excluded: chain LH residue 84 VAL Chi-restraints excluded: chain LH residue 95 VAL Chi-restraints excluded: chain LH residue 102 ASN Chi-restraints excluded: chain LH residue 104 VAL Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LH residue 183 GLU Chi-restraints excluded: chain LI residue 26 VAL Chi-restraints excluded: chain LI residue 53 VAL Chi-restraints excluded: chain LI residue 113 THR Chi-restraints excluded: chain LI residue 135 ILE Chi-restraints excluded: chain LI residue 142 LEU Chi-restraints excluded: chain LI residue 144 ASN Chi-restraints excluded: chain LI residue 150 GLU Chi-restraints excluded: chain LI residue 166 HIS Chi-restraints excluded: chain LI residue 213 HIS Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 101 ASP Chi-restraints excluded: chain LJ residue 104 ASN Chi-restraints excluded: chain LJ residue 111 GLU Chi-restraints excluded: chain LJ residue 132 VAL Chi-restraints excluded: chain LJ residue 155 HIS Chi-restraints excluded: chain LL residue 8 MET Chi-restraints excluded: chain LL residue 168 VAL Chi-restraints excluded: chain LL residue 175 ASN Chi-restraints excluded: chain LM residue 15 VAL Chi-restraints excluded: chain LM residue 27 ILE Chi-restraints excluded: chain LM residue 43 THR Chi-restraints excluded: chain LM residue 83 ASN Chi-restraints excluded: chain LM residue 96 GLU Chi-restraints excluded: chain LM residue 113 MET Chi-restraints excluded: chain LM residue 127 VAL Chi-restraints excluded: chain LN residue 27 CYS Chi-restraints excluded: chain LN residue 80 THR Chi-restraints excluded: chain LN residue 135 ILE Chi-restraints excluded: chain LN residue 147 ASP Chi-restraints excluded: chain LN residue 151 ILE Chi-restraints excluded: chain LN residue 174 LEU Chi-restraints excluded: chain LO residue 34 VAL Chi-restraints excluded: chain LO residue 67 SER Chi-restraints excluded: chain LO residue 106 ASP Chi-restraints excluded: chain LO residue 132 THR Chi-restraints excluded: chain LO residue 153 THR Chi-restraints excluded: chain LO residue 167 HIS Chi-restraints excluded: chain LO residue 190 ASP Chi-restraints excluded: chain LP residue 15 CYS Chi-restraints excluded: chain LP residue 29 THR Chi-restraints excluded: chain LP residue 32 THR Chi-restraints excluded: chain LP residue 52 THR Chi-restraints excluded: chain LP residue 67 VAL Chi-restraints excluded: chain LP residue 103 GLU Chi-restraints excluded: chain LP residue 114 ILE Chi-restraints excluded: chain LP residue 146 ILE Chi-restraints excluded: chain LQ residue 5 ILE Chi-restraints excluded: chain LQ residue 10 ASP Chi-restraints excluded: chain LQ residue 13 VAL Chi-restraints excluded: chain LQ residue 39 THR Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LQ residue 134 CYS Chi-restraints excluded: chain LQ residue 162 HIS Chi-restraints excluded: chain LR residue 10 LEU Chi-restraints excluded: chain LR residue 47 ASP Chi-restraints excluded: chain LR residue 57 VAL Chi-restraints excluded: chain LR residue 115 ILE Chi-restraints excluded: chain LS residue 36 ASN Chi-restraints excluded: chain LS residue 62 VAL Chi-restraints excluded: chain LS residue 112 ASP Chi-restraints excluded: chain LS residue 129 VAL Chi-restraints excluded: chain LS residue 154 LEU Chi-restraints excluded: chain LT residue 33 ILE Chi-restraints excluded: chain LT residue 68 THR Chi-restraints excluded: chain LT residue 89 ILE Chi-restraints excluded: chain LT residue 109 VAL Chi-restraints excluded: chain LT residue 150 LEU Chi-restraints excluded: chain LU residue 29 VAL Chi-restraints excluded: chain LU residue 40 GLU Chi-restraints excluded: chain LU residue 62 THR Chi-restraints excluded: chain LW residue 44 ARG Chi-restraints excluded: chain LX residue 54 LEU Chi-restraints excluded: chain LX residue 76 ILE Chi-restraints excluded: chain LX residue 90 ILE Chi-restraints excluded: chain LX residue 128 ILE Chi-restraints excluded: chain LX residue 144 TYR Chi-restraints excluded: chain LY residue 109 LEU Chi-restraints excluded: chain LZ residue 47 ASP Chi-restraints excluded: chain LZ residue 68 ILE Chi-restraints excluded: chain LZ residue 81 MET Chi-restraints excluded: chain LZ residue 106 LEU Chi-restraints excluded: chain LZ residue 132 GLN Chi-restraints excluded: chain La residue 34 ASN Chi-restraints excluded: chain La residue 58 MET Chi-restraints excluded: chain La residue 76 ASP Chi-restraints excluded: chain La residue 78 LEU Chi-restraints excluded: chain La residue 95 THR Chi-restraints excluded: chain La residue 146 LEU Chi-restraints excluded: chain La residue 147 VAL Chi-restraints excluded: chain Lb residue 65 MET Chi-restraints excluded: chain Lc residue 20 LEU Chi-restraints excluded: chain Lc residue 71 VAL Chi-restraints excluded: chain Lc residue 73 HIS Chi-restraints excluded: chain Ld residue 59 THR Chi-restraints excluded: chain Ld residue 65 ASP Chi-restraints excluded: chain Ld residue 107 THR Chi-restraints excluded: chain Ld residue 111 VAL Chi-restraints excluded: chain Ld residue 116 ASN Chi-restraints excluded: chain Ld residue 119 THR Chi-restraints excluded: chain Le residue 57 ASN Chi-restraints excluded: chain Le residue 91 CYS Chi-restraints excluded: chain Lf residue 10 ILE Chi-restraints excluded: chain Lf residue 25 THR Chi-restraints excluded: chain Lf residue 27 LEU Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lf residue 84 VAL Chi-restraints excluded: chain Lf residue 97 ILE Chi-restraints excluded: chain Lg residue 11 LEU Chi-restraints excluded: chain Lh residue 4 ILE Chi-restraints excluded: chain Lh residue 23 ASP Chi-restraints excluded: chain Lh residue 104 THR Chi-restraints excluded: chain Li residue 47 VAL Chi-restraints excluded: chain Li residue 61 LEU Chi-restraints excluded: chain Li residue 88 GLU Chi-restraints excluded: chain Lj residue 13 ASN Chi-restraints excluded: chain Lj residue 17 THR Chi-restraints excluded: chain Lj residue 24 SER Chi-restraints excluded: chain Lk residue 8 ILE Chi-restraints excluded: chain Lk residue 32 VAL Chi-restraints excluded: chain Lk residue 36 VAL Chi-restraints excluded: chain Lk residue 46 VAL Chi-restraints excluded: chain Lk residue 47 ILE Chi-restraints excluded: chain Lk residue 60 LEU Chi-restraints excluded: chain Lk residue 64 LEU Chi-restraints excluded: chain Ll residue 6 THR Chi-restraints excluded: chain Lm residue 103 LEU Chi-restraints excluded: chain Lm residue 108 VAL Chi-restraints excluded: chain Lm residue 127 VAL Chi-restraints excluded: chain Lo residue 10 THR Chi-restraints excluded: chain Lo residue 24 THR Chi-restraints excluded: chain Lo residue 76 ASN Chi-restraints excluded: chain Lp residue 16 THR Chi-restraints excluded: chain Lp residue 72 ASN Chi-restraints excluded: chain Lr residue 21 ASN Chi-restraints excluded: chain Lr residue 64 ILE Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain Lr residue 81 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 203 GLN Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 323 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1019 random chunks: chunk 950 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 chunk 561 optimal weight: 8.9990 chunk 719 optimal weight: 2.9990 chunk 557 optimal weight: 0.9990 chunk 829 optimal weight: 5.9990 chunk 550 optimal weight: 6.9990 chunk 982 optimal weight: 5.9990 chunk 614 optimal weight: 7.9990 chunk 598 optimal weight: 6.9990 chunk 453 optimal weight: 0.1980 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LA 215 ASN ** LD 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 128 HIS ** LF 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LG 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LG 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LG 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LI 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LL 188 ASN LM 56 GLN LN 149 GLN ** LO 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 7 HIS LR 130 ASN ** LT 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** La 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** La 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lc 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lc 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lc 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Le 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lf 20 ASN Lf 91 ASN ** Lh 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ll 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lm 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Lr 83 ASN ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 147758 Z= 0.221 Angle : 0.630 15.423 218687 Z= 0.317 Chirality : 0.035 0.340 27382 Planarity : 0.005 0.101 12914 Dihedral : 25.088 179.625 70126 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.23 % Favored : 91.73 % Rotamer: Outliers : 4.10 % Allowed : 22.43 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.05 % Twisted Proline : 0.73 % Twisted General : 0.03 % 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: -2.11 (0.10), residues: 6315 helix: -0.63 (0.11), residues: 2016 sheet: -1.69 (0.17), residues: 867 loop : -1.80 (0.11), residues: 3432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRPLC 267 HIS 0.024 0.001 HISLI 166 PHE 0.026 0.001 PHELk 11 TYR 0.041 0.002 TYRLZ 49 ARG 0.007 0.000 ARGLB 378 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12630 Ramachandran restraints generated. 6315 Oldfield, 0 Emsley, 6315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12630 Ramachandran restraints generated. 6315 Oldfield, 0 Emsley, 6315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1116 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 891 time to evaluate : 6.786 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: LA 132 ASN cc_start: 0.7797 (m110) cc_final: 0.7510 (m110) REVERT: LA 133 TYR cc_start: 0.8393 (p90) cc_final: 0.8027 (p90) REVERT: LA 160 SER cc_start: 0.9133 (t) cc_final: 0.8882 (p) REVERT: LB 66 LYS cc_start: 0.7153 (pttt) cc_final: 0.6538 (mptt) REVERT: LD 158 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8073 (mmtp) REVERT: LE 62 MET cc_start: 0.8970 (mmm) cc_final: 0.8725 (tpp) REVERT: LE 115 TYR cc_start: 0.8817 (t80) cc_final: 0.8537 (t80) REVERT: LE 242 ILE cc_start: 0.9324 (OUTLIER) cc_final: 0.8861 (tt) REVERT: LF 57 TYR cc_start: 0.8393 (m-10) cc_final: 0.8163 (m-80) REVERT: LF 152 GLU cc_start: 0.8116 (pp20) cc_final: 0.7847 (pp20) REVERT: LG 39 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.7608 (p90) REVERT: LG 204 PHE cc_start: 0.7893 (OUTLIER) cc_final: 0.7029 (m-80) REVERT: LH 8 GLN cc_start: 0.7771 (mt0) cc_final: 0.7513 (tt0) REVERT: LH 58 ASP cc_start: 0.7744 (p0) cc_final: 0.7460 (p0) REVERT: LH 74 CYS cc_start: 0.8388 (m) cc_final: 0.8061 (m) REVERT: LI 87 MET cc_start: 0.6439 (tmm) cc_final: 0.6229 (tmm) REVERT: LJ 25 CYS cc_start: 0.7008 (OUTLIER) cc_final: 0.6661 (p) REVERT: LJ 111 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6628 (tm-30) REVERT: LJ 155 HIS cc_start: 0.7208 (OUTLIER) cc_final: 0.6846 (m170) REVERT: LJ 159 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8674 (tptm) REVERT: LM 44 GLN cc_start: 0.8348 (mm-40) cc_final: 0.7885 (mm-40) REVERT: LN 46 ASP cc_start: 0.7970 (p0) cc_final: 0.7734 (p0) REVERT: LR 140 GLU cc_start: 0.8568 (pp20) cc_final: 0.8224 (pp20) REVERT: LT 109 VAL cc_start: 0.8207 (OUTLIER) cc_final: 0.7987 (p) REVERT: LX 155 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7549 (tt) REVERT: LZ 68 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.7752 (mp) REVERT: La 108 TYR cc_start: 0.8227 (m-80) cc_final: 0.8024 (m-80) REVERT: Lc 61 GLU cc_start: 0.8846 (tp30) cc_final: 0.8447 (tp30) REVERT: Lc 90 ARG cc_start: 0.8706 (mpp80) cc_final: 0.8381 (mpp80) REVERT: Ld 93 ASN cc_start: 0.6809 (t0) cc_final: 0.6234 (t0) REVERT: Le 113 GLU cc_start: 0.8005 (pp20) cc_final: 0.7799 (pp20) REVERT: Lf 28 LEU cc_start: 0.9096 (pp) cc_final: 0.8893 (pp) REVERT: Li 7 MET cc_start: 0.8078 (pmm) cc_final: 0.7727 (pmm) REVERT: Lk 12 LEU cc_start: 0.9166 (tp) cc_final: 0.8863 (tp) REVERT: Ll 29 MET cc_start: 0.8448 (pmm) cc_final: 0.8155 (pmm) REVERT: A 157 VAL cc_start: 0.6914 (OUTLIER) cc_final: 0.6593 (t) outliers start: 225 outliers final: 166 residues processed: 1034 average time/residue: 1.1200 time to fit residues: 2090.7526 Evaluate side-chains 1010 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 832 time to evaluate : 6.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LA residue 45 VAL Chi-restraints excluded: chain LA residue 50 HIS Chi-restraints excluded: chain LA residue 62 VAL Chi-restraints excluded: chain LA residue 138 SER Chi-restraints excluded: chain LA residue 157 VAL Chi-restraints excluded: chain LA residue 165 VAL Chi-restraints excluded: chain LA residue 224 THR Chi-restraints excluded: chain LB residue 73 VAL Chi-restraints excluded: chain LB residue 90 VAL Chi-restraints excluded: chain LB residue 105 VAL Chi-restraints excluded: chain LB residue 147 GLU Chi-restraints excluded: chain LB residue 329 ASP Chi-restraints excluded: chain LC residue 24 LEU Chi-restraints excluded: chain LC residue 111 TRP Chi-restraints excluded: chain LC residue 116 ASN Chi-restraints excluded: chain LC residue 128 LEU Chi-restraints excluded: chain LC residue 294 LYS Chi-restraints excluded: chain LC residue 334 THR Chi-restraints excluded: chain LD residue 28 THR Chi-restraints excluded: chain LD residue 55 VAL Chi-restraints excluded: chain LD residue 100 CYS Chi-restraints excluded: chain LD residue 110 LEU Chi-restraints excluded: chain LD residue 158 LYS Chi-restraints excluded: chain LD residue 171 LEU Chi-restraints excluded: chain LD residue 185 SER Chi-restraints excluded: chain LD residue 203 ASN Chi-restraints excluded: chain LD residue 252 VAL Chi-restraints excluded: chain LE residue 49 VAL Chi-restraints excluded: chain LE residue 202 ASP Chi-restraints excluded: chain LE residue 212 LEU Chi-restraints excluded: chain LE residue 242 ILE Chi-restraints excluded: chain LF residue 83 VAL Chi-restraints excluded: chain LF residue 121 THR Chi-restraints excluded: chain LF residue 170 THR Chi-restraints excluded: chain LF residue 175 ILE Chi-restraints excluded: chain LF residue 186 CYS Chi-restraints excluded: chain LF residue 228 VAL Chi-restraints excluded: chain LG residue 33 GLU Chi-restraints excluded: chain LG residue 39 PHE Chi-restraints excluded: chain LG residue 63 LEU Chi-restraints excluded: chain LG residue 149 ASN Chi-restraints excluded: chain LG residue 160 ASP Chi-restraints excluded: chain LG residue 204 PHE Chi-restraints excluded: chain LG residue 231 ASP Chi-restraints excluded: chain LH residue 95 VAL Chi-restraints excluded: chain LH residue 104 VAL Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LH residue 183 GLU Chi-restraints excluded: chain LI residue 26 VAL Chi-restraints excluded: chain LI residue 53 VAL Chi-restraints excluded: chain LI residue 113 THR Chi-restraints excluded: chain LI residue 135 ILE Chi-restraints excluded: chain LI residue 142 LEU Chi-restraints excluded: chain LI residue 144 ASN Chi-restraints excluded: chain LI residue 150 GLU Chi-restraints excluded: chain LI residue 213 HIS Chi-restraints excluded: chain LJ residue 25 CYS Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 104 ASN Chi-restraints excluded: chain LJ residue 111 GLU Chi-restraints excluded: chain LJ residue 132 VAL Chi-restraints excluded: chain LJ residue 155 HIS Chi-restraints excluded: chain LJ residue 159 LYS Chi-restraints excluded: chain LL residue 168 VAL Chi-restraints excluded: chain LL residue 175 ASN Chi-restraints excluded: chain LL residue 194 ILE Chi-restraints excluded: chain LM residue 15 VAL Chi-restraints excluded: chain LM residue 27 ILE Chi-restraints excluded: chain LM residue 43 THR Chi-restraints excluded: chain LM residue 83 ASN Chi-restraints excluded: chain LM residue 96 GLU Chi-restraints excluded: chain LM residue 113 MET Chi-restraints excluded: chain LM residue 127 VAL Chi-restraints excluded: chain LN residue 80 THR Chi-restraints excluded: chain LN residue 135 ILE Chi-restraints excluded: chain LN residue 147 ASP Chi-restraints excluded: chain LN residue 151 ILE Chi-restraints excluded: chain LN residue 174 LEU Chi-restraints excluded: chain LO residue 34 VAL Chi-restraints excluded: chain LO residue 67 SER Chi-restraints excluded: chain LO residue 106 ASP Chi-restraints excluded: chain LO residue 132 THR Chi-restraints excluded: chain LO residue 153 THR Chi-restraints excluded: chain LO residue 167 HIS Chi-restraints excluded: chain LO residue 190 ASP Chi-restraints excluded: chain LP residue 15 CYS Chi-restraints excluded: chain LP residue 29 THR Chi-restraints excluded: chain LP residue 32 THR Chi-restraints excluded: chain LP residue 52 THR Chi-restraints excluded: chain LP residue 67 VAL Chi-restraints excluded: chain LP residue 103 GLU Chi-restraints excluded: chain LP residue 114 ILE Chi-restraints excluded: chain LP residue 117 ILE Chi-restraints excluded: chain LQ residue 5 ILE Chi-restraints excluded: chain LQ residue 10 ASP Chi-restraints excluded: chain LQ residue 13 VAL Chi-restraints excluded: chain LQ residue 39 THR Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LQ residue 134 CYS Chi-restraints excluded: chain LQ residue 160 HIS Chi-restraints excluded: chain LR residue 10 LEU Chi-restraints excluded: chain LR residue 47 ASP Chi-restraints excluded: chain LR residue 57 VAL Chi-restraints excluded: chain LR residue 115 ILE Chi-restraints excluded: chain LS residue 62 VAL Chi-restraints excluded: chain LS residue 90 THR Chi-restraints excluded: chain LS residue 112 ASP Chi-restraints excluded: chain LS residue 129 VAL Chi-restraints excluded: chain LS residue 154 LEU Chi-restraints excluded: chain LT residue 103 ASP Chi-restraints excluded: chain LT residue 109 VAL Chi-restraints excluded: chain LT residue 150 LEU Chi-restraints excluded: chain LU residue 29 VAL Chi-restraints excluded: chain LU residue 62 THR Chi-restraints excluded: chain LW residue 44 ARG Chi-restraints excluded: chain LX residue 54 LEU Chi-restraints excluded: chain LX residue 76 ILE Chi-restraints excluded: chain LX residue 90 ILE Chi-restraints excluded: chain LX residue 128 ILE Chi-restraints excluded: chain LX residue 155 ILE Chi-restraints excluded: chain LY residue 109 LEU Chi-restraints excluded: chain LZ residue 47 ASP Chi-restraints excluded: chain LZ residue 68 ILE Chi-restraints excluded: chain LZ residue 106 LEU Chi-restraints excluded: chain LZ residue 132 GLN Chi-restraints excluded: chain La residue 58 MET Chi-restraints excluded: chain La residue 76 ASP Chi-restraints excluded: chain La residue 78 LEU Chi-restraints excluded: chain La residue 95 THR Chi-restraints excluded: chain La residue 144 CYS Chi-restraints excluded: chain La residue 147 VAL Chi-restraints excluded: chain Lc residue 14 ILE Chi-restraints excluded: chain Lc residue 71 VAL Chi-restraints excluded: chain Lc residue 73 HIS Chi-restraints excluded: chain Ld residue 59 THR Chi-restraints excluded: chain Ld residue 65 ASP Chi-restraints excluded: chain Ld residue 107 THR Chi-restraints excluded: chain Ld residue 116 ASN Chi-restraints excluded: chain Le residue 57 ASN Chi-restraints excluded: chain Le residue 122 VAL Chi-restraints excluded: chain Lf residue 10 ILE Chi-restraints excluded: chain Lf residue 25 THR Chi-restraints excluded: chain Lf residue 27 LEU Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lf residue 84 VAL Chi-restraints excluded: chain Lf residue 97 ILE Chi-restraints excluded: chain Lg residue 11 LEU Chi-restraints excluded: chain Lh residue 4 ILE Chi-restraints excluded: chain Lh residue 23 ASP Chi-restraints excluded: chain Lh residue 104 THR Chi-restraints excluded: chain Li residue 47 VAL Chi-restraints excluded: chain Li residue 61 LEU Chi-restraints excluded: chain Li residue 88 GLU Chi-restraints excluded: chain Lj residue 13 ASN Chi-restraints excluded: chain Lj residue 18 LEU Chi-restraints excluded: chain Lj residue 24 SER Chi-restraints excluded: chain Lk residue 32 VAL Chi-restraints excluded: chain Lk residue 36 VAL Chi-restraints excluded: chain Lk residue 46 VAL Chi-restraints excluded: chain Lk residue 64 LEU Chi-restraints excluded: chain Ll residue 6 THR Chi-restraints excluded: chain Lm residue 103 LEU Chi-restraints excluded: chain Lm residue 108 VAL Chi-restraints excluded: chain Lm residue 127 VAL Chi-restraints excluded: chain Lo residue 10 THR Chi-restraints excluded: chain Lo residue 24 THR Chi-restraints excluded: chain Lp residue 10 ILE Chi-restraints excluded: chain Lp residue 72 ASN Chi-restraints excluded: chain Lr residue 64 ILE Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 323 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1019 random chunks: chunk 607 optimal weight: 8.9990 chunk 392 optimal weight: 10.0000 chunk 586 optimal weight: 6.9990 chunk 295 optimal weight: 10.0000 chunk 192 optimal weight: 20.0000 chunk 190 optimal weight: 10.0000 chunk 624 optimal weight: 5.9990 chunk 669 optimal weight: 0.8980 chunk 485 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 771 optimal weight: 10.0000 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** LD 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LG 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LG 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 240 ASN ** LI 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LL 188 ASN LM 33 GLN ** LO 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 28 ASN ** LP 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LR 130 ASN ** LT 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LW 48 GLN ** La 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** La 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lc 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lc 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lc 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Le 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lf 20 ASN Lf 91 ASN ** Lh 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lj 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ll 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lm 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Lr 30 ASN A 171 ASN ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 147758 Z= 0.354 Angle : 0.693 15.571 218687 Z= 0.346 Chirality : 0.038 0.320 27382 Planarity : 0.005 0.104 12914 Dihedral : 25.067 179.957 70126 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 22.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.93 % Favored : 90.04 % Rotamer: Outliers : 4.52 % Allowed : 22.74 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.05 % Twisted Proline : 0.73 % Twisted General : 0.05 % 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: -2.18 (0.10), residues: 6315 helix: -0.66 (0.11), residues: 2012 sheet: -1.77 (0.17), residues: 895 loop : -1.85 (0.11), residues: 3408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPLb 16 HIS 0.007 0.001 HISLI 147 PHE 0.040 0.002 PHELU 39 TYR 0.038 0.002 TYRLP 63 ARG 0.016 0.000 ARGLH 89 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12630 Ramachandran restraints generated. 6315 Oldfield, 0 Emsley, 6315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12630 Ramachandran restraints generated. 6315 Oldfield, 0 Emsley, 6315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1060 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 812 time to evaluate : 6.983 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: LA 132 ASN cc_start: 0.7802 (m110) cc_final: 0.7495 (m110) REVERT: LA 133 TYR cc_start: 0.8494 (p90) cc_final: 0.8070 (p90) REVERT: LA 160 SER cc_start: 0.9223 (t) cc_final: 0.8945 (p) REVERT: LB 66 LYS cc_start: 0.7162 (pttt) cc_final: 0.6565 (mptt) REVERT: LD 158 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8080 (mmtp) REVERT: LD 235 MET cc_start: 0.8207 (ppp) cc_final: 0.7595 (ppp) REVERT: LD 236 MET cc_start: 0.7744 (ptt) cc_final: 0.7311 (ptt) REVERT: LE 62 MET cc_start: 0.9008 (mmm) cc_final: 0.8581 (tpp) REVERT: LE 115 TYR cc_start: 0.8866 (t80) cc_final: 0.8578 (t80) REVERT: LF 57 TYR cc_start: 0.8472 (m-10) cc_final: 0.8227 (m-80) REVERT: LF 152 GLU cc_start: 0.8199 (pp20) cc_final: 0.7922 (pp20) REVERT: LG 39 PHE cc_start: 0.8509 (OUTLIER) cc_final: 0.7959 (p90) REVERT: LG 204 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7093 (m-80) REVERT: LH 74 CYS cc_start: 0.8461 (m) cc_final: 0.8162 (m) REVERT: LI 87 MET cc_start: 0.6538 (tmm) cc_final: 0.6315 (tmm) REVERT: LJ 25 CYS cc_start: 0.7224 (OUTLIER) cc_final: 0.6901 (p) REVERT: LJ 104 ASN cc_start: 0.8427 (OUTLIER) cc_final: 0.8014 (m-40) REVERT: LJ 111 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.6539 (tm-30) REVERT: LN 9 GLU cc_start: 0.7659 (pp20) cc_final: 0.7378 (pp20) REVERT: LN 46 ASP cc_start: 0.8041 (p0) cc_final: 0.7818 (p0) REVERT: LT 109 VAL cc_start: 0.8247 (OUTLIER) cc_final: 0.8006 (p) REVERT: La 108 TYR cc_start: 0.8282 (m-80) cc_final: 0.8034 (m-80) REVERT: Lc 61 GLU cc_start: 0.8871 (tp30) cc_final: 0.8581 (tp30) REVERT: Lc 90 ARG cc_start: 0.8742 (mpp80) cc_final: 0.8359 (mpp80) REVERT: Ld 93 ASN cc_start: 0.6824 (t0) cc_final: 0.6021 (t0) REVERT: Li 7 MET cc_start: 0.8091 (pmm) cc_final: 0.7724 (pmm) REVERT: Lk 12 LEU cc_start: 0.9159 (tp) cc_final: 0.8787 (tp) REVERT: Ll 29 MET cc_start: 0.8500 (pmm) cc_final: 0.8086 (pmm) REVERT: Lo 82 MET cc_start: 0.5129 (ptt) cc_final: 0.4738 (ptt) REVERT: Lr 82 ILE cc_start: 0.9033 (mm) cc_final: 0.8727 (mm) REVERT: A 157 VAL cc_start: 0.6918 (OUTLIER) cc_final: 0.6605 (t) outliers start: 248 outliers final: 204 residues processed: 976 average time/residue: 1.0771 time to fit residues: 1901.8597 Evaluate side-chains 996 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 784 time to evaluate : 6.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LA residue 45 VAL Chi-restraints excluded: chain LA residue 50 HIS Chi-restraints excluded: chain LA residue 62 VAL Chi-restraints excluded: chain LA residue 104 VAL Chi-restraints excluded: chain LA residue 138 SER Chi-restraints excluded: chain LA residue 157 VAL Chi-restraints excluded: chain LA residue 165 VAL Chi-restraints excluded: chain LA residue 224 THR Chi-restraints excluded: chain LB residue 73 VAL Chi-restraints excluded: chain LB residue 90 VAL Chi-restraints excluded: chain LB residue 105 VAL Chi-restraints excluded: chain LB residue 147 GLU Chi-restraints excluded: chain LB residue 222 VAL Chi-restraints excluded: chain LB residue 329 ASP Chi-restraints excluded: chain LB residue 340 THR Chi-restraints excluded: chain LB residue 345 LEU Chi-restraints excluded: chain LC residue 24 LEU Chi-restraints excluded: chain LC residue 85 HIS Chi-restraints excluded: chain LC residue 92 PHE Chi-restraints excluded: chain LC residue 111 TRP Chi-restraints excluded: chain LC residue 116 ASN Chi-restraints excluded: chain LC residue 128 LEU Chi-restraints excluded: chain LC residue 294 LYS Chi-restraints excluded: chain LC residue 334 THR Chi-restraints excluded: chain LD residue 28 THR Chi-restraints excluded: chain LD residue 55 VAL Chi-restraints excluded: chain LD residue 73 MET Chi-restraints excluded: chain LD residue 100 CYS Chi-restraints excluded: chain LD residue 155 THR Chi-restraints excluded: chain LD residue 158 LYS Chi-restraints excluded: chain LD residue 171 LEU Chi-restraints excluded: chain LD residue 185 SER Chi-restraints excluded: chain LD residue 203 ASN Chi-restraints excluded: chain LD residue 252 VAL Chi-restraints excluded: chain LE residue 49 VAL Chi-restraints excluded: chain LE residue 202 ASP Chi-restraints excluded: chain LE residue 212 LEU Chi-restraints excluded: chain LE residue 242 ILE Chi-restraints excluded: chain LE residue 258 LEU Chi-restraints excluded: chain LF residue 83 VAL Chi-restraints excluded: chain LF residue 105 VAL Chi-restraints excluded: chain LF residue 121 THR Chi-restraints excluded: chain LF residue 170 THR Chi-restraints excluded: chain LF residue 175 ILE Chi-restraints excluded: chain LF residue 186 CYS Chi-restraints excluded: chain LF residue 228 VAL Chi-restraints excluded: chain LG residue 33 GLU Chi-restraints excluded: chain LG residue 39 PHE Chi-restraints excluded: chain LG residue 63 LEU Chi-restraints excluded: chain LG residue 69 ILE Chi-restraints excluded: chain LG residue 149 ASN Chi-restraints excluded: chain LG residue 160 ASP Chi-restraints excluded: chain LG residue 204 PHE Chi-restraints excluded: chain LG residue 231 ASP Chi-restraints excluded: chain LH residue 84 VAL Chi-restraints excluded: chain LH residue 95 VAL Chi-restraints excluded: chain LH residue 102 ASN Chi-restraints excluded: chain LH residue 104 VAL Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LH residue 183 GLU Chi-restraints excluded: chain LI residue 26 VAL Chi-restraints excluded: chain LI residue 53 VAL Chi-restraints excluded: chain LI residue 113 THR Chi-restraints excluded: chain LI residue 125 THR Chi-restraints excluded: chain LI residue 135 ILE Chi-restraints excluded: chain LI residue 142 LEU Chi-restraints excluded: chain LI residue 144 ASN Chi-restraints excluded: chain LI residue 150 GLU Chi-restraints excluded: chain LI residue 207 ASP Chi-restraints excluded: chain LI residue 213 HIS Chi-restraints excluded: chain LJ residue 17 ILE Chi-restraints excluded: chain LJ residue 25 CYS Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 104 ASN Chi-restraints excluded: chain LJ residue 111 GLU Chi-restraints excluded: chain LJ residue 132 VAL Chi-restraints excluded: chain LJ residue 155 HIS Chi-restraints excluded: chain LJ residue 159 LYS Chi-restraints excluded: chain LL residue 8 MET Chi-restraints excluded: chain LL residue 168 VAL Chi-restraints excluded: chain LL residue 175 ASN Chi-restraints excluded: chain LM residue 15 VAL Chi-restraints excluded: chain LM residue 27 ILE Chi-restraints excluded: chain LM residue 43 THR Chi-restraints excluded: chain LM residue 83 ASN Chi-restraints excluded: chain LM residue 96 GLU Chi-restraints excluded: chain LM residue 113 MET Chi-restraints excluded: chain LM residue 127 VAL Chi-restraints excluded: chain LN residue 27 CYS Chi-restraints excluded: chain LN residue 80 THR Chi-restraints excluded: chain LN residue 135 ILE Chi-restraints excluded: chain LN residue 147 ASP Chi-restraints excluded: chain LN residue 151 ILE Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LN residue 174 LEU Chi-restraints excluded: chain LO residue 34 VAL Chi-restraints excluded: chain LO residue 67 SER Chi-restraints excluded: chain LO residue 106 ASP Chi-restraints excluded: chain LO residue 132 THR Chi-restraints excluded: chain LO residue 153 THR Chi-restraints excluded: chain LO residue 166 ILE Chi-restraints excluded: chain LO residue 167 HIS Chi-restraints excluded: chain LO residue 190 ASP Chi-restraints excluded: chain LP residue 15 CYS Chi-restraints excluded: chain LP residue 29 THR Chi-restraints excluded: chain LP residue 32 THR Chi-restraints excluded: chain LP residue 52 THR Chi-restraints excluded: chain LP residue 67 VAL Chi-restraints excluded: chain LP residue 70 CYS Chi-restraints excluded: chain LP residue 103 GLU Chi-restraints excluded: chain LP residue 114 ILE Chi-restraints excluded: chain LP residue 117 ILE Chi-restraints excluded: chain LQ residue 5 ILE Chi-restraints excluded: chain LQ residue 10 ASP Chi-restraints excluded: chain LQ residue 13 VAL Chi-restraints excluded: chain LQ residue 39 THR Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LQ residue 134 CYS Chi-restraints excluded: chain LQ residue 160 HIS Chi-restraints excluded: chain LQ residue 162 HIS Chi-restraints excluded: chain LR residue 10 LEU Chi-restraints excluded: chain LR residue 47 ASP Chi-restraints excluded: chain LR residue 57 VAL Chi-restraints excluded: chain LR residue 101 ILE Chi-restraints excluded: chain LR residue 115 ILE Chi-restraints excluded: chain LS residue 36 ASN Chi-restraints excluded: chain LS residue 62 VAL Chi-restraints excluded: chain LS residue 77 ASN Chi-restraints excluded: chain LS residue 90 THR Chi-restraints excluded: chain LS residue 112 ASP Chi-restraints excluded: chain LS residue 129 VAL Chi-restraints excluded: chain LS residue 154 LEU Chi-restraints excluded: chain LT residue 68 THR Chi-restraints excluded: chain LT residue 89 ILE Chi-restraints excluded: chain LT residue 103 ASP Chi-restraints excluded: chain LT residue 109 VAL Chi-restraints excluded: chain LT residue 150 LEU Chi-restraints excluded: chain LU residue 29 VAL Chi-restraints excluded: chain LU residue 47 ILE Chi-restraints excluded: chain LU residue 62 THR Chi-restraints excluded: chain LW residue 44 ARG Chi-restraints excluded: chain LX residue 54 LEU Chi-restraints excluded: chain LX residue 76 ILE Chi-restraints excluded: chain LX residue 81 LEU Chi-restraints excluded: chain LX residue 90 ILE Chi-restraints excluded: chain LX residue 128 ILE Chi-restraints excluded: chain LY residue 109 LEU Chi-restraints excluded: chain LZ residue 47 ASP Chi-restraints excluded: chain LZ residue 106 LEU Chi-restraints excluded: chain LZ residue 132 GLN Chi-restraints excluded: chain La residue 34 ASN Chi-restraints excluded: chain La residue 38 LEU Chi-restraints excluded: chain La residue 58 MET Chi-restraints excluded: chain La residue 76 ASP Chi-restraints excluded: chain La residue 78 LEU Chi-restraints excluded: chain La residue 95 THR Chi-restraints excluded: chain La residue 147 VAL Chi-restraints excluded: chain Lb residue 65 MET Chi-restraints excluded: chain Lc residue 14 ILE Chi-restraints excluded: chain Lc residue 20 LEU Chi-restraints excluded: chain Lc residue 71 VAL Chi-restraints excluded: chain Ld residue 59 THR Chi-restraints excluded: chain Ld residue 65 ASP Chi-restraints excluded: chain Ld residue 107 THR Chi-restraints excluded: chain Ld residue 116 ASN Chi-restraints excluded: chain Le residue 41 ILE Chi-restraints excluded: chain Le residue 57 ASN Chi-restraints excluded: chain Le residue 91 CYS Chi-restraints excluded: chain Le residue 122 VAL Chi-restraints excluded: chain Lf residue 5 LEU Chi-restraints excluded: chain Lf residue 10 ILE Chi-restraints excluded: chain Lf residue 25 THR Chi-restraints excluded: chain Lf residue 27 LEU Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lf residue 84 VAL Chi-restraints excluded: chain Lf residue 97 ILE Chi-restraints excluded: chain Lh residue 4 ILE Chi-restraints excluded: chain Lh residue 23 ASP Chi-restraints excluded: chain Lh residue 104 THR Chi-restraints excluded: chain Li residue 47 VAL Chi-restraints excluded: chain Li residue 61 LEU Chi-restraints excluded: chain Li residue 88 GLU Chi-restraints excluded: chain Lj residue 13 ASN Chi-restraints excluded: chain Lj residue 24 SER Chi-restraints excluded: chain Lk residue 32 VAL Chi-restraints excluded: chain Lk residue 36 VAL Chi-restraints excluded: chain Lk residue 46 VAL Chi-restraints excluded: chain Lk residue 47 ILE Chi-restraints excluded: chain Lk residue 64 LEU Chi-restraints excluded: chain Ll residue 6 THR Chi-restraints excluded: chain Ll residue 27 ILE Chi-restraints excluded: chain Lm residue 103 LEU Chi-restraints excluded: chain Lm residue 108 VAL Chi-restraints excluded: chain Lm residue 127 VAL Chi-restraints excluded: chain Lo residue 10 THR Chi-restraints excluded: chain Lo residue 24 THR Chi-restraints excluded: chain Lo residue 76 ASN Chi-restraints excluded: chain Lp residue 16 THR Chi-restraints excluded: chain Lp residue 72 ASN Chi-restraints excluded: chain Lr residue 64 ILE Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 208 GLN Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 323 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1019 random chunks: chunk 893 optimal weight: 0.9980 chunk 940 optimal weight: 10.0000 chunk 858 optimal weight: 3.9990 chunk 915 optimal weight: 8.9990 chunk 550 optimal weight: 6.9990 chunk 398 optimal weight: 7.9990 chunk 718 optimal weight: 6.9990 chunk 280 optimal weight: 20.0000 chunk 827 optimal weight: 8.9990 chunk 865 optimal weight: 3.9990 chunk 912 optimal weight: 1.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LA 215 ASN ** LD 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LG 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LG 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LG 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LI 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LL 188 ASN ** LM 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LO 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LR 130 ASN ** LT 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** La 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** La 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lc 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lc 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lc 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lc 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Le 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lf 20 ASN Lf 91 ASN ** Lh 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ll 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lm 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Lr 30 ASN Lr 83 ASN A 171 ASN ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 147758 Z= 0.235 Angle : 0.638 15.760 218687 Z= 0.320 Chirality : 0.036 0.333 27382 Planarity : 0.005 0.096 12914 Dihedral : 25.030 179.485 70126 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.55 % Favored : 91.42 % Rotamer: Outliers : 4.05 % Allowed : 23.71 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.05 % Twisted Proline : 0.73 % Twisted General : 0.05 % 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: -2.09 (0.10), residues: 6315 helix: -0.59 (0.11), residues: 2019 sheet: -1.72 (0.17), residues: 917 loop : -1.78 (0.11), residues: 3379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPLC 267 HIS 0.005 0.001 HISLf 78 PHE 0.037 0.001 PHELU 39 TYR 0.046 0.002 TYRLZ 49 ARG 0.010 0.000 ARGLI 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12630 Ramachandran restraints generated. 6315 Oldfield, 0 Emsley, 6315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12630 Ramachandran restraints generated. 6315 Oldfield, 0 Emsley, 6315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1088 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 866 time to evaluate : 6.862 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: LA 132 ASN cc_start: 0.7782 (m110) cc_final: 0.7516 (m110) REVERT: LA 133 TYR cc_start: 0.8420 (p90) cc_final: 0.8007 (p90) REVERT: LA 160 SER cc_start: 0.9131 (t) cc_final: 0.8844 (p) REVERT: LB 66 LYS cc_start: 0.7124 (pttt) cc_final: 0.6523 (mptt) REVERT: LD 158 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8003 (mmtm) REVERT: LD 235 MET cc_start: 0.8271 (ppp) cc_final: 0.7747 (ppp) REVERT: LD 236 MET cc_start: 0.7677 (ptt) cc_final: 0.7332 (ptt) REVERT: LE 62 MET cc_start: 0.8971 (mmm) cc_final: 0.8590 (mmm) REVERT: LE 115 TYR cc_start: 0.8837 (t80) cc_final: 0.8593 (t80) REVERT: LF 152 GLU cc_start: 0.8163 (pp20) cc_final: 0.7889 (pp20) REVERT: LG 39 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.7658 (p90) REVERT: LG 204 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.7027 (m-80) REVERT: LH 74 CYS cc_start: 0.8436 (m) cc_final: 0.8168 (m) REVERT: LI 87 MET cc_start: 0.6509 (tmm) cc_final: 0.6191 (tmm) REVERT: LJ 25 CYS cc_start: 0.7132 (OUTLIER) cc_final: 0.6715 (p) REVERT: LJ 104 ASN cc_start: 0.8395 (OUTLIER) cc_final: 0.7992 (m-40) REVERT: LJ 111 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.6640 (tm-30) REVERT: LJ 155 HIS cc_start: 0.7229 (OUTLIER) cc_final: 0.6861 (m170) REVERT: LJ 159 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8655 (tptm) REVERT: LN 46 ASP cc_start: 0.7976 (p0) cc_final: 0.7746 (p0) REVERT: LR 140 GLU cc_start: 0.8600 (pp20) cc_final: 0.8261 (pp20) REVERT: LR 148 ASP cc_start: 0.8561 (p0) cc_final: 0.8330 (p0) REVERT: LT 65 TYR cc_start: 0.8208 (p90) cc_final: 0.7899 (p90) REVERT: LZ 49 TYR cc_start: 0.7908 (m-10) cc_final: 0.7425 (m-10) REVERT: La 108 TYR cc_start: 0.8245 (m-80) cc_final: 0.8043 (m-80) REVERT: Lc 61 GLU cc_start: 0.8884 (tp30) cc_final: 0.8507 (tp30) REVERT: Lc 90 ARG cc_start: 0.8703 (mpp80) cc_final: 0.8323 (mpp80) REVERT: Ld 93 ASN cc_start: 0.6726 (t0) cc_final: 0.6101 (t0) REVERT: Lf 28 LEU cc_start: 0.9119 (pp) cc_final: 0.8906 (pp) REVERT: Li 7 MET cc_start: 0.8099 (pmm) cc_final: 0.7718 (pmm) REVERT: Lk 12 LEU cc_start: 0.9081 (tp) cc_final: 0.8881 (tp) REVERT: Ll 29 MET cc_start: 0.8421 (pmm) cc_final: 0.8095 (pmm) REVERT: Lo 82 MET cc_start: 0.4832 (ptt) cc_final: 0.4491 (ptt) REVERT: Lr 82 ILE cc_start: 0.9038 (mm) cc_final: 0.8744 (mm) REVERT: A 157 VAL cc_start: 0.6908 (OUTLIER) cc_final: 0.6585 (t) outliers start: 222 outliers final: 193 residues processed: 1007 average time/residue: 1.1460 time to fit residues: 2093.1274 Evaluate side-chains 1021 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 819 time to evaluate : 6.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LA residue 45 VAL Chi-restraints excluded: chain LA residue 50 HIS Chi-restraints excluded: chain LA residue 62 VAL Chi-restraints excluded: chain LA residue 138 SER Chi-restraints excluded: chain LA residue 157 VAL Chi-restraints excluded: chain LA residue 165 VAL Chi-restraints excluded: chain LA residue 224 THR Chi-restraints excluded: chain LB residue 73 VAL Chi-restraints excluded: chain LB residue 90 VAL Chi-restraints excluded: chain LB residue 105 VAL Chi-restraints excluded: chain LB residue 147 GLU Chi-restraints excluded: chain LB residue 222 VAL Chi-restraints excluded: chain LB residue 329 ASP Chi-restraints excluded: chain LB residue 336 CYS Chi-restraints excluded: chain LB residue 340 THR Chi-restraints excluded: chain LB residue 345 LEU Chi-restraints excluded: chain LC residue 24 LEU Chi-restraints excluded: chain LC residue 62 THR Chi-restraints excluded: chain LC residue 92 PHE Chi-restraints excluded: chain LC residue 111 TRP Chi-restraints excluded: chain LC residue 116 ASN Chi-restraints excluded: chain LC residue 128 LEU Chi-restraints excluded: chain LC residue 145 GLU Chi-restraints excluded: chain LC residue 294 LYS Chi-restraints excluded: chain LC residue 334 THR Chi-restraints excluded: chain LD residue 28 THR Chi-restraints excluded: chain LD residue 55 VAL Chi-restraints excluded: chain LD residue 73 MET Chi-restraints excluded: chain LD residue 100 CYS Chi-restraints excluded: chain LD residue 155 THR Chi-restraints excluded: chain LD residue 158 LYS Chi-restraints excluded: chain LD residue 171 LEU Chi-restraints excluded: chain LD residue 185 SER Chi-restraints excluded: chain LD residue 203 ASN Chi-restraints excluded: chain LD residue 252 VAL Chi-restraints excluded: chain LE residue 49 VAL Chi-restraints excluded: chain LE residue 202 ASP Chi-restraints excluded: chain LE residue 212 LEU Chi-restraints excluded: chain LE residue 242 ILE Chi-restraints excluded: chain LF residue 83 VAL Chi-restraints excluded: chain LF residue 105 VAL Chi-restraints excluded: chain LF residue 121 THR Chi-restraints excluded: chain LF residue 170 THR Chi-restraints excluded: chain LF residue 175 ILE Chi-restraints excluded: chain LF residue 186 CYS Chi-restraints excluded: chain LF residue 228 VAL Chi-restraints excluded: chain LG residue 33 GLU Chi-restraints excluded: chain LG residue 39 PHE Chi-restraints excluded: chain LG residue 63 LEU Chi-restraints excluded: chain LG residue 149 ASN Chi-restraints excluded: chain LG residue 160 ASP Chi-restraints excluded: chain LG residue 198 THR Chi-restraints excluded: chain LG residue 204 PHE Chi-restraints excluded: chain LG residue 231 ASP Chi-restraints excluded: chain LH residue 84 VAL Chi-restraints excluded: chain LH residue 95 VAL Chi-restraints excluded: chain LH residue 102 ASN Chi-restraints excluded: chain LH residue 104 VAL Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LH residue 183 GLU Chi-restraints excluded: chain LI residue 26 VAL Chi-restraints excluded: chain LI residue 53 VAL Chi-restraints excluded: chain LI residue 113 THR Chi-restraints excluded: chain LI residue 125 THR Chi-restraints excluded: chain LI residue 135 ILE Chi-restraints excluded: chain LI residue 142 LEU Chi-restraints excluded: chain LI residue 144 ASN Chi-restraints excluded: chain LI residue 150 GLU Chi-restraints excluded: chain LI residue 207 ASP Chi-restraints excluded: chain LI residue 213 HIS Chi-restraints excluded: chain LJ residue 17 ILE Chi-restraints excluded: chain LJ residue 25 CYS Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 104 ASN Chi-restraints excluded: chain LJ residue 111 GLU Chi-restraints excluded: chain LJ residue 132 VAL Chi-restraints excluded: chain LJ residue 155 HIS Chi-restraints excluded: chain LJ residue 159 LYS Chi-restraints excluded: chain LL residue 8 MET Chi-restraints excluded: chain LL residue 168 VAL Chi-restraints excluded: chain LL residue 175 ASN Chi-restraints excluded: chain LL residue 194 ILE Chi-restraints excluded: chain LM residue 15 VAL Chi-restraints excluded: chain LM residue 27 ILE Chi-restraints excluded: chain LM residue 43 THR Chi-restraints excluded: chain LM residue 83 ASN Chi-restraints excluded: chain LM residue 96 GLU Chi-restraints excluded: chain LM residue 113 MET Chi-restraints excluded: chain LM residue 127 VAL Chi-restraints excluded: chain LN residue 27 CYS Chi-restraints excluded: chain LN residue 80 THR Chi-restraints excluded: chain LN residue 135 ILE Chi-restraints excluded: chain LN residue 147 ASP Chi-restraints excluded: chain LN residue 151 ILE Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LN residue 174 LEU Chi-restraints excluded: chain LO residue 34 VAL Chi-restraints excluded: chain LO residue 67 SER Chi-restraints excluded: chain LO residue 106 ASP Chi-restraints excluded: chain LO residue 132 THR Chi-restraints excluded: chain LO residue 153 THR Chi-restraints excluded: chain LO residue 167 HIS Chi-restraints excluded: chain LO residue 190 ASP Chi-restraints excluded: chain LP residue 15 CYS Chi-restraints excluded: chain LP residue 29 THR Chi-restraints excluded: chain LP residue 31 GLU Chi-restraints excluded: chain LP residue 32 THR Chi-restraints excluded: chain LP residue 52 THR Chi-restraints excluded: chain LP residue 67 VAL Chi-restraints excluded: chain LP residue 70 CYS Chi-restraints excluded: chain LP residue 103 GLU Chi-restraints excluded: chain LP residue 114 ILE Chi-restraints excluded: chain LP residue 117 ILE Chi-restraints excluded: chain LQ residue 5 ILE Chi-restraints excluded: chain LQ residue 10 ASP Chi-restraints excluded: chain LQ residue 13 VAL Chi-restraints excluded: chain LQ residue 39 THR Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LQ residue 134 CYS Chi-restraints excluded: chain LQ residue 160 HIS Chi-restraints excluded: chain LR residue 10 LEU Chi-restraints excluded: chain LR residue 47 ASP Chi-restraints excluded: chain LR residue 57 VAL Chi-restraints excluded: chain LR residue 115 ILE Chi-restraints excluded: chain LS residue 36 ASN Chi-restraints excluded: chain LS residue 62 VAL Chi-restraints excluded: chain LS residue 77 ASN Chi-restraints excluded: chain LS residue 90 THR Chi-restraints excluded: chain LS residue 112 ASP Chi-restraints excluded: chain LS residue 129 VAL Chi-restraints excluded: chain LS residue 154 LEU Chi-restraints excluded: chain LT residue 68 THR Chi-restraints excluded: chain LT residue 103 ASP Chi-restraints excluded: chain LT residue 150 LEU Chi-restraints excluded: chain LU residue 29 VAL Chi-restraints excluded: chain LU residue 62 THR Chi-restraints excluded: chain LW residue 44 ARG Chi-restraints excluded: chain LX residue 54 LEU Chi-restraints excluded: chain LX residue 76 ILE Chi-restraints excluded: chain LX residue 81 LEU Chi-restraints excluded: chain LX residue 90 ILE Chi-restraints excluded: chain LX residue 128 ILE Chi-restraints excluded: chain LY residue 109 LEU Chi-restraints excluded: chain LZ residue 47 ASP Chi-restraints excluded: chain LZ residue 106 LEU Chi-restraints excluded: chain LZ residue 132 GLN Chi-restraints excluded: chain La residue 38 LEU Chi-restraints excluded: chain La residue 58 MET Chi-restraints excluded: chain La residue 76 ASP Chi-restraints excluded: chain La residue 78 LEU Chi-restraints excluded: chain La residue 95 THR Chi-restraints excluded: chain La residue 147 VAL Chi-restraints excluded: chain Lc residue 14 ILE Chi-restraints excluded: chain Lc residue 71 VAL Chi-restraints excluded: chain Ld residue 59 THR Chi-restraints excluded: chain Ld residue 65 ASP Chi-restraints excluded: chain Ld residue 107 THR Chi-restraints excluded: chain Ld residue 116 ASN Chi-restraints excluded: chain Le residue 57 ASN Chi-restraints excluded: chain Le residue 91 CYS Chi-restraints excluded: chain Le residue 122 VAL Chi-restraints excluded: chain Lf residue 5 LEU Chi-restraints excluded: chain Lf residue 10 ILE Chi-restraints excluded: chain Lf residue 25 THR Chi-restraints excluded: chain Lf residue 27 LEU Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lf residue 84 VAL Chi-restraints excluded: chain Lf residue 97 ILE Chi-restraints excluded: chain Lh residue 4 ILE Chi-restraints excluded: chain Lh residue 23 ASP Chi-restraints excluded: chain Lh residue 104 THR Chi-restraints excluded: chain Li residue 47 VAL Chi-restraints excluded: chain Li residue 61 LEU Chi-restraints excluded: chain Li residue 88 GLU Chi-restraints excluded: chain Lj residue 13 ASN Chi-restraints excluded: chain Lj residue 24 SER Chi-restraints excluded: chain Lk residue 32 VAL Chi-restraints excluded: chain Lk residue 36 VAL Chi-restraints excluded: chain Lk residue 46 VAL Chi-restraints excluded: chain Lk residue 47 ILE Chi-restraints excluded: chain Lk residue 64 LEU Chi-restraints excluded: chain Ll residue 6 THR Chi-restraints excluded: chain Lm residue 103 LEU Chi-restraints excluded: chain Lm residue 108 VAL Chi-restraints excluded: chain Lm residue 127 VAL Chi-restraints excluded: chain Lo residue 10 THR Chi-restraints excluded: chain Lo residue 24 THR Chi-restraints excluded: chain Lo residue 76 ASN Chi-restraints excluded: chain Lp residue 10 ILE Chi-restraints excluded: chain Lp residue 16 THR Chi-restraints excluded: chain Lp residue 72 ASN Chi-restraints excluded: chain Lr residue 64 ILE Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain Lr residue 83 ASN Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 323 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1019 random chunks: chunk 601 optimal weight: 5.9990 chunk 967 optimal weight: 8.9990 chunk 590 optimal weight: 7.9990 chunk 459 optimal weight: 0.8980 chunk 672 optimal weight: 2.9990 chunk 1015 optimal weight: 6.9990 chunk 934 optimal weight: 10.0000 chunk 808 optimal weight: 1.9990 chunk 83 optimal weight: 20.0000 chunk 624 optimal weight: 5.9990 chunk 495 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** LA 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LC 142 HIS ** LD 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LG 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LG 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LG 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 240 ASN LH 98 HIS ** LI 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LN 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LO 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 56 GLN ** LP 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LR 130 ASN ** LT 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LW 48 GLN ** LX 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** La 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** La 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lc 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lc 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lc 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lc 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Le 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lf 20 ASN ** Lh 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ll 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lm 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Lr 83 ASN A 171 ASN ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 147758 Z= 0.239 Angle : 0.639 16.356 218687 Z= 0.320 Chirality : 0.035 0.331 27382 Planarity : 0.005 0.094 12914 Dihedral : 24.967 179.751 70126 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 20.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.82 % Favored : 91.15 % Rotamer: Outliers : 3.88 % Allowed : 24.00 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.05 % Twisted Proline : 0.73 % Twisted General : 0.03 % 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: -2.03 (0.10), residues: 6315 helix: -0.55 (0.11), residues: 2019 sheet: -1.66 (0.17), residues: 900 loop : -1.76 (0.11), residues: 3396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRPLH 61 HIS 0.016 0.001 HISLl 43 PHE 0.036 0.002 PHELU 39 TYR 0.036 0.002 TYRLZ 49 ARG 0.019 0.000 ARGLl 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12630 Ramachandran restraints generated. 6315 Oldfield, 0 Emsley, 6315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12630 Ramachandran restraints generated. 6315 Oldfield, 0 Emsley, 6315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1055 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 842 time to evaluate : 6.796 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: LA 132 ASN cc_start: 0.7782 (m110) cc_final: 0.7542 (m110) REVERT: LA 133 TYR cc_start: 0.8418 (p90) cc_final: 0.7916 (p90) REVERT: LA 160 SER cc_start: 0.9184 (t) cc_final: 0.8893 (p) REVERT: LB 66 LYS cc_start: 0.7130 (pttt) cc_final: 0.6530 (mptt) REVERT: LC 95 MET cc_start: 0.8763 (ptp) cc_final: 0.8327 (ptp) REVERT: LD 235 MET cc_start: 0.8312 (ppp) cc_final: 0.7821 (ppp) REVERT: LD 236 MET cc_start: 0.7721 (ptt) cc_final: 0.7433 (ptt) REVERT: LD 271 MET cc_start: 0.7865 (pmm) cc_final: 0.7333 (pmm) REVERT: LE 62 MET cc_start: 0.8974 (mmm) cc_final: 0.8601 (mmm) REVERT: LE 68 MET cc_start: 0.8356 (mmm) cc_final: 0.8128 (mmm) REVERT: LE 242 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8783 (tt) REVERT: LF 57 TYR cc_start: 0.8456 (m-10) cc_final: 0.8248 (m-80) REVERT: LF 152 GLU cc_start: 0.8181 (pp20) cc_final: 0.7942 (pp20) REVERT: LF 195 TYR cc_start: 0.8627 (t80) cc_final: 0.8349 (t80) REVERT: LG 39 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.7579 (p90) REVERT: LG 204 PHE cc_start: 0.7895 (OUTLIER) cc_final: 0.6976 (m-80) REVERT: LH 74 CYS cc_start: 0.8442 (m) cc_final: 0.8181 (m) REVERT: LI 87 MET cc_start: 0.6593 (tmm) cc_final: 0.6298 (tmm) REVERT: LJ 25 CYS cc_start: 0.7263 (OUTLIER) cc_final: 0.6847 (p) REVERT: LJ 104 ASN cc_start: 0.8407 (OUTLIER) cc_final: 0.7996 (m-40) REVERT: LJ 111 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.6615 (tm-30) REVERT: LJ 155 HIS cc_start: 0.7194 (OUTLIER) cc_final: 0.6829 (m170) REVERT: LJ 159 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8658 (tptm) REVERT: LN 46 ASP cc_start: 0.7991 (p0) cc_final: 0.7750 (p0) REVERT: LO 118 MET cc_start: 0.7962 (tpp) cc_final: 0.7723 (mmt) REVERT: LP 31 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7755 (tp30) REVERT: LR 140 GLU cc_start: 0.8665 (pp20) cc_final: 0.8413 (pp20) REVERT: LR 148 ASP cc_start: 0.8533 (p0) cc_final: 0.8309 (p0) REVERT: LT 65 TYR cc_start: 0.8149 (p90) cc_final: 0.7850 (p90) REVERT: LT 106 LEU cc_start: 0.8838 (pp) cc_final: 0.8481 (mm) REVERT: La 108 TYR cc_start: 0.8256 (m-80) cc_final: 0.8022 (m-80) REVERT: Lc 61 GLU cc_start: 0.8855 (tp30) cc_final: 0.8606 (tp30) REVERT: Lc 90 ARG cc_start: 0.8701 (mpp80) cc_final: 0.8319 (mpp80) REVERT: Ld 93 ASN cc_start: 0.6870 (t0) cc_final: 0.5975 (t0) REVERT: Li 7 MET cc_start: 0.8119 (pmm) cc_final: 0.7777 (pmm) REVERT: Lk 12 LEU cc_start: 0.9050 (tp) cc_final: 0.8837 (tp) REVERT: Ll 29 MET cc_start: 0.8437 (pmm) cc_final: 0.8046 (pmm) REVERT: Lo 34 TYR cc_start: 0.8022 (m-80) cc_final: 0.7685 (t80) REVERT: Lo 82 MET cc_start: 0.4812 (ptt) cc_final: 0.4451 (ptt) REVERT: Lr 82 ILE cc_start: 0.9152 (mm) cc_final: 0.8869 (mm) REVERT: A 157 VAL cc_start: 0.6898 (OUTLIER) cc_final: 0.6580 (t) outliers start: 213 outliers final: 184 residues processed: 981 average time/residue: 1.1163 time to fit residues: 1978.1136 Evaluate side-chains 1015 residues out of total 5556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 821 time to evaluate : 6.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LA residue 45 VAL Chi-restraints excluded: chain LA residue 50 HIS Chi-restraints excluded: chain LA residue 62 VAL Chi-restraints excluded: chain LA residue 138 SER Chi-restraints excluded: chain LA residue 157 VAL Chi-restraints excluded: chain LA residue 165 VAL Chi-restraints excluded: chain LA residue 224 THR Chi-restraints excluded: chain LB residue 73 VAL Chi-restraints excluded: chain LB residue 90 VAL Chi-restraints excluded: chain LB residue 105 VAL Chi-restraints excluded: chain LB residue 147 GLU Chi-restraints excluded: chain LB residue 222 VAL Chi-restraints excluded: chain LB residue 329 ASP Chi-restraints excluded: chain LB residue 336 CYS Chi-restraints excluded: chain LB residue 340 THR Chi-restraints excluded: chain LB residue 345 LEU Chi-restraints excluded: chain LC residue 24 LEU Chi-restraints excluded: chain LC residue 62 THR Chi-restraints excluded: chain LC residue 92 PHE Chi-restraints excluded: chain LC residue 111 TRP Chi-restraints excluded: chain LC residue 116 ASN Chi-restraints excluded: chain LC residue 128 LEU Chi-restraints excluded: chain LC residue 334 THR Chi-restraints excluded: chain LD residue 28 THR Chi-restraints excluded: chain LD residue 55 VAL Chi-restraints excluded: chain LD residue 73 MET Chi-restraints excluded: chain LD residue 100 CYS Chi-restraints excluded: chain LD residue 155 THR Chi-restraints excluded: chain LD residue 171 LEU Chi-restraints excluded: chain LD residue 185 SER Chi-restraints excluded: chain LD residue 203 ASN Chi-restraints excluded: chain LD residue 252 VAL Chi-restraints excluded: chain LE residue 49 VAL Chi-restraints excluded: chain LE residue 202 ASP Chi-restraints excluded: chain LE residue 212 LEU Chi-restraints excluded: chain LE residue 242 ILE Chi-restraints excluded: chain LF residue 83 VAL Chi-restraints excluded: chain LF residue 121 THR Chi-restraints excluded: chain LF residue 170 THR Chi-restraints excluded: chain LF residue 175 ILE Chi-restraints excluded: chain LF residue 186 CYS Chi-restraints excluded: chain LF residue 228 VAL Chi-restraints excluded: chain LG residue 33 GLU Chi-restraints excluded: chain LG residue 39 PHE Chi-restraints excluded: chain LG residue 63 LEU Chi-restraints excluded: chain LG residue 149 ASN Chi-restraints excluded: chain LG residue 160 ASP Chi-restraints excluded: chain LG residue 198 THR Chi-restraints excluded: chain LG residue 204 PHE Chi-restraints excluded: chain LG residue 231 ASP Chi-restraints excluded: chain LH residue 84 VAL Chi-restraints excluded: chain LH residue 95 VAL Chi-restraints excluded: chain LH residue 98 HIS Chi-restraints excluded: chain LH residue 102 ASN Chi-restraints excluded: chain LH residue 104 VAL Chi-restraints excluded: chain LH residue 128 MET Chi-restraints excluded: chain LH residue 183 GLU Chi-restraints excluded: chain LI residue 26 VAL Chi-restraints excluded: chain LI residue 53 VAL Chi-restraints excluded: chain LI residue 113 THR Chi-restraints excluded: chain LI residue 125 THR Chi-restraints excluded: chain LI residue 135 ILE Chi-restraints excluded: chain LI residue 142 LEU Chi-restraints excluded: chain LI residue 144 ASN Chi-restraints excluded: chain LI residue 207 ASP Chi-restraints excluded: chain LI residue 213 HIS Chi-restraints excluded: chain LJ residue 17 ILE Chi-restraints excluded: chain LJ residue 25 CYS Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 104 ASN Chi-restraints excluded: chain LJ residue 111 GLU Chi-restraints excluded: chain LJ residue 132 VAL Chi-restraints excluded: chain LJ residue 155 HIS Chi-restraints excluded: chain LJ residue 159 LYS Chi-restraints excluded: chain LL residue 8 MET Chi-restraints excluded: chain LL residue 168 VAL Chi-restraints excluded: chain LL residue 175 ASN Chi-restraints excluded: chain LL residue 194 ILE Chi-restraints excluded: chain LM residue 15 VAL Chi-restraints excluded: chain LM residue 27 ILE Chi-restraints excluded: chain LM residue 43 THR Chi-restraints excluded: chain LM residue 83 ASN Chi-restraints excluded: chain LM residue 96 GLU Chi-restraints excluded: chain LM residue 113 MET Chi-restraints excluded: chain LM residue 127 VAL Chi-restraints excluded: chain LN residue 27 CYS Chi-restraints excluded: chain LN residue 80 THR Chi-restraints excluded: chain LN residue 135 ILE Chi-restraints excluded: chain LN residue 147 ASP Chi-restraints excluded: chain LN residue 151 ILE Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LN residue 174 LEU Chi-restraints excluded: chain LO residue 34 VAL Chi-restraints excluded: chain LO residue 67 SER Chi-restraints excluded: chain LO residue 106 ASP Chi-restraints excluded: chain LO residue 153 THR Chi-restraints excluded: chain LO residue 167 HIS Chi-restraints excluded: chain LO residue 190 ASP Chi-restraints excluded: chain LP residue 15 CYS Chi-restraints excluded: chain LP residue 29 THR Chi-restraints excluded: chain LP residue 31 GLU Chi-restraints excluded: chain LP residue 32 THR Chi-restraints excluded: chain LP residue 67 VAL Chi-restraints excluded: chain LP residue 70 CYS Chi-restraints excluded: chain LP residue 103 GLU Chi-restraints excluded: chain LP residue 114 ILE Chi-restraints excluded: chain LP residue 117 ILE Chi-restraints excluded: chain LQ residue 5 ILE Chi-restraints excluded: chain LQ residue 10 ASP Chi-restraints excluded: chain LQ residue 13 VAL Chi-restraints excluded: chain LQ residue 39 THR Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LQ residue 134 CYS Chi-restraints excluded: chain LQ residue 160 HIS Chi-restraints excluded: chain LR residue 10 LEU Chi-restraints excluded: chain LR residue 47 ASP Chi-restraints excluded: chain LR residue 57 VAL Chi-restraints excluded: chain LS residue 36 ASN Chi-restraints excluded: chain LS residue 62 VAL Chi-restraints excluded: chain LS residue 73 LEU Chi-restraints excluded: chain LS residue 77 ASN Chi-restraints excluded: chain LS residue 90 THR Chi-restraints excluded: chain LS residue 112 ASP Chi-restraints excluded: chain LS residue 129 VAL Chi-restraints excluded: chain LS residue 154 LEU Chi-restraints excluded: chain LT residue 33 ILE Chi-restraints excluded: chain LT residue 68 THR Chi-restraints excluded: chain LT residue 103 ASP Chi-restraints excluded: chain LT residue 150 LEU Chi-restraints excluded: chain LU residue 29 VAL Chi-restraints excluded: chain LU residue 62 THR Chi-restraints excluded: chain LW residue 44 ARG Chi-restraints excluded: chain LX residue 54 LEU Chi-restraints excluded: chain LX residue 76 ILE Chi-restraints excluded: chain LX residue 81 LEU Chi-restraints excluded: chain LX residue 128 ILE Chi-restraints excluded: chain LY residue 109 LEU Chi-restraints excluded: chain LZ residue 47 ASP Chi-restraints excluded: chain LZ residue 106 LEU Chi-restraints excluded: chain LZ residue 132 GLN Chi-restraints excluded: chain La residue 38 LEU Chi-restraints excluded: chain La residue 76 ASP Chi-restraints excluded: chain La residue 78 LEU Chi-restraints excluded: chain La residue 95 THR Chi-restraints excluded: chain La residue 147 VAL Chi-restraints excluded: chain Lc residue 14 ILE Chi-restraints excluded: chain Lc residue 71 VAL Chi-restraints excluded: chain Lc residue 73 HIS Chi-restraints excluded: chain Ld residue 59 THR Chi-restraints excluded: chain Ld residue 65 ASP Chi-restraints excluded: chain Ld residue 107 THR Chi-restraints excluded: chain Ld residue 116 ASN Chi-restraints excluded: chain Ld residue 119 THR Chi-restraints excluded: chain Le residue 57 ASN Chi-restraints excluded: chain Le residue 91 CYS Chi-restraints excluded: chain Le residue 122 VAL Chi-restraints excluded: chain Lf residue 5 LEU Chi-restraints excluded: chain Lf residue 10 ILE Chi-restraints excluded: chain Lf residue 25 THR Chi-restraints excluded: chain Lf residue 27 LEU Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lf residue 84 VAL Chi-restraints excluded: chain Lf residue 97 ILE Chi-restraints excluded: chain Lh residue 4 ILE Chi-restraints excluded: chain Lh residue 23 ASP Chi-restraints excluded: chain Lh residue 104 THR Chi-restraints excluded: chain Li residue 47 VAL Chi-restraints excluded: chain Li residue 61 LEU Chi-restraints excluded: chain Li residue 88 GLU Chi-restraints excluded: chain Lj residue 13 ASN Chi-restraints excluded: chain Lj residue 24 SER Chi-restraints excluded: chain Lk residue 32 VAL Chi-restraints excluded: chain Lk residue 36 VAL Chi-restraints excluded: chain Lk residue 46 VAL Chi-restraints excluded: chain Lk residue 47 ILE Chi-restraints excluded: chain Lk residue 64 LEU Chi-restraints excluded: chain Ll residue 6 THR Chi-restraints excluded: chain Lm residue 108 VAL Chi-restraints excluded: chain Lm residue 127 VAL Chi-restraints excluded: chain Lo residue 24 THR Chi-restraints excluded: chain Lo residue 76 ASN Chi-restraints excluded: chain Lp residue 10 ILE Chi-restraints excluded: chain Lp residue 16 THR Chi-restraints excluded: chain Lp residue 72 ASN Chi-restraints excluded: chain Lr residue 64 ILE Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 323 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1019 random chunks: chunk 642 optimal weight: 10.0000 chunk 861 optimal weight: 2.9990 chunk 247 optimal weight: 10.0000 chunk 745 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 224 optimal weight: 10.0000 chunk 809 optimal weight: 0.0870 chunk 338 optimal weight: 10.0000 chunk 831 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 chunk 149 optimal weight: 10.0000 overall best weight: 5.2168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** LA 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LC 317 ASN ** LD 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LG 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LG 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 240 ASN ** LH 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LI 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LL 188 ASN ** LM 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LN 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LO 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LP 56 GLN ** LP 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LR 130 ASN ** LT 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** La 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** La 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lc 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lc 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lc 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lc 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Le 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lf 20 ASN Lf 91 ASN ** Lh 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lj 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ll 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lm 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Lr 83 ASN A 171 ASN ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.045676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.036890 restraints weight = 1001616.811| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.10 r_work: 0.2956 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 147758 Z= 0.316 Angle : 0.676 16.062 218687 Z= 0.339 Chirality : 0.037 0.318 27382 Planarity : 0.005 0.098 12914 Dihedral : 24.966 179.636 70126 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 21.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.36 % Favored : 90.61 % Rotamer: Outliers : 3.90 % Allowed : 24.25 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.36 % Cis-general : 0.05 % Twisted Proline : 0.73 % Twisted General : 0.03 % 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: -2.11 (0.10), residues: 6315 helix: -0.64 (0.11), residues: 2041 sheet: -1.75 (0.17), residues: 875 loop : -1.79 (0.11), residues: 3399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPLb 16 HIS 0.007 0.001 HISLl 43 PHE 0.035 0.002 PHELU 39 TYR 0.039 0.002 TYRLc 31 ARG 0.018 0.000 ARGLl 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32864.06 seconds wall clock time: 576 minutes 54.48 seconds (34614.48 seconds total)