Starting phenix.real_space_refine on Sun Jun 30 16:54:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip9_35635/06_2024/8ip9_35635_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip9_35635/06_2024/8ip9_35635.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip9_35635/06_2024/8ip9_35635_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip9_35635/06_2024/8ip9_35635_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip9_35635/06_2024/8ip9_35635_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip9_35635/06_2024/8ip9_35635.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip9_35635/06_2024/8ip9_35635.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip9_35635/06_2024/8ip9_35635_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ip9_35635/06_2024/8ip9_35635_updated.pdb" } resolution = 3.0 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= 0.002 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 2 6.06 5 P 1770 5.49 5 Mg 84 5.21 5 S 167 5.16 5 C 39063 2.51 5 N 13403 2.21 5 O 18539 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "ba PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ba PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ba ARG 48": "NH1" <-> "NH2" Residue "ba TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ba PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ba PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ba PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ba PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ba GLU 92": "OE1" <-> "OE2" Residue "ca ARG 5": "NH1" <-> "NH2" Residue "ca GLU 28": "OE1" <-> "OE2" Residue "ca ARG 45": "NH1" <-> "NH2" Residue "ca ARG 46": "NH1" <-> "NH2" Residue "ca ASP 81": "OD1" <-> "OD2" Residue "ca TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ca ARG 160": "NH1" <-> "NH2" Residue "ca ARG 169": "NH1" <-> "NH2" Residue "ca GLU 176": "OE1" <-> "OE2" Residue "ca ARG 197": "NH1" <-> "NH2" Residue "ca GLU 207": "OE1" <-> "OE2" Residue "ca PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ca ARG 213": "NH1" <-> "NH2" Residue "da GLU 10": "OE1" <-> "OE2" Residue "da TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "da GLU 18": "OE1" <-> "OE2" Residue "da ASP 26": "OD1" <-> "OD2" Residue "da TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "da GLU 53": "OE1" <-> "OE2" Residue "da TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "da GLU 57": "OE1" <-> "OE2" Residue "da TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "da ASP 71": "OD1" <-> "OD2" Residue "ga TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ga GLU 35": "OE1" <-> "OE2" Residue "ga PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ga ASP 87": "OD1" <-> "OD2" Residue "ga GLU 95": "OE1" <-> "OE2" Residue "ga ASP 97": "OD1" <-> "OD2" Residue "ga GLU 98": "OE1" <-> "OE2" Residue "ga ASP 113": "OD1" <-> "OD2" Residue "ga GLU 138": "OE1" <-> "OE2" Residue "ha GLU 6": "OE1" <-> "OE2" Residue "ha TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ha ARG 15": "NH1" <-> "NH2" Residue "ha ASP 29": "OD1" <-> "OD2" Residue "ha PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ha ASP 57": "OD1" <-> "OD2" Residue "ha GLU 61": "OE1" <-> "OE2" Residue "ha TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ha PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ha ARG 68": "NH1" <-> "NH2" Residue "ha PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ha GLU 96": "OE1" <-> "OE2" Residue "ha ARG 110": "NH1" <-> "NH2" Residue "ha GLU 115": "OE1" <-> "OE2" Residue "ha ASP 126": "OD1" <-> "OD2" Residue "ha ASP 136": "OD1" <-> "OD2" Residue "ha ARG 137": "NH1" <-> "NH2" Residue "ha GLU 147": "OE1" <-> "OE2" Residue "ha TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ha ASP 155": "OD1" <-> "OD2" Residue "ha GLU 160": "OE1" <-> "OE2" Residue "ha ARG 187": "NH1" <-> "NH2" Residue "ha ARG 200": "NH1" <-> "NH2" Residue "ha TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ha ASP 218": "OD1" <-> "OD2" Residue "ha ASP 228": "OD1" <-> "OD2" Residue "ha GLU 238": "OE1" <-> "OE2" Residue "ha ARG 241": "NH1" <-> "NH2" Residue "ha TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ha ASP 246": "OD1" <-> "OD2" Residue "ha PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ha TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ha ASP 275": "OD1" <-> "OD2" Residue "ha ASP 284": "OD1" <-> "OD2" Residue "ha ARG 286": "NH1" <-> "NH2" Residue "ha TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ha TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ia PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ia TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ia GLU 20": "OE1" <-> "OE2" Residue "ia GLU 23": "OE1" <-> "OE2" Residue "ia ASP 32": "OD1" <-> "OD2" Residue "ia TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ia GLU 61": "OE1" <-> "OE2" Residue "ia TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ia GLU 89": "OE1" <-> "OE2" Residue "ia GLU 103": "OE1" <-> "OE2" Residue "ia TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ia GLU 135": "OE1" <-> "OE2" Residue "ia PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ia TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ia GLU 166": "OE1" <-> "OE2" Residue "ia ASP 206": "OD1" <-> "OD2" Residue "ja ARG 3": "NH1" <-> "NH2" Residue "ja ARG 11": "NH1" <-> "NH2" Residue "ja PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ja ARG 39": "NH1" <-> "NH2" Residue "ja ARG 49": "NH1" <-> "NH2" Residue "ja ARG 51": "NH1" <-> "NH2" Residue "ja ARG 59": "NH1" <-> "NH2" Residue "ja ARG 68": "NH1" <-> "NH2" Residue "ja ARG 77": "NH1" <-> "NH2" Residue "ja ASP 79": "OD1" <-> "OD2" Residue "ja GLU 97": "OE1" <-> "OE2" Residue "ja ARG 100": "NH1" <-> "NH2" Residue "ja TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ja ARG 108": "NH1" <-> "NH2" Residue "ja ARG 110": "NH1" <-> "NH2" Residue "ja ARG 115": "NH1" <-> "NH2" Residue "ja ASP 116": "OD1" <-> "OD2" Residue "ja GLU 117": "OE1" <-> "OE2" Residue "ja ASP 118": "OD1" <-> "OD2" Residue "ja ARG 127": "NH1" <-> "NH2" Residue "ja ARG 145": "NH1" <-> "NH2" Residue "ja ARG 148": "NH1" <-> "NH2" Residue "ja ASP 151": "OD1" <-> "OD2" Residue "ja ASP 163": "OD1" <-> "OD2" Residue "ja PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ja PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ja ASP 176": "OD1" <-> "OD2" Residue "ja ARG 187": "NH1" <-> "NH2" Residue "ja ARG 191": "NH1" <-> "NH2" Residue "ja ARG 198": "NH1" <-> "NH2" Residue "ja GLU 199": "OE1" <-> "OE2" Residue "ja GLU 206": "OE1" <-> "OE2" Residue "ja PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ja ARG 221": "NH1" <-> "NH2" Residue "ja PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ja GLU 251": "OE1" <-> "OE2" Residue "ja ARG 253": "NH1" <-> "NH2" Residue "ja ARG 255": "NH1" <-> "NH2" Residue "ja ASP 256": "OD1" <-> "OD2" Residue "ka ASP 27": "OD1" <-> "OD2" Residue "ka ASP 32": "OD1" <-> "OD2" Residue "ka TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ka TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ka PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ka GLU 66": "OE1" <-> "OE2" Residue "ka GLU 119": "OE1" <-> "OE2" Residue "ka ASP 120": "OD1" <-> "OD2" Residue "ka ARG 123": "NH1" <-> "NH2" Residue "ka ARG 131": "NH1" <-> "NH2" Residue "ka ARG 132": "NH1" <-> "NH2" Residue "ka GLU 156": "OE1" <-> "OE2" Residue "ka GLU 167": "OE1" <-> "OE2" Residue "ka ASP 171": "OD1" <-> "OD2" Residue "ka GLU 172": "OE1" <-> "OE2" Residue "ka TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ka GLU 193": "OE1" <-> "OE2" Residue "la ARG 46": "NH1" <-> "NH2" Residue "la GLU 56": "OE1" <-> "OE2" Residue "la ASP 70": "OD1" <-> "OD2" Residue "la ARG 76": "NH1" <-> "NH2" Residue "la TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "la TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "la GLU 113": "OE1" <-> "OE2" Residue "la ASP 119": "OD1" <-> "OD2" Residue "la GLU 131": "OE1" <-> "OE2" Residue "ma ARG 27": "NH1" <-> "NH2" Residue "ma GLU 41": "OE1" <-> "OE2" Residue "ma GLU 80": "OE1" <-> "OE2" Residue "ma ASP 86": "OD1" <-> "OD2" Residue "ma GLU 89": "OE1" <-> "OE2" Residue "ma ARG 91": "NH1" <-> "NH2" Residue "ma GLU 119": "OE1" <-> "OE2" Residue "ma ASP 126": "OD1" <-> "OD2" Residue "na PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "na ASP 46": "OD1" <-> "OD2" Residue "na ARG 50": "NH1" <-> "NH2" Residue "na GLU 51": "OE1" <-> "OE2" Residue "na ASP 65": "OD1" <-> "OD2" Residue "na ASP 67": "OD1" <-> "OD2" Residue "na TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "na ARG 117": "NH1" <-> "NH2" Residue "na ARG 141": "NH1" <-> "NH2" Residue "na ARG 150": "NH1" <-> "NH2" Residue "oa GLU 7": "OE1" <-> "OE2" Residue "oa PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "oa GLU 58": "OE1" <-> "OE2" Residue "oa GLU 63": "OE1" <-> "OE2" Residue "oa PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "oa PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "oa ASP 104": "OD1" <-> "OD2" Residue "oa GLU 112": "OE1" <-> "OE2" Residue "pa ASP 34": "OD1" <-> "OD2" Residue "pa GLU 35": "OE1" <-> "OE2" Residue "pa GLU 83": "OE1" <-> "OE2" Residue "pa GLU 86": "OE1" <-> "OE2" Residue "pa TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "pa GLU 103": "OE1" <-> "OE2" Residue "pa ASP 110": "OD1" <-> "OD2" Residue "pa ARG 131": "NH1" <-> "NH2" Residue "qa GLU 18": "OE1" <-> "OE2" Residue "qa ARG 23": "NH1" <-> "NH2" Residue "qa GLU 37": "OE1" <-> "OE2" Residue "qa PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "qa ARG 59": "NH1" <-> "NH2" Residue "qa GLU 75": "OE1" <-> "OE2" Residue "qa GLU 76": "OE1" <-> "OE2" Residue "qa GLU 79": "OE1" <-> "OE2" Residue "qa GLU 95": "OE1" <-> "OE2" Residue "qa ARG 97": "NH1" <-> "NH2" Residue "qa ASP 99": "OD1" <-> "OD2" Residue "qa ASP 113": "OD1" <-> "OD2" Residue "qa GLU 118": "OE1" <-> "OE2" Residue "qa ARG 119": "NH1" <-> "NH2" Residue "ra TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ra GLU 45": "OE1" <-> "OE2" Residue "ra PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ra ASP 62": "OD1" <-> "OD2" Residue "ra TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ra TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ra TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ra PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ra ASP 127": "OD1" <-> "OD2" Residue "ra ARG 142": "NH1" <-> "NH2" Residue "sa PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "sa TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "sa PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "sa GLU 115": "OE1" <-> "OE2" Residue "sa TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ta GLU 35": "OE1" <-> "OE2" Residue "ta PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ta ASP 44": "OD1" <-> "OD2" Residue "ta GLU 68": "OE1" <-> "OE2" Residue "ta ARG 69": "NH1" <-> "NH2" Residue "ta ARG 79": "NH1" <-> "NH2" Residue "ta ASP 83": "OD1" <-> "OD2" Residue "ta GLU 86": "OE1" <-> "OE2" Residue "ta PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ua PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ua ASP 53": "OD1" <-> "OD2" Residue "ua ASP 54": "OD1" <-> "OD2" Residue "ua ASP 71": "OD1" <-> "OD2" Residue "va ARG 4": "NH1" <-> "NH2" Residue "va ARG 11": "NH1" <-> "NH2" Residue "va ARG 19": "NH1" <-> "NH2" Residue "va ARG 43": "NH1" <-> "NH2" Residue "va TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "va PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "va GLU 50": "OE1" <-> "OE2" Residue "va PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "va ARG 56": "NH1" <-> "NH2" Residue "va ARG 67": "NH1" <-> "NH2" Residue "va GLU 84": "OE1" <-> "OE2" Residue "va TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "va ARG 89": "NH1" <-> "NH2" Residue "va ARG 91": "NH1" <-> "NH2" Residue "va TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "va GLU 114": "OE1" <-> "OE2" Residue "va ARG 117": "NH1" <-> "NH2" Residue "wa PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "wa ASP 49": "OD1" <-> "OD2" Residue "xa GLU 15": "OE1" <-> "OE2" Residue "xa PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "xa GLU 77": "OE1" <-> "OE2" Residue "xa PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "za TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "za ASP 48": "OD1" <-> "OD2" Residue "za TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "za GLU 60": "OE1" <-> "OE2" Residue "za GLU 73": "OE1" <-> "OE2" Residue "za ASP 77": "OD1" <-> "OD2" Residue "za PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "za ASP 130": "OD1" <-> "OD2" Residue "za PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "za ASP 162": "OD1" <-> "OD2" Residue "za ARG 172": "NH1" <-> "NH2" Residue "za ASP 200": "OD1" <-> "OD2" Residue "za ASP 204": "OD1" <-> "OD2" Residue "za TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "bb PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "bb TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "bb PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "bb ASP 72": "OD1" <-> "OD2" Residue "bb ASP 76": "OD1" <-> "OD2" Residue "bb GLU 77": "OE1" <-> "OE2" Residue "bb TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "bb ASP 104": "OD1" <-> "OD2" Residue "bb PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "bb ASP 108": "OD1" <-> "OD2" Residue "bb ARG 115": "NH1" <-> "NH2" Residue "bb ASP 131": "OD1" <-> "OD2" Residue "bb TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "bb PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "bb ASP 180": "OD1" <-> "OD2" Residue "bb GLU 191": "OE1" <-> "OE2" Residue "bb GLU 196": "OE1" <-> "OE2" Residue "bb GLU 198": "OE1" <-> "OE2" Residue "bb TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "bb ASP 224": "OD1" <-> "OD2" Residue "cb GLU 4": "OE1" <-> "OE2" Residue "cb TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "cb TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "db ARG 5": "NH1" <-> "NH2" Residue "db ARG 10": "NH1" <-> "NH2" Residue "db ARG 38": "NH1" <-> "NH2" Residue "db ASP 52": "OD1" <-> "OD2" Residue "db GLU 55": "OE1" <-> "OE2" Residue "db ASP 60": "OD1" <-> "OD2" Residue "db GLU 90": "OE1" <-> "OE2" Residue "eb TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "eb ARG 18": "NH1" <-> "NH2" Residue "eb ARG 19": "NH1" <-> "NH2" Residue "eb ASP 27": "OD1" <-> "OD2" Residue "eb TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "eb ASP 65": "OD1" <-> "OD2" Residue "eb GLU 74": "OE1" <-> "OE2" Residue "eb GLU 104": "OE1" <-> "OE2" Residue "eb PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "eb GLU 153": "OE1" <-> "OE2" Residue "eb GLU 155": "OE1" <-> "OE2" Residue "eb PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "fb GLU 57": "OE1" <-> "OE2" Residue "fb GLU 80": "OE1" <-> "OE2" Residue "fb ASP 88": "OD1" <-> "OD2" Residue "fb GLU 89": "OE1" <-> "OE2" Residue "fb GLU 130": "OE1" <-> "OE2" Residue "fb TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "fb TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "fb ASP 238": "OD1" <-> "OD2" Residue "gb GLU 17": "OE1" <-> "OE2" Residue "gb ASP 20": "OD1" <-> "OD2" Residue "gb TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "gb PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "gb ASP 57": "OD1" <-> "OD2" Residue "gb PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "gb ARG 89": "NH1" <-> "NH2" Residue "gb GLU 93": "OE1" <-> "OE2" Residue "gb ARG 95": "NH1" <-> "NH2" Residue "gb GLU 209": "OE1" <-> "OE2" Residue "gb GLU 212": "OE1" <-> "OE2" Residue "hb PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "hb ASP 21": "OD1" <-> "OD2" Residue "hb PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "hb GLU 31": "OE1" <-> "OE2" Residue "hb TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "hb TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "hb GLU 83": "OE1" <-> "OE2" Residue "hb PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "hb GLU 135": "OE1" <-> "OE2" Residue "hb TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "hb GLU 159": "OE1" <-> "OE2" Residue "hb GLU 168": "OE1" <-> "OE2" Residue "hb TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "hb ASP 181": "OD1" <-> "OD2" Residue "hb GLU 185": "OE1" <-> "OE2" Residue "hb TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ib GLU 6": "OE1" <-> "OE2" Residue "ib PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ib PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ib PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ib TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ib ARG 70": "NH1" <-> "NH2" Residue "ib TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ib GLU 102": "OE1" <-> "OE2" Residue "ib PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ib ARG 117": "NH1" <-> "NH2" Residue "ib GLU 120": "OE1" <-> "OE2" Residue "IB ARG 21": "NH1" <-> "NH2" Residue "IB ARG 23": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 73028 Number of models: 1 Model: "" Number of chains: 41 Chain: "aa" Number of atoms: 36156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1695, 36156 Inner-chain residues flagged as termini: ['pdbres=" Caa 700 "'] Classifications: {'RNA': 1695} Modifications used: {'5*END': 2, 'rna2p_pur': 153, 'rna2p_pyr': 130, 'rna3p_pur': 747, 'rna3p_pyr': 665} Link IDs: {'rna2p': 282, 'rna3p': 1412} Chain breaks: 3 Chain: "ba" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 929 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain: "ca" Number of atoms: 1443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1443 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 3, 'TRANS': 174} Chain breaks: 1 Chain: "da" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 703 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "ga" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1070 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "ha" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2473 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 10, 'TRANS': 311} Chain: "ia" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1673 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 8, 'TRANS': 204} Chain: "ja" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2082 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 12, 'TRANS': 248} Chain: "ka" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1516 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain: "la" Number of atoms: 1119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1119 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain: "ma" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 806 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 97} Chain: "na" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 941 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "oa" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1114 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 2, 'TRANS': 133} Chain: "pa" Number of atoms: 1195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1195 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 140} Chain: "qa" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 975 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "ra" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1065 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "sa" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 807 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 8, 'TRANS': 91} Chain: "ta" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 618 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "ua" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 513 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "va" Number of atoms: 1039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1039 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "wa" Number of atoms: 314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 314 Classifications: {'peptide': 39} Modifications used: {'COO': 1} Link IDs: {'TRANS': 38} Chain: "xa" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 546 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "ya" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 322 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 2, 'TRANS': 36} Chain: "za" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1609 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 11, 'TRANS': 190} Chain: "bb" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1720 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 5, 'TRANS': 205} Chain: "cb" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 596 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "db" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 771 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "eb" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1493 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain: "fb" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1660 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} Chain: "gb" Number of atoms: 1199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1199 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 4, 'TRANS': 146} Chain breaks: 1 Chain: "hb" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1389 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 8, 'TRANS': 160} Chain: "ib" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1166 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 8, 'TRANS': 136} Chain: "IB" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 237 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "al" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 61 Classifications: {'RNA': 3} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "cl" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1622 Classifications: {'RNA': 75} Modifications used: {'p5*END': 1, 'rna2p': 4, 'rna2p_pur': 6, 'rna2p_pyr': 1, 'rna3p': 7, 'rna3p_pur': 30, 'rna3p_pyr': 27} Link IDs: {'rna2p': 10, 'rna3p': 64} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 6 Chain: "aa" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Unusual residues: {' MG': 80} Classifications: {'undetermined': 80} Link IDs: {None: 79} Chain: "ja" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "wa" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "db" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "al" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "cl" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 58267 SG CYSwa 21 60.254 92.371 61.380 1.00 65.98 S ATOM 58291 SG CYSwa 24 63.505 93.867 60.145 1.00 68.00 S ATOM 58403 SG CYSwa 39 63.419 91.535 63.174 1.00 66.51 S ATOM 58429 SG CYSwa 42 62.354 94.879 63.654 1.00 63.62 S ATOM 63529 SG CYSdb 23 116.387 80.807 114.102 1.00 56.49 S ATOM 63549 SG CYSdb 26 117.755 80.281 110.499 1.00 55.57 S ATOM 63930 SG CYSdb 74 115.859 83.443 111.556 1.00 54.77 S ATOM 63949 SG CYSdb 77 114.061 80.321 111.016 1.00 53.98 S Time building chain proxies: 32.79, per 1000 atoms: 0.45 Number of scatterers: 73028 At special positions: 0 Unit cell: (231.672, 229.308, 189.12, 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 2 29.99 S 167 16.00 P 1770 15.00 Mg 84 11.99 O 18539 8.00 N 13403 7.00 C 39063 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: 29.32 Conformation dependent library (CDL) restraints added in 5.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNdb 201 " pdb="ZN ZNdb 201 " - pdb=" SG CYSdb 26 " pdb="ZN ZNdb 201 " - pdb=" SG CYSdb 77 " pdb="ZN ZNdb 201 " - pdb=" SG CYSdb 74 " pdb="ZN ZNdb 201 " - pdb=" SG CYSdb 23 " pdb=" ZNwa 101 " pdb="ZN ZNwa 101 " - pdb=" SG CYSwa 39 " pdb="ZN ZNwa 101 " - pdb=" SG CYSwa 24 " pdb="ZN ZNwa 101 " - pdb=" SG CYSwa 42 " pdb="ZN ZNwa 101 " - pdb=" SG CYSwa 21 " Number of angles added : 12 8650 Ramachandran restraints generated. 4325 Oldfield, 0 Emsley, 4325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8128 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 150 helices and 47 sheets defined 29.4% alpha, 16.3% beta 498 base pairs and 870 stacking pairs defined. Time for finding SS restraints: 29.51 Creating SS restraints... Processing helix chain 'ba' and resid 42 through 53 Processing helix chain 'ba' and resid 85 through 90 Processing helix chain 'ba' and resid 94 through 100 Processing helix chain 'ba' and resid 116 through 119 Processing helix chain 'ca' and resid 26 through 28 No H-bonds generated for 'chain 'ca' and resid 26 through 28' Processing helix chain 'ca' and resid 50 through 52 No H-bonds generated for 'chain 'ca' and resid 50 through 52' Processing helix chain 'ca' and resid 89 through 93 Processing helix chain 'ca' and resid 108 through 115 Processing helix chain 'ca' and resid 156 through 162 Processing helix chain 'ca' and resid 173 through 181 removed outlier: 3.524A pdb=" N GLNca 178 " --> pdb=" O HISca 174 " (cutoff:3.500A) Processing helix chain 'ca' and resid 192 through 195 No H-bonds generated for 'chain 'ca' and resid 192 through 195' Processing helix chain 'ca' and resid 205 through 215 Processing helix chain 'da' and resid 5 through 17 Processing helix chain 'da' and resid 40 through 51 removed outlier: 3.622A pdb=" N SERda 48 " --> pdb=" O LYSda 44 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SERda 51 " --> pdb=" O GLNda 47 " (cutoff:3.500A) Processing helix chain 'da' and resid 70 through 77 removed outlier: 4.010A pdb=" N GLUda 74 " --> pdb=" O ASNda 70 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHEda 75 " --> pdb=" O ASPda 71 " (cutoff:3.500A) Processing helix chain 'ga' and resid 10 through 23 removed outlier: 4.371A pdb=" N TRPga 22 " --> pdb=" O ARGga 18 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALAga 23 " --> pdb=" O ASNga 19 " (cutoff:3.500A) Processing helix chain 'ga' and resid 25 through 31 Processing helix chain 'ga' and resid 89 through 91 No H-bonds generated for 'chain 'ga' and resid 89 through 91' Processing helix chain 'ga' and resid 129 through 133 Processing helix chain 'ia' and resid 7 through 28 removed outlier: 4.461A pdb=" N ARGia 27 " --> pdb=" O GLUia 23 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLUia 28 " --> pdb=" O METia 24 " (cutoff:3.500A) Processing helix chain 'ia' and resid 30 through 32 No H-bonds generated for 'chain 'ia' and resid 30 through 32' Processing helix chain 'ia' and resid 55 through 59 Processing helix chain 'ia' and resid 64 through 76 Processing helix chain 'ia' and resid 94 through 96 No H-bonds generated for 'chain 'ia' and resid 94 through 96' Processing helix chain 'ia' and resid 98 through 111 Processing helix chain 'ia' and resid 115 through 128 Processing helix chain 'ia' and resid 162 through 167 removed outlier: 3.898A pdb=" N TYRia 167 " --> pdb=" O VALia 164 " (cutoff:3.500A) Processing helix chain 'ja' and resid 11 through 13 No H-bonds generated for 'chain 'ja' and resid 11 through 13' Processing helix chain 'ja' and resid 16 through 18 No H-bonds generated for 'chain 'ja' and resid 16 through 18' Processing helix chain 'ja' and resid 44 through 48 Processing helix chain 'ja' and resid 58 through 67 removed outlier: 3.883A pdb=" N GLNja 67 " --> pdb=" O SERja 63 " (cutoff:3.500A) Processing helix chain 'ja' and resid 117 through 119 No H-bonds generated for 'chain 'ja' and resid 117 through 119' Processing helix chain 'ja' and resid 133 through 135 No H-bonds generated for 'chain 'ja' and resid 133 through 135' Processing helix chain 'ja' and resid 186 through 188 No H-bonds generated for 'chain 'ja' and resid 186 through 188' Processing helix chain 'ja' and resid 222 through 224 No H-bonds generated for 'chain 'ja' and resid 222 through 224' Processing helix chain 'ja' and resid 248 through 259 Processing helix chain 'ka' and resid 14 through 16 No H-bonds generated for 'chain 'ka' and resid 14 through 16' Processing helix chain 'ka' and resid 39 through 41 No H-bonds generated for 'chain 'ka' and resid 39 through 41' Processing helix chain 'ka' and resid 58 through 60 No H-bonds generated for 'chain 'ka' and resid 58 through 60' Processing helix chain 'ka' and resid 64 through 72 Processing helix chain 'ka' and resid 82 through 100 Processing helix chain 'ka' and resid 104 through 114 Processing helix chain 'ka' and resid 139 through 158 Processing helix chain 'ka' and resid 165 through 178 Processing helix chain 'ka' and resid 184 through 199 removed outlier: 3.802A pdb=" N ASNka 199 " --> pdb=" O VALka 195 " (cutoff:3.500A) Processing helix chain 'la' and resid 42 through 44 No H-bonds generated for 'chain 'la' and resid 42 through 44' Processing helix chain 'la' and resid 51 through 61 Proline residue: la 57 - end of helix Processing helix chain 'la' and resid 63 through 66 Processing helix chain 'la' and resid 80 through 101 Processing helix chain 'la' and resid 105 through 118 removed outlier: 3.673A pdb=" N VALla 111 " --> pdb=" O ALAla 107 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYRla 118 " --> pdb=" O ILEla 114 " (cutoff:3.500A) Processing helix chain 'la' and resid 120 through 122 No H-bonds generated for 'chain 'la' and resid 120 through 122' Processing helix chain 'ma' and resid 37 through 52 removed outlier: 3.594A pdb=" N VALma 43 " --> pdb=" O ASNma 39 " (cutoff:3.500A) Processing helix chain 'ma' and resid 103 through 109 Processing helix chain 'na' and resid 58 through 60 No H-bonds generated for 'chain 'na' and resid 58 through 60' Processing helix chain 'na' and resid 65 through 67 No H-bonds generated for 'chain 'na' and resid 65 through 67' Processing helix chain 'na' and resid 71 through 86 Processing helix chain 'na' and resid 112 through 121 Processing helix chain 'oa' and resid 15 through 17 No H-bonds generated for 'chain 'oa' and resid 15 through 17' Processing helix chain 'oa' and resid 26 through 32 removed outlier: 4.409A pdb=" N THRoa 31 " --> pdb=" O METoa 27 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N SERoa 32 " --> pdb=" O PHEoa 28 " (cutoff:3.500A) Processing helix chain 'oa' and resid 38 through 47 Processing helix chain 'oa' and resid 61 through 72 Processing helix chain 'oa' and resid 81 through 83 No H-bonds generated for 'chain 'oa' and resid 81 through 83' Processing helix chain 'oa' and resid 100 through 117 removed outlier: 4.325A pdb=" N ASPoa 104 " --> pdb=" O SERoa 100 " (cutoff:3.500A) Processing helix chain 'oa' and resid 120 through 127 Processing helix chain 'pa' and resid 30 through 42 Processing helix chain 'pa' and resid 47 through 56 Processing helix chain 'pa' and resid 63 through 66 No H-bonds generated for 'chain 'pa' and resid 63 through 66' Processing helix chain 'pa' and resid 71 through 77 Processing helix chain 'pa' and resid 86 through 104 removed outlier: 3.914A pdb=" N ARGpa 104 " --> pdb=" O LYSpa 100 " (cutoff:3.500A) Processing helix chain 'pa' and resid 109 through 131 Processing helix chain 'pa' and resid 144 through 146 No H-bonds generated for 'chain 'pa' and resid 144 through 146' Processing helix chain 'qa' and resid 7 through 19 removed outlier: 3.628A pdb=" N LYSqa 19 " --> pdb=" O GLNqa 15 " (cutoff:3.500A) Processing helix chain 'qa' and resid 28 through 37 Processing helix chain 'qa' and resid 44 through 63 removed outlier: 3.778A pdb=" N HISqa 56 " --> pdb=" O GLYqa 52 " (cutoff:3.500A) Processing helix chain 'qa' and resid 72 through 75 No H-bonds generated for 'chain 'qa' and resid 72 through 75' Processing helix chain 'qa' and resid 77 through 80 No H-bonds generated for 'chain 'qa' and resid 77 through 80' Processing helix chain 'qa' and resid 100 through 108 Processing helix chain 'ra' and resid 19 through 21 No H-bonds generated for 'chain 'ra' and resid 19 through 21' Processing helix chain 'ra' and resid 24 through 37 removed outlier: 3.688A pdb=" N VALra 28 " --> pdb=" O PROra 24 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYSra 36 " --> pdb=" O SERra 32 " (cutoff:3.500A) Processing helix chain 'ra' and resid 63 through 78 removed outlier: 4.725A pdb=" N TYRra 66 " --> pdb=" O ALAra 63 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TYRra 67 " --> pdb=" O ASPra 64 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SERra 72 " --> pdb=" O ARGra 69 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALAra 74 " --> pdb=" O ALAra 71 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARGra 75 " --> pdb=" O SERra 72 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILEra 77 " --> pdb=" O ALAra 74 " (cutoff:3.500A) Processing helix chain 'ra' and resid 85 through 92 removed outlier: 4.434A pdb=" N LYSra 90 " --> pdb=" O GLYra 86 " (cutoff:3.500A) Processing helix chain 'ra' and resid 110 through 121 Processing helix chain 'ra' and resid 138 through 150 removed outlier: 3.705A pdb=" N THRra 150 " --> pdb=" O GLNra 146 " (cutoff:3.500A) Processing helix chain 'sa' and resid 39 through 45 removed outlier: 3.650A pdb=" N GLNsa 44 " --> pdb=" O ASPsa 40 " (cutoff:3.500A) Processing helix chain 'sa' and resid 48 through 55 Processing helix chain 'sa' and resid 60 through 75 removed outlier: 3.787A pdb=" N LYSsa 67 " --> pdb=" O METsa 63 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYSsa 68 " --> pdb=" O ALAsa 64 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEUsa 69 " --> pdb=" O LEUsa 65 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARGsa 70 " --> pdb=" O VALsa 66 " (cutoff:3.500A) Processing helix chain 'sa' and resid 96 through 98 No H-bonds generated for 'chain 'sa' and resid 96 through 98' Processing helix chain 'sa' and resid 125 through 128 removed outlier: 3.605A pdb=" N PHEsa 128 " --> pdb=" O LEUsa 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'sa' and resid 125 through 128' Processing helix chain 'ta' and resid 35 through 38 removed outlier: 4.440A pdb=" N ASNta 38 " --> pdb=" O GLUta 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'ta' and resid 35 through 38' Processing helix chain 'ta' and resid 57 through 59 No H-bonds generated for 'chain 'ta' and resid 57 through 59' Processing helix chain 'ta' and resid 82 through 87 Processing helix chain 'va' and resid 8 through 19 Processing helix chain 'va' and resid 31 through 43 Processing helix chain 'va' and resid 85 through 92 Processing helix chain 'va' and resid 112 through 118 Processing helix chain 'wa' and resid 33 through 35 No H-bonds generated for 'chain 'wa' and resid 33 through 35' Processing helix chain 'wa' and resid 40 through 45 removed outlier: 3.670A pdb=" N ARGwa 44 " --> pdb=" O ARGwa 40 " (cutoff:3.500A) Processing helix chain 'wa' and resid 47 through 50 No H-bonds generated for 'chain 'wa' and resid 47 through 50' Processing helix chain 'xa' and resid 17 through 19 No H-bonds generated for 'chain 'xa' and resid 17 through 19' Processing helix chain 'ya' and resid 13 through 17 Processing helix chain 'ya' and resid 33 through 43 Processing helix chain 'za' and resid 14 through 24 Processing helix chain 'za' and resid 55 through 70 Processing helix chain 'za' and resid 75 through 77 No H-bonds generated for 'chain 'za' and resid 75 through 77' Processing helix chain 'za' and resid 85 through 98 removed outlier: 3.692A pdb=" N GLNza 88 " --> pdb=" O PROza 85 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ARGza 89 " --> pdb=" O TYRza 86 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALAza 90 " --> pdb=" O GLYza 87 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEUza 92 " --> pdb=" O ARGza 89 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHEza 94 " --> pdb=" O VALza 91 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N HISza 97 " --> pdb=" O PHEza 94 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THRza 98 " --> pdb=" O ALAza 95 " (cutoff:3.500A) Processing helix chain 'za' and resid 135 through 143 removed outlier: 3.510A pdb=" N ALAza 142 " --> pdb=" O ILEza 138 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEUza 143 " --> pdb=" O LYSza 139 " (cutoff:3.500A) Processing helix chain 'za' and resid 172 through 190 removed outlier: 3.804A pdb=" N GLYza 176 " --> pdb=" O ARGza 172 " (cutoff:3.500A) Processing helix chain 'za' and resid 203 through 205 No H-bonds generated for 'chain 'za' and resid 203 through 205' Processing helix chain 'bb' and resid 58 through 61 No H-bonds generated for 'chain 'bb' and resid 58 through 61' Processing helix chain 'bb' and resid 71 through 74 No H-bonds generated for 'chain 'bb' and resid 71 through 74' Processing helix chain 'bb' and resid 77 through 79 No H-bonds generated for 'chain 'bb' and resid 77 through 79' Processing helix chain 'bb' and resid 107 through 113 Processing helix chain 'bb' and resid 160 through 175 Processing helix chain 'bb' and resid 181 through 189 Processing helix chain 'bb' and resid 192 through 200 Processing helix chain 'bb' and resid 225 through 231 Processing helix chain 'cb' and resid 56 through 61 Processing helix chain 'cb' and resid 64 through 72 Processing helix chain 'db' and resid 47 through 49 No H-bonds generated for 'chain 'db' and resid 47 through 49' Processing helix chain 'db' and resid 51 through 56 removed outlier: 4.608A pdb=" N ALAdb 56 " --> pdb=" O ASPdb 52 " (cutoff:3.500A) Processing helix chain 'db' and resid 75 through 80 Processing helix chain 'db' and resid 91 through 93 No H-bonds generated for 'chain 'db' and resid 91 through 93' Processing helix chain 'eb' and resid 23 through 35 removed outlier: 3.521A pdb=" N LEUeb 32 " --> pdb=" O ALAeb 28 " (cutoff:3.500A) Processing helix chain 'eb' and resid 41 through 63 removed outlier: 3.548A pdb=" N VALeb 47 " --> pdb=" O GLUeb 43 " (cutoff:3.500A) Processing helix chain 'eb' and resid 69 through 84 Processing helix chain 'eb' and resid 103 through 109 removed outlier: 3.697A pdb=" N ARGeb 109 " --> pdb=" O ASNeb 105 " (cutoff:3.500A) Processing helix chain 'eb' and resid 111 through 117 Processing helix chain 'eb' and resid 124 through 133 removed outlier: 3.521A pdb=" N GLNeb 133 " --> pdb=" O VALeb 129 " (cutoff:3.500A) Processing helix chain 'eb' and resid 173 through 182 removed outlier: 3.541A pdb=" N GLNeb 179 " --> pdb=" O LYSeb 175 " (cutoff:3.500A) Processing helix chain 'fb' and resid 50 through 56 Processing helix chain 'fb' and resid 64 through 67 No H-bonds generated for 'chain 'fb' and resid 64 through 67' Processing helix chain 'fb' and resid 76 through 82 removed outlier: 3.838A pdb=" N THRfb 81 " --> pdb=" O ILEfb 78 " (cutoff:3.500A) Processing helix chain 'fb' and resid 131 through 144 Processing helix chain 'fb' and resid 192 through 201 Processing helix chain 'fb' and resid 217 through 232 removed outlier: 3.767A pdb=" N THRfb 231 " --> pdb=" O CYSfb 227 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TYRfb 232 " --> pdb=" O LEUfb 228 " (cutoff:3.500A) Processing helix chain 'fb' and resid 237 through 239 No H-bonds generated for 'chain 'fb' and resid 237 through 239' Processing helix chain 'fb' and resid 249 through 252 No H-bonds generated for 'chain 'fb' and resid 249 through 252' Processing helix chain 'gb' and resid 22 through 24 No H-bonds generated for 'chain 'gb' and resid 22 through 24' Processing helix chain 'gb' and resid 38 through 41 No H-bonds generated for 'chain 'gb' and resid 38 through 41' Processing helix chain 'gb' and resid 43 through 45 No H-bonds generated for 'chain 'gb' and resid 43 through 45' Processing helix chain 'gb' and resid 58 through 60 No H-bonds generated for 'chain 'gb' and resid 58 through 60' Processing helix chain 'gb' and resid 186 through 212 removed outlier: 3.681A pdb=" N LYSgb 201 " --> pdb=" O ALAgb 197 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILEgb 203 " --> pdb=" O LYSgb 199 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALAgb 211 " --> pdb=" O LYSgb 207 " (cutoff:3.500A) Processing helix chain 'hb' and resid 20 through 28 Processing helix chain 'hb' and resid 35 through 37 No H-bonds generated for 'chain 'hb' and resid 35 through 37' Processing helix chain 'hb' and resid 70 through 75 Processing helix chain 'hb' and resid 83 through 85 No H-bonds generated for 'chain 'hb' and resid 83 through 85' Processing helix chain 'hb' and resid 119 through 130 Processing helix chain 'hb' and resid 167 through 177 removed outlier: 3.552A pdb=" N LEUhb 177 " --> pdb=" O VALhb 173 " (cutoff:3.500A) Processing helix chain 'ib' and resid 47 through 50 No H-bonds generated for 'chain 'ib' and resid 47 through 50' Processing helix chain 'IB' and resid 2 through 23 Processing sheet with id= A, first strand: chain 'ba' and resid 18 through 20 Processing sheet with id= B, first strand: chain 'ca' and resid 73 through 78 removed outlier: 3.507A pdb=" N VALca 73 " --> pdb=" O TRPca 68 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASPca 81 " --> pdb=" O GLNca 104 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'ca' and resid 43 through 48 removed outlier: 6.494A pdb=" N ARGca 45 " --> pdb=" O ALAca 58 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ALAca 58 " --> pdb=" O ARGca 45 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VALca 47 " --> pdb=" O TRPca 56 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N TRPca 56 " --> pdb=" O VALca 47 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'da' and resid 20 through 22 Processing sheet with id= E, first strand: chain 'ga' and resid 98 through 102 removed outlier: 6.814A pdb=" N ARGga 70 " --> pdb=" O LEUga 51 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LYSga 53 " --> pdb=" O CYSga 68 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N CYSga 68 " --> pdb=" O LYSga 53 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N PHEga 119 " --> pdb=" O PHEga 83 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEUga 100 " --> pdb=" O VALga 122 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'ha' and resid 21 through 25 removed outlier: 6.541A pdb=" N SERha 37 " --> pdb=" O THRha 22 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILEha 24 " --> pdb=" O VALha 35 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VALha 35 " --> pdb=" O ILEha 24 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N ASPha 47 " --> pdb=" O PROha 65 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'ha' and resid 76 through 81 removed outlier: 6.902A pdb=" N GLYha 91 " --> pdb=" O GLNha 77 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VALha 79 " --> pdb=" O LEUha 89 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEUha 89 " --> pdb=" O VALha 79 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEUha 99 " --> pdb=" O ARGha 109 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARGha 109 " --> pdb=" O LEUha 99 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ASPha 101 " --> pdb=" O THRha 107 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N THRha 107 " --> pdb=" O ASPha 101 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'ha' and resid 118 through 122 removed outlier: 6.622A pdb=" N ALAha 133 " --> pdb=" O LEUha 119 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VALha 121 " --> pdb=" O VALha 131 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VALha 131 " --> pdb=" O VALha 121 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYRha 150 " --> pdb=" O LEUha 141 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'ha' and resid 166 through 171 removed outlier: 6.647A pdb=" N GLYha 183 " --> pdb=" O SERha 167 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VALha 169 " --> pdb=" O VALha 181 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VALha 181 " --> pdb=" O VALha 169 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N PHEha 171 " --> pdb=" O THRha 179 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THRha 179 " --> pdb=" O PHEha 171 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILEha 180 " --> pdb=" O TRPha 192 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VALha 189 " --> pdb=" O LEUha 203 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYSha 201 " --> pdb=" O VALha 191 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASNha 193 " --> pdb=" O LEUha 199 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEUha 199 " --> pdb=" O ASNha 193 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'ha' and resid 230 through 232 Processing sheet with id= K, first strand: chain 'ha' and resid 254 through 256 removed outlier: 3.528A pdb=" N GLNha 283 " --> pdb=" O ILEha 273 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'ha' and resid 8 through 15 removed outlier: 3.899A pdb=" N ALAha 11 " --> pdb=" O ILEha 322 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ILEha 322 " --> pdb=" O ALAha 11 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VALha 13 " --> pdb=" O ILEha 320 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILEha 320 " --> pdb=" O VALha 13 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THRha 319 " --> pdb=" O TYRha 315 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'ia' and resid 84 through 90 removed outlier: 6.356A pdb=" N THRia 46 " --> pdb=" O GLUia 85 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N TYRia 87 " --> pdb=" O THRia 46 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILEia 48 " --> pdb=" O TYRia 87 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N GLUia 89 " --> pdb=" O ILEia 48 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILEia 50 " --> pdb=" O GLUia 89 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARGia 45 " --> pdb=" O THRia 42 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'ia' and resid 148 through 155 removed outlier: 3.653A pdb=" N GLYia 133 " --> pdb=" O METia 189 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'ja' and resid 41 through 43 removed outlier: 3.642A pdb=" N ALAja 84 " --> pdb=" O LEUja 42 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'ja' and resid 70 through 72 Processing sheet with id= Q, first strand: chain 'ja' and resid 121 through 125 removed outlier: 3.889A pdb=" N ASPja 171 " --> pdb=" O LYSja 161 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ASPja 163 " --> pdb=" O ILEja 169 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILEja 169 " --> pdb=" O ASPja 163 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'ja' and resid 146 through 148 removed outlier: 3.516A pdb=" N SERja 128 " --> pdb=" O ASNja 140 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'ja' and resid 225 through 229 removed outlier: 7.136A pdb=" N VALja 180 " --> pdb=" O ILEja 228 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N HISja 209 " --> pdb=" O LYSja 196 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ARGja 198 " --> pdb=" O THRja 207 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THRja 207 " --> pdb=" O ARGja 198 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'ka' and resid 119 through 126 Processing sheet with id= U, first strand: chain 'la' and resid 14 through 18 Processing sheet with id= V, first strand: chain 'ma' and resid 28 through 34 removed outlier: 4.451A pdb=" N LYSma 94 " --> pdb=" O METma 64 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'ma' and resid 67 through 74 Processing sheet with id= X, first strand: chain 'na' and resid 52 through 57 removed outlier: 7.049A pdb=" N VALna 44 " --> pdb=" O LEUna 53 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARGna 55 " --> pdb=" O ILEna 42 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILEna 42 " --> pdb=" O ARGna 55 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N THRna 57 " --> pdb=" O THRna 40 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THRna 40 " --> pdb=" O THRna 57 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASPna 39 " --> pdb=" O SERna 36 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALAna 92 " --> pdb=" O GLYna 29 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ALAna 31 " --> pdb=" O ALAna 92 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N HISna 94 " --> pdb=" O ALAna 31 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILEna 33 " --> pdb=" O HISna 94 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LYSna 96 " --> pdb=" O ILEna 33 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ALAna 35 " --> pdb=" O LYSna 96 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ARGna 98 " --> pdb=" O ALAna 35 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'qa' and resid 96 through 98 removed outlier: 3.867A pdb=" N GLUqa 118 " --> pdb=" O ILEqa 96 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'ra' and resid 94 through 96 Processing sheet with id= AA, first strand: chain 'ra' and resid 126 through 128 Processing sheet with id= AB, first strand: chain 'ua' and resid 72 through 75 removed outlier: 7.098A pdb=" N ARGua 48 " --> pdb=" O VALua 32 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VALua 34 " --> pdb=" O GLNua 46 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N GLNua 46 " --> pdb=" O VALua 34 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'ua' and resid 36 through 38 Processing sheet with id= AD, first strand: chain 'va' and resid 23 through 26 Processing sheet with id= AE, first strand: chain 'va' and resid 70 through 73 removed outlier: 6.823A pdb=" N VALva 102 " --> pdb=" O LEUva 125 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TYRva 127 " --> pdb=" O TYRva 100 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N TYRva 100 " --> pdb=" O TYRva 127 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'xa' and resid 46 through 49 Processing sheet with id= AG, first strand: chain 'za' and resid 101 through 104 removed outlier: 3.646A pdb=" N SERza 82 " --> pdb=" O ILEza 103 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEUza 125 " --> pdb=" O ILEza 79 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N GLNza 81 " --> pdb=" O LEUza 125 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILEza 127 " --> pdb=" O GLNza 81 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILEza 163 " --> pdb=" O ALAza 150 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N CYSza 152 " --> pdb=" O ILEza 163 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ILEza 165 " --> pdb=" O CYSza 152 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'za' and resid 42 through 45 removed outlier: 6.783A pdb=" N ILEza 52 " --> pdb=" O TYRza 43 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'bb' and resid 44 through 49 removed outlier: 3.815A pdb=" N GLYbb 44 " --> pdb=" O ILEbb 32 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'bb' and resid 65 through 69 removed outlier: 5.349A pdb=" N ARGbb 87 " --> pdb=" O PHEbb 100 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N PHEbb 100 " --> pdb=" O ARGbb 87 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'bb' and resid 120 through 128 removed outlier: 5.866A pdb=" N ARGbb 136 " --> pdb=" O ILEbb 217 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ILEbb 217 " --> pdb=" O ARGbb 136 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N PHEbb 138 " --> pdb=" O VALbb 215 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N VALbb 215 " --> pdb=" O PHEbb 138 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'cb' and resid 32 through 37 Processing sheet with id= AM, first strand: chain 'db' and resid 20 through 22 Processing sheet with id= AN, first strand: chain 'db' and resid 36 through 43 Processing sheet with id= AO, first strand: chain 'fb' and resid 122 through 128 removed outlier: 3.744A pdb=" N LYSfb 92 " --> pdb=" O PHEfb 111 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VALfb 113 " --> pdb=" O VALfb 90 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N VALfb 90 " --> pdb=" O VALfb 113 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'fb' and resid 168 through 172 Processing sheet with id= AQ, first strand: chain 'gb' and resid 12 through 17 removed outlier: 3.638A pdb=" N ILEgb 115 " --> pdb=" O ALAgb 6 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILEgb 49 " --> pdb=" O VALgb 116 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'gb' and resid 72 through 78 removed outlier: 3.548A pdb=" N ARGgb 95 " --> pdb=" O LEUgb 77 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'hb' and resid 92 through 97 removed outlier: 3.726A pdb=" N ASPhb 92 " --> pdb=" O LYShb 59 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THRhb 48 " --> pdb=" O HIShb 64 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'hb' and resid 182 through 186 removed outlier: 7.905A pdb=" N VALhb 183 " --> pdb=" O LYShb 149 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILEhb 151 " --> pdb=" O VALhb 183 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N GLUhb 185 " --> pdb=" O ILEhb 151 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ILEhb 153 " --> pdb=" O GLUhb 185 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'ib' and resid 100 through 111 removed outlier: 5.425A pdb=" N ARGib 88 " --> pdb=" O CYSib 76 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N CYSib 76 " --> pdb=" O ARGib 88 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ASNib 90 " --> pdb=" O GLYib 74 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N GLYib 74 " --> pdb=" O ASNib 90 " (cutoff:3.500A) removed outlier: 15.082A pdb=" N LEUib 92 " --> pdb=" O ILEib 72 " (cutoff:3.500A) removed outlier: 16.098A pdb=" N ILEib 72 " --> pdb=" O LEUib 92 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLYib 127 " --> pdb=" O VALib 140 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VALib 140 " --> pdb=" O GLYib 127 " (cutoff:3.500A) 1068 hydrogen bonds defined for protein. 3021 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1222 hydrogen bonds 1916 hydrogen bond angles 0 basepair planarities 498 basepair parallelities 870 stacking parallelities Total time for adding SS restraints: 58.33 Time building geometry restraints manager: 31.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 8282 1.31 - 1.44: 31081 1.44 - 1.57: 34862 1.57 - 1.70: 3540 1.70 - 1.83: 264 Bond restraints: 78029 Sorted by residual: bond pdb=" C LYSya 28 " pdb=" N GLNya 29 " ideal model delta sigma weight residual 1.331 1.276 0.055 2.07e-02 2.33e+03 7.08e+00 bond pdb=" CG1 ILEla 91 " pdb=" CD1 ILEla 91 " ideal model delta sigma weight residual 1.513 1.422 0.091 3.90e-02 6.57e+02 5.46e+00 bond pdb=" CB PROgb 70 " pdb=" CG PROgb 70 " ideal model delta sigma weight residual 1.492 1.607 -0.115 5.00e-02 4.00e+02 5.29e+00 bond pdb=" C2 G7Mcl 46 " pdb=" N2 G7Mcl 46 " ideal model delta sigma weight residual 1.452 1.497 -0.045 2.00e-02 2.50e+03 5.05e+00 bond pdb=" N1 1MAcl 58 " pdb=" CM1 1MAcl 58 " ideal model delta sigma weight residual 1.506 1.466 0.040 2.00e-02 2.50e+03 4.08e+00 ... (remaining 78024 not shown) Histogram of bond angle deviations from ideal: 91.50 - 101.82: 1591 101.82 - 112.14: 48425 112.14 - 122.46: 50000 122.46 - 132.78: 13739 132.78 - 143.10: 116 Bond angle restraints: 113871 Sorted by residual: angle pdb=" C1' 1MAcl 58 " pdb=" N9 1MAcl 58 " pdb=" C8 1MAcl 58 " ideal model delta sigma weight residual 100.68 143.10 -42.42 3.00e+00 1.11e-01 2.00e+02 angle pdb=" C1' 1MAcl 58 " pdb=" N9 1MAcl 58 " pdb=" C4 1MAcl 58 " ideal model delta sigma weight residual 142.33 107.86 34.47 3.00e+00 1.11e-01 1.32e+02 angle pdb=" CA PROgb 70 " pdb=" N PROgb 70 " pdb=" CD PROgb 70 " ideal model delta sigma weight residual 112.00 98.83 13.17 1.40e+00 5.10e-01 8.85e+01 angle pdb=" N HISva 55 " pdb=" CA HISva 55 " pdb=" C HISva 55 " ideal model delta sigma weight residual 110.80 91.50 19.30 2.13e+00 2.20e-01 8.21e+01 angle pdb=" C PROva 54 " pdb=" N HISva 55 " pdb=" CA HISva 55 " ideal model delta sigma weight residual 121.54 135.92 -14.38 1.91e+00 2.74e-01 5.67e+01 ... (remaining 113866 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 43786 35.96 - 71.92: 5050 71.92 - 107.88: 526 107.88 - 143.84: 30 143.84 - 179.80: 47 Dihedral angle restraints: 49439 sinusoidal: 36828 harmonic: 12611 Sorted by residual: dihedral pdb=" CA ARGla 46 " pdb=" C ARGla 46 " pdb=" N PROla 47 " pdb=" CA PROla 47 " ideal model delta harmonic sigma weight residual 180.00 127.98 52.02 0 5.00e+00 4.00e-02 1.08e+02 dihedral pdb=" O4' Uaa1294 " pdb=" C1' Uaa1294 " pdb=" N1 Uaa1294 " pdb=" C2 Uaa1294 " ideal model delta sinusoidal sigma weight residual -160.00 17.19 -177.19 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' Uaa1087 " pdb=" C1' Uaa1087 " pdb=" N1 Uaa1087 " pdb=" C2 Uaa1087 " ideal model delta sinusoidal sigma weight residual -160.00 14.94 -174.94 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 49436 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 12645 0.079 - 0.157: 1337 0.157 - 0.236: 100 0.236 - 0.315: 14 0.315 - 0.394: 5 Chirality restraints: 14101 Sorted by residual: chirality pdb=" CB VALua 32 " pdb=" CA VALua 32 " pdb=" CG1 VALua 32 " pdb=" CG2 VALua 32 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" C3' Uaa1771 " pdb=" C4' Uaa1771 " pdb=" O3' Uaa1771 " pdb=" C2' Uaa1771 " both_signs ideal model delta sigma weight residual False -2.74 -2.36 -0.38 2.00e-01 2.50e+01 3.64e+00 chirality pdb=" CB ILEda 35 " pdb=" CA ILEda 35 " pdb=" CG1 ILEda 35 " pdb=" CG2 ILEda 35 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.42e+00 ... (remaining 14098 not shown) Planarity restraints: 7899 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MGcl 26 " 0.085 2.00e-02 2.50e+03 6.39e-01 9.20e+03 pdb=" C4' 2MGcl 26 " 0.470 2.00e-02 2.50e+03 pdb=" O4' 2MGcl 26 " 0.737 2.00e-02 2.50e+03 pdb=" C3' 2MGcl 26 " -0.592 2.00e-02 2.50e+03 pdb=" O3' 2MGcl 26 " -0.685 2.00e-02 2.50e+03 pdb=" C2' 2MGcl 26 " -0.178 2.00e-02 2.50e+03 pdb=" O2' 2MGcl 26 " 0.995 2.00e-02 2.50e+03 pdb=" C1' 2MGcl 26 " 0.186 2.00e-02 2.50e+03 pdb=" N9 2MGcl 26 " -1.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MCcl 48 " -0.950 2.00e-02 2.50e+03 6.23e-01 8.73e+03 pdb=" C4' 5MCcl 48 " 0.181 2.00e-02 2.50e+03 pdb=" O4' 5MCcl 48 " 0.816 2.00e-02 2.50e+03 pdb=" C3' 5MCcl 48 " -0.230 2.00e-02 2.50e+03 pdb=" O3' 5MCcl 48 " 0.922 2.00e-02 2.50e+03 pdb=" C2' 5MCcl 48 " -0.615 2.00e-02 2.50e+03 pdb=" O2' 5MCcl 48 " -0.624 2.00e-02 2.50e+03 pdb=" C1' 5MCcl 48 " 0.467 2.00e-02 2.50e+03 pdb=" N1 5MCcl 48 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MGcl 10 " -0.047 2.00e-02 2.50e+03 6.16e-01 8.54e+03 pdb=" C4' 2MGcl 10 " -0.470 2.00e-02 2.50e+03 pdb=" O4' 2MGcl 10 " -0.790 2.00e-02 2.50e+03 pdb=" C3' 2MGcl 10 " 0.584 2.00e-02 2.50e+03 pdb=" O3' 2MGcl 10 " 0.599 2.00e-02 2.50e+03 pdb=" C2' 2MGcl 10 " 0.226 2.00e-02 2.50e+03 pdb=" O2' 2MGcl 10 " -0.904 2.00e-02 2.50e+03 pdb=" C1' 2MGcl 10 " -0.183 2.00e-02 2.50e+03 pdb=" N9 2MGcl 10 " 0.984 2.00e-02 2.50e+03 ... (remaining 7896 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 436 2.46 - 3.07: 46263 3.07 - 3.68: 129048 3.68 - 4.29: 197262 4.29 - 4.90: 277267 Nonbonded interactions: 650276 Sorted by model distance: nonbonded pdb=" OP1 Gaa1114 " pdb="MG MGaa5021 " model vdw 1.852 2.170 nonbonded pdb=" OP2 Uaa1455 " pdb="MG MGaa5049 " model vdw 1.909 2.170 nonbonded pdb=" OP1 Gaa1205 " pdb="MG MGaa5052 " model vdw 1.921 2.170 nonbonded pdb=" OP2 Aaa 101 " pdb="MG MGaa5004 " model vdw 1.929 2.170 nonbonded pdb=" OP2 Caa1209 " pdb="MG MGaa5053 " model vdw 1.933 2.170 ... (remaining 650271 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=0.00 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: 11.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 37.890 Check model and map are aligned: 0.450 Set scattering table: 0.550 Process input model: 218.100 Find NCS groups from input model: 1.530 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 281.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 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 0.115 78029 Z= 0.431 Angle : 0.912 42.423 113871 Z= 0.470 Chirality : 0.049 0.394 14101 Planarity : 0.017 0.639 7899 Dihedral : 23.993 179.804 41311 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.28 % Favored : 92.58 % Rotamer: Outliers : 3.10 % Allowed : 41.69 % Favored : 55.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.24 % 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: -2.21 (0.12), residues: 4325 helix: -1.13 (0.13), residues: 1333 sheet: -0.94 (0.17), residues: 876 loop : -1.88 (0.12), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRPha 165 HIS 0.009 0.002 HISeb 125 PHE 0.036 0.003 PHEoa 28 TYR 0.042 0.004 TYRsa 106 ARG 0.024 0.002 ARGha 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8650 Ramachandran restraints generated. 4325 Oldfield, 0 Emsley, 4325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8650 Ramachandran restraints generated. 4325 Oldfield, 0 Emsley, 4325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 989 residues out of total 3778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 872 time to evaluate : 4.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: da 16 PHE cc_start: 0.6416 (t80) cc_final: 0.6000 (t80) REVERT: da 53 GLU cc_start: 0.7402 (pm20) cc_final: 0.6668 (tm-30) REVERT: da 71 ASP cc_start: 0.7515 (t70) cc_final: 0.7088 (t0) REVERT: da 73 ILE cc_start: 0.6018 (OUTLIER) cc_final: 0.5600 (tt) REVERT: ha 137 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.7274 (mtp180) REVERT: ha 300 THR cc_start: 0.7666 (OUTLIER) cc_final: 0.7331 (p) REVERT: ia 68 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7617 (mt-10) REVERT: ia 184 ILE cc_start: 0.8868 (mm) cc_final: 0.8617 (mt) REVERT: ja 40 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7570 (pp20) REVERT: la 58 ILE cc_start: 0.8971 (mt) cc_final: 0.8744 (mp) REVERT: na 84 ARG cc_start: 0.7884 (tmt170) cc_final: 0.7610 (tpt170) REVERT: oa 99 VAL cc_start: 0.7529 (t) cc_final: 0.7175 (p) REVERT: oa 108 ARG cc_start: 0.6601 (ppp-140) cc_final: 0.6123 (tmt-80) REVERT: qa 24 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7534 (mpt) REVERT: qa 101 GLU cc_start: 0.7754 (mp0) cc_final: 0.7436 (mp0) REVERT: ra 122 LYS cc_start: 0.8246 (mttt) cc_final: 0.8007 (ttmm) REVERT: ua 27 LYS cc_start: 0.8310 (mttm) cc_final: 0.7914 (mmtp) REVERT: xa 57 VAL cc_start: 0.7430 (m) cc_final: 0.7066 (p) REVERT: za 16 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7908 (mt-10) REVERT: za 174 SER cc_start: 0.7774 (p) cc_final: 0.7204 (t) REVERT: bb 28 GLN cc_start: 0.7448 (mp10) cc_final: 0.7215 (mm110) REVERT: bb 31 ASP cc_start: 0.7829 (t0) cc_final: 0.7605 (t0) REVERT: bb 50 ARG cc_start: 0.6245 (mtt180) cc_final: 0.5998 (mtt180) REVERT: bb 132 ASN cc_start: 0.7596 (m-40) cc_final: 0.6903 (t0) REVERT: bb 229 MET cc_start: 0.7624 (mmm) cc_final: 0.7349 (mmm) REVERT: db 42 ARG cc_start: 0.7641 (ptp90) cc_final: 0.7334 (ptm-80) REVERT: db 45 VAL cc_start: 0.7772 (t) cc_final: 0.7532 (t) REVERT: hb 37 LEU cc_start: 0.5242 (OUTLIER) cc_final: 0.5005 (pt) REVERT: hb 84 LEU cc_start: 0.5799 (OUTLIER) cc_final: 0.5442 (tm) REVERT: hb 117 ARG cc_start: 0.6709 (ptp90) cc_final: 0.6329 (mtm180) REVERT: ib 37 LYS cc_start: 0.8252 (ptmt) cc_final: 0.7731 (pttt) outliers start: 117 outliers final: 51 residues processed: 941 average time/residue: 1.5203 time to fit residues: 1885.9434 Evaluate side-chains 830 residues out of total 3778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 772 time to evaluate : 4.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain ba residue 19 THR Chi-restraints excluded: chain ba residue 32 VAL Chi-restraints excluded: chain ca residue 54 VAL Chi-restraints excluded: chain ca residue 89 ASN Chi-restraints excluded: chain da residue 73 ILE Chi-restraints excluded: chain ga residue 136 LYS Chi-restraints excluded: chain ha residue 20 VAL Chi-restraints excluded: chain ha residue 132 SER Chi-restraints excluded: chain ha residue 137 ARG Chi-restraints excluded: chain ha residue 189 VAL Chi-restraints excluded: chain ha residue 300 THR Chi-restraints excluded: chain ha residue 302 LEU Chi-restraints excluded: chain ia residue 169 ASP Chi-restraints excluded: chain ia residue 202 THR Chi-restraints excluded: chain ia residue 210 ILE Chi-restraints excluded: chain ja residue 40 GLU Chi-restraints excluded: chain ja residue 163 ASP Chi-restraints excluded: chain ka residue 19 THR Chi-restraints excluded: chain ka residue 38 SER Chi-restraints excluded: chain ka residue 45 LEU Chi-restraints excluded: chain ka residue 119 GLU Chi-restraints excluded: chain la residue 69 ILE Chi-restraints excluded: chain la residue 121 THR Chi-restraints excluded: chain ma residue 30 ILE Chi-restraints excluded: chain ma residue 31 THR Chi-restraints excluded: chain ma residue 113 THR Chi-restraints excluded: chain na residue 57 THR Chi-restraints excluded: chain oa residue 32 SER Chi-restraints excluded: chain oa residue 96 SER Chi-restraints excluded: chain oa residue 100 SER Chi-restraints excluded: chain pa residue 34 ASP Chi-restraints excluded: chain pa residue 49 GLN Chi-restraints excluded: chain pa residue 80 LEU Chi-restraints excluded: chain qa residue 8 THR Chi-restraints excluded: chain qa residue 16 VAL Chi-restraints excluded: chain qa residue 24 MET Chi-restraints excluded: chain qa residue 25 THR Chi-restraints excluded: chain qa residue 70 SER Chi-restraints excluded: chain sa residue 85 VAL Chi-restraints excluded: chain sa residue 129 SER Chi-restraints excluded: chain va residue 52 PHE Chi-restraints excluded: chain za residue 29 LEU Chi-restraints excluded: chain za residue 177 CYS Chi-restraints excluded: chain bb residue 122 GLU Chi-restraints excluded: chain bb residue 129 THR Chi-restraints excluded: chain cb residue 12 TYR Chi-restraints excluded: chain db residue 76 SER Chi-restraints excluded: chain eb residue 113 THR Chi-restraints excluded: chain eb residue 149 MET Chi-restraints excluded: chain eb residue 152 VAL Chi-restraints excluded: chain fb residue 133 THR Chi-restraints excluded: chain fb residue 149 VAL Chi-restraints excluded: chain gb residue 12 CYS Chi-restraints excluded: chain gb residue 56 CYS Chi-restraints excluded: chain gb residue 113 LEU Chi-restraints excluded: chain hb residue 37 LEU Chi-restraints excluded: chain hb residue 84 LEU Chi-restraints excluded: chain ib residue 75 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 508 optimal weight: 0.7980 chunk 456 optimal weight: 1.9990 chunk 253 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 307 optimal weight: 8.9990 chunk 243 optimal weight: 5.9990 chunk 471 optimal weight: 10.0000 chunk 182 optimal weight: 0.0870 chunk 286 optimal weight: 5.9990 chunk 351 optimal weight: 5.9990 chunk 546 optimal weight: 6.9990 overall best weight: 2.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** ca 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** da 7 ASN da 39 ASN ** da 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ga 91 ASN ha 17 HIS ** ha 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ia 211 HIS ka 79 ASN ** ma 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ma 39 ASN ** na 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** oa 97 GLN oa 120 HIS ra 81 GLN ** ra 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** sa 113 GLN va 48 ASN va 65 GLN ** za 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** db 11 ASN db 13 HIS db 94 ASN eb 9 ASN eb 60 HIS eb 68 ASN ** eb 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** gb 7 ASN ** hb 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ib 107 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.0804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 78029 Z= 0.246 Angle : 0.736 15.899 113871 Z= 0.388 Chirality : 0.041 0.323 14101 Planarity : 0.007 0.141 7899 Dihedral : 23.910 179.945 32441 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.50 % Favored : 93.39 % Rotamer: Outliers : 9.26 % Allowed : 31.95 % Favored : 58.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.12), residues: 4325 helix: -0.53 (0.14), residues: 1335 sheet: -0.86 (0.17), residues: 868 loop : -1.61 (0.13), residues: 2122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRPha 165 HIS 0.007 0.001 HISoa 120 PHE 0.025 0.002 PHEoa 28 TYR 0.023 0.002 TYRhb 132 ARG 0.010 0.001 ARGha 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8650 Ramachandran restraints generated. 4325 Oldfield, 0 Emsley, 4325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8650 Ramachandran restraints generated. 4325 Oldfield, 0 Emsley, 4325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1187 residues out of total 3778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 350 poor density : 837 time to evaluate : 4.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: ba 54 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7282 (mp0) REVERT: ca 169 ARG cc_start: 0.5056 (OUTLIER) cc_final: 0.3512 (mtp-110) REVERT: da 53 GLU cc_start: 0.7320 (pm20) cc_final: 0.6726 (tm-30) REVERT: da 57 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6402 (tp30) REVERT: da 71 ASP cc_start: 0.7570 (t70) cc_final: 0.7152 (t0) REVERT: da 78 ASN cc_start: 0.7262 (p0) cc_final: 0.6518 (t160) REVERT: ga 53 LYS cc_start: 0.8417 (mtmt) cc_final: 0.8198 (mtmm) REVERT: ha 102 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8233 (mt) REVERT: ha 123 PHE cc_start: 0.7246 (m-80) cc_final: 0.5667 (m-80) REVERT: ha 300 THR cc_start: 0.7556 (OUTLIER) cc_final: 0.7233 (p) REVERT: ha 322 ILE cc_start: 0.7212 (pp) cc_final: 0.6817 (mp) REVERT: ia 32 ASP cc_start: 0.5988 (m-30) cc_final: 0.5612 (m-30) REVERT: ia 65 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.6404 (ttt180) REVERT: ia 68 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7603 (mt-10) REVERT: ia 89 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.5642 (mp0) REVERT: ia 93 ASN cc_start: 0.7179 (OUTLIER) cc_final: 0.6950 (m-40) REVERT: ia 101 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7484 (mp10) REVERT: ja 40 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7264 (pp20) REVERT: ja 87 MET cc_start: 0.8072 (tpp) cc_final: 0.7866 (mtt) REVERT: ka 51 ARG cc_start: 0.7757 (ttm110) cc_final: 0.7539 (mtp180) REVERT: ka 98 LEU cc_start: 0.7937 (tm) cc_final: 0.7576 (tm) REVERT: ka 156 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7303 (mt-10) REVERT: la 58 ILE cc_start: 0.8971 (mt) cc_final: 0.8743 (mp) REVERT: ma 27 ARG cc_start: 0.6006 (OUTLIER) cc_final: 0.5797 (mmt90) REVERT: na 51 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7289 (mt-10) REVERT: na 56 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8542 (mm) REVERT: oa 108 ARG cc_start: 0.6496 (ppp-140) cc_final: 0.5865 (tmt170) REVERT: oa 112 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6386 (mp0) REVERT: qa 100 LYS cc_start: 0.7071 (OUTLIER) cc_final: 0.6776 (ttpm) REVERT: qa 119 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7338 (mtp-110) REVERT: ra 36 LYS cc_start: 0.8583 (mmmt) cc_final: 0.8373 (mmmm) REVERT: ra 122 LYS cc_start: 0.8224 (mttt) cc_final: 0.7961 (ttmm) REVERT: ta 69 ARG cc_start: 0.3615 (OUTLIER) cc_final: 0.2086 (mtp180) REVERT: ua 27 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7916 (mmtp) REVERT: ua 69 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6932 (mt-10) REVERT: va 67 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7957 (pmm-80) REVERT: va 86 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7548 (tm-30) REVERT: xa 37 VAL cc_start: 0.7616 (OUTLIER) cc_final: 0.7231 (t) REVERT: xa 57 VAL cc_start: 0.7534 (m) cc_final: 0.7176 (p) REVERT: za 12 LEU cc_start: 0.6072 (OUTLIER) cc_final: 0.5803 (mp) REVERT: za 15 LYS cc_start: 0.8540 (tptm) cc_final: 0.7834 (ttpp) REVERT: za 16 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7850 (mt-10) REVERT: za 174 SER cc_start: 0.7820 (OUTLIER) cc_final: 0.7253 (t) REVERT: za 197 HIS cc_start: 0.4754 (OUTLIER) cc_final: 0.2818 (p90) REVERT: bb 28 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.7268 (mm110) REVERT: bb 31 ASP cc_start: 0.7835 (t0) cc_final: 0.7527 (t0) REVERT: bb 111 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.8010 (mmp80) REVERT: bb 132 ASN cc_start: 0.7535 (m-40) cc_final: 0.6843 (t0) REVERT: bb 159 SER cc_start: 0.7804 (OUTLIER) cc_final: 0.7570 (p) REVERT: bb 189 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7944 (mt) REVERT: cb 2 GLN cc_start: 0.8270 (mt0) cc_final: 0.8052 (tt0) REVERT: db 19 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8115 (mtpm) REVERT: db 45 VAL cc_start: 0.7776 (OUTLIER) cc_final: 0.7501 (t) REVERT: eb 46 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7566 (ptp-170) REVERT: eb 60 HIS cc_start: 0.7919 (t70) cc_final: 0.7638 (t-90) REVERT: fb 205 ASP cc_start: 0.7851 (m-30) cc_final: 0.7392 (m-30) REVERT: gb 56 CYS cc_start: 0.7096 (p) cc_final: 0.6755 (p) REVERT: gb 91 VAL cc_start: 0.8289 (OUTLIER) cc_final: 0.7874 (t) REVERT: hb 37 LEU cc_start: 0.4933 (OUTLIER) cc_final: 0.4609 (pt) REVERT: hb 82 ARG cc_start: 0.6391 (mmp80) cc_final: 0.6179 (mmp80) REVERT: hb 84 LEU cc_start: 0.5728 (OUTLIER) cc_final: 0.5396 (tm) REVERT: hb 117 ARG cc_start: 0.6625 (ptp90) cc_final: 0.6213 (mtm180) REVERT: ib 37 LYS cc_start: 0.8250 (ptmt) cc_final: 0.7869 (pttt) REVERT: IB 20 MET cc_start: 0.4758 (OUTLIER) cc_final: 0.4471 (mpt) outliers start: 350 outliers final: 137 residues processed: 1064 average time/residue: 1.4821 time to fit residues: 2094.8918 Evaluate side-chains 961 residues out of total 3778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 790 time to evaluate : 4.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain ba residue 19 THR Chi-restraints excluded: chain ba residue 32 VAL Chi-restraints excluded: chain ba residue 54 GLU Chi-restraints excluded: chain ba residue 68 THR Chi-restraints excluded: chain ca residue 43 THR Chi-restraints excluded: chain ca residue 63 THR Chi-restraints excluded: chain ca residue 73 VAL Chi-restraints excluded: chain ca residue 83 VAL Chi-restraints excluded: chain ca residue 94 THR Chi-restraints excluded: chain ca residue 169 ARG Chi-restraints excluded: chain da residue 57 GLU Chi-restraints excluded: chain ga residue 35 GLU Chi-restraints excluded: chain ga residue 72 GLN Chi-restraints excluded: chain ga residue 90 LEU Chi-restraints excluded: chain ha residue 20 VAL Chi-restraints excluded: chain ha residue 28 ILE Chi-restraints excluded: chain ha residue 102 LEU Chi-restraints excluded: chain ha residue 103 SER Chi-restraints excluded: chain ha residue 118 VAL Chi-restraints excluded: chain ha residue 155 ASP Chi-restraints excluded: chain ha residue 189 VAL Chi-restraints excluded: chain ha residue 231 THR Chi-restraints excluded: chain ha residue 296 MET Chi-restraints excluded: chain ha residue 300 THR Chi-restraints excluded: chain ha residue 302 LEU Chi-restraints excluded: chain ha residue 303 SER Chi-restraints excluded: chain ha residue 305 SER Chi-restraints excluded: chain ia residue 65 ARG Chi-restraints excluded: chain ia residue 84 VAL Chi-restraints excluded: chain ia residue 89 GLU Chi-restraints excluded: chain ia residue 91 VAL Chi-restraints excluded: chain ia residue 93 ASN Chi-restraints excluded: chain ia residue 101 GLN Chi-restraints excluded: chain ia residue 123 LEU Chi-restraints excluded: chain ia residue 179 GLN Chi-restraints excluded: chain ia residue 207 LEU Chi-restraints excluded: chain ja residue 33 SER Chi-restraints excluded: chain ja residue 40 GLU Chi-restraints excluded: chain ja residue 163 ASP Chi-restraints excluded: chain ja residue 237 SER Chi-restraints excluded: chain ka residue 19 THR Chi-restraints excluded: chain ka residue 36 VAL Chi-restraints excluded: chain ka residue 45 LEU Chi-restraints excluded: chain ka residue 74 MET Chi-restraints excluded: chain ka residue 92 THR Chi-restraints excluded: chain ka residue 136 ASP Chi-restraints excluded: chain ka residue 156 GLU Chi-restraints excluded: chain ka residue 180 SER Chi-restraints excluded: chain la residue 32 ARG Chi-restraints excluded: chain la residue 49 MET Chi-restraints excluded: chain la residue 69 ILE Chi-restraints excluded: chain la residue 121 THR Chi-restraints excluded: chain la residue 123 LEU Chi-restraints excluded: chain ma residue 27 ARG Chi-restraints excluded: chain ma residue 30 ILE Chi-restraints excluded: chain ma residue 31 THR Chi-restraints excluded: chain ma residue 49 LYS Chi-restraints excluded: chain ma residue 52 LYS Chi-restraints excluded: chain ma residue 73 THR Chi-restraints excluded: chain ma residue 113 THR Chi-restraints excluded: chain ma residue 126 ASP Chi-restraints excluded: chain na residue 40 THR Chi-restraints excluded: chain na residue 47 LEU Chi-restraints excluded: chain na residue 54 VAL Chi-restraints excluded: chain na residue 56 ILE Chi-restraints excluded: chain na residue 57 THR Chi-restraints excluded: chain na residue 81 VAL Chi-restraints excluded: chain na residue 88 LEU Chi-restraints excluded: chain na residue 91 THR Chi-restraints excluded: chain na residue 107 THR Chi-restraints excluded: chain oa residue 112 GLU Chi-restraints excluded: chain oa residue 136 THR Chi-restraints excluded: chain pa residue 33 VAL Chi-restraints excluded: chain pa residue 87 ASP Chi-restraints excluded: chain pa residue 138 THR Chi-restraints excluded: chain qa residue 8 THR Chi-restraints excluded: chain qa residue 16 VAL Chi-restraints excluded: chain qa residue 25 THR Chi-restraints excluded: chain qa residue 43 SER Chi-restraints excluded: chain qa residue 100 LYS Chi-restraints excluded: chain qa residue 105 MET Chi-restraints excluded: chain qa residue 114 LEU Chi-restraints excluded: chain qa residue 119 ARG Chi-restraints excluded: chain ra residue 57 GLU Chi-restraints excluded: chain sa residue 43 VAL Chi-restraints excluded: chain sa residue 85 VAL Chi-restraints excluded: chain sa residue 88 HIS Chi-restraints excluded: chain ta residue 33 GLN Chi-restraints excluded: chain ta residue 45 GLN Chi-restraints excluded: chain ta residue 69 ARG Chi-restraints excluded: chain ua residue 27 LYS Chi-restraints excluded: chain ua residue 45 THR Chi-restraints excluded: chain ua residue 54 ASP Chi-restraints excluded: chain ua residue 67 VAL Chi-restraints excluded: chain va residue 8 ASP Chi-restraints excluded: chain va residue 17 GLU Chi-restraints excluded: chain va residue 23 THR Chi-restraints excluded: chain va residue 42 HIS Chi-restraints excluded: chain va residue 57 VAL Chi-restraints excluded: chain va residue 67 ARG Chi-restraints excluded: chain va residue 79 ASP Chi-restraints excluded: chain va residue 81 ARG Chi-restraints excluded: chain va residue 83 THR Chi-restraints excluded: chain wa residue 30 LEU Chi-restraints excluded: chain xa residue 37 VAL Chi-restraints excluded: chain xa residue 54 THR Chi-restraints excluded: chain xa residue 65 LEU Chi-restraints excluded: chain xa residue 77 GLU Chi-restraints excluded: chain ya residue 8 LEU Chi-restraints excluded: chain za residue 12 LEU Chi-restraints excluded: chain za residue 23 LEU Chi-restraints excluded: chain za residue 29 LEU Chi-restraints excluded: chain za residue 40 ARG Chi-restraints excluded: chain za residue 118 THR Chi-restraints excluded: chain za residue 141 SER Chi-restraints excluded: chain za residue 162 ASP Chi-restraints excluded: chain za residue 174 SER Chi-restraints excluded: chain za residue 177 CYS Chi-restraints excluded: chain za residue 197 HIS Chi-restraints excluded: chain bb residue 24 PHE Chi-restraints excluded: chain bb residue 28 GLN Chi-restraints excluded: chain bb residue 37 LEU Chi-restraints excluded: chain bb residue 40 SER Chi-restraints excluded: chain bb residue 69 SER Chi-restraints excluded: chain bb residue 91 VAL Chi-restraints excluded: chain bb residue 98 THR Chi-restraints excluded: chain bb residue 108 ASP Chi-restraints excluded: chain bb residue 111 ARG Chi-restraints excluded: chain bb residue 129 THR Chi-restraints excluded: chain bb residue 148 ASN Chi-restraints excluded: chain bb residue 159 SER Chi-restraints excluded: chain bb residue 180 ASP Chi-restraints excluded: chain bb residue 189 ILE Chi-restraints excluded: chain cb residue 12 TYR Chi-restraints excluded: chain cb residue 36 ILE Chi-restraints excluded: chain cb residue 67 SER Chi-restraints excluded: chain db residue 19 LYS Chi-restraints excluded: chain db residue 24 SER Chi-restraints excluded: chain db residue 41 VAL Chi-restraints excluded: chain db residue 45 VAL Chi-restraints excluded: chain db residue 55 GLU Chi-restraints excluded: chain eb residue 46 ARG Chi-restraints excluded: chain eb residue 52 SER Chi-restraints excluded: chain eb residue 113 THR Chi-restraints excluded: chain eb residue 143 VAL Chi-restraints excluded: chain eb residue 158 ILE Chi-restraints excluded: chain fb residue 133 THR Chi-restraints excluded: chain fb residue 149 VAL Chi-restraints excluded: chain fb residue 213 SER Chi-restraints excluded: chain fb residue 229 MET Chi-restraints excluded: chain fb residue 238 ASP Chi-restraints excluded: chain gb residue 50 PHE Chi-restraints excluded: chain gb residue 52 ILE Chi-restraints excluded: chain gb residue 67 VAL Chi-restraints excluded: chain gb residue 68 LEU Chi-restraints excluded: chain gb residue 91 VAL Chi-restraints excluded: chain gb residue 113 LEU Chi-restraints excluded: chain gb residue 205 LYS Chi-restraints excluded: chain hb residue 37 LEU Chi-restraints excluded: chain hb residue 84 LEU Chi-restraints excluded: chain hb residue 116 THR Chi-restraints excluded: chain hb residue 118 THR Chi-restraints excluded: chain hb residue 130 VAL Chi-restraints excluded: chain hb residue 137 VAL Chi-restraints excluded: chain hb residue 155 LEU Chi-restraints excluded: chain hb residue 182 VAL Chi-restraints excluded: chain ib residue 21 LYS Chi-restraints excluded: chain ib residue 87 VAL Chi-restraints excluded: chain ib residue 88 ARG Chi-restraints excluded: chain ib residue 122 ASP Chi-restraints excluded: chain IB residue 20 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 303 optimal weight: 9.9990 chunk 169 optimal weight: 6.9990 chunk 454 optimal weight: 10.0000 chunk 372 optimal weight: 0.6980 chunk 150 optimal weight: 10.0000 chunk 547 optimal weight: 9.9990 chunk 591 optimal weight: 10.0000 chunk 487 optimal weight: 5.9990 chunk 543 optimal weight: 9.9990 chunk 186 optimal weight: 4.9990 chunk 439 optimal weight: 3.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ba 34 HIS ca 166 GLN ca 174 HIS da 7 ASN ** da 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ga 91 ASN ** ha 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ja 67 GLN ** ma 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ma 39 ASN ** na 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** oa 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** oa 120 HIS ra 81 GLN ** ra 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** sa 113 GLN va 42 HIS va 48 ASN va 65 GLN xa 67 GLN ya 24 GLN za 20 GLN za 63 GLN za 96 GLN za 188 GLN bb 232 HIS db 94 ASN eb 9 ASN eb 68 ASN eb 92 GLN ** eb 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** gb 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** hb 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ib 99 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 78029 Z= 0.327 Angle : 0.758 14.064 113871 Z= 0.400 Chirality : 0.044 0.365 14101 Planarity : 0.007 0.128 7899 Dihedral : 23.805 179.701 32390 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.10 % Favored : 92.79 % Rotamer: Outliers : 10.35 % Allowed : 29.88 % Favored : 59.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.12), residues: 4325 helix: -0.36 (0.14), residues: 1339 sheet: -0.80 (0.17), residues: 860 loop : -1.56 (0.13), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPha 165 HIS 0.013 0.002 HISva 42 PHE 0.026 0.002 PHEoa 28 TYR 0.029 0.002 TYRpa 18 ARG 0.009 0.001 ARGfb 59 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8650 Ramachandran restraints generated. 4325 Oldfield, 0 Emsley, 4325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8650 Ramachandran restraints generated. 4325 Oldfield, 0 Emsley, 4325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1204 residues out of total 3778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 391 poor density : 813 time to evaluate : 4.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: ba 51 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7408 (mptp) REVERT: ca 18 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7687 (tt0) REVERT: ca 159 GLN cc_start: 0.6243 (mp10) cc_final: 0.5454 (pt0) REVERT: ca 164 LYS cc_start: 0.7517 (tptm) cc_final: 0.7298 (mppt) REVERT: ca 169 ARG cc_start: 0.5176 (OUTLIER) cc_final: 0.3585 (mtp-110) REVERT: da 7 ASN cc_start: 0.6675 (m110) cc_final: 0.6084 (m-40) REVERT: da 10 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7179 (mp0) REVERT: da 53 GLU cc_start: 0.7356 (pm20) cc_final: 0.6732 (tm-30) REVERT: da 57 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6367 (tp30) REVERT: da 71 ASP cc_start: 0.7484 (t70) cc_final: 0.7039 (t0) REVERT: ga 53 LYS cc_start: 0.8316 (mtmt) cc_final: 0.8092 (mtmm) REVERT: ga 118 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.7790 (ptm160) REVERT: ha 102 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8242 (mt) REVERT: ha 103 SER cc_start: 0.8170 (OUTLIER) cc_final: 0.7961 (t) REVERT: ha 123 PHE cc_start: 0.7391 (m-80) cc_final: 0.5774 (m-80) REVERT: ha 272 LYS cc_start: 0.6189 (OUTLIER) cc_final: 0.5817 (ttpt) REVERT: ia 5 ILE cc_start: 0.8492 (OUTLIER) cc_final: 0.8283 (mp) REVERT: ia 65 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.6535 (ttt180) REVERT: ia 68 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7638 (mt-10) REVERT: ia 89 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.5743 (mp0) REVERT: ia 101 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7540 (mp10) REVERT: ia 135 GLU cc_start: 0.7939 (tt0) cc_final: 0.7620 (tt0) REVERT: ja 40 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7375 (pp20) REVERT: ka 51 ARG cc_start: 0.7732 (ttm110) cc_final: 0.7475 (mtp180) REVERT: ka 98 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7529 (tm) REVERT: ka 120 ASP cc_start: 0.7504 (t0) cc_final: 0.7296 (t0) REVERT: ka 156 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7310 (mt-10) REVERT: ka 167 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7461 (mt-10) REVERT: la 12 THR cc_start: 0.8028 (t) cc_final: 0.7626 (m) REVERT: la 58 ILE cc_start: 0.9033 (mt) cc_final: 0.8807 (mp) REVERT: la 76 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.7083 (ttt90) REVERT: ma 27 ARG cc_start: 0.6179 (OUTLIER) cc_final: 0.5845 (mmt90) REVERT: na 47 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8412 (mm) REVERT: na 56 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8552 (mm) REVERT: oa 108 ARG cc_start: 0.6503 (OUTLIER) cc_final: 0.5966 (tmt170) REVERT: oa 112 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6571 (mp0) REVERT: pa 60 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8363 (mm) REVERT: qa 24 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7574 (mpt) REVERT: qa 56 HIS cc_start: 0.7544 (OUTLIER) cc_final: 0.6862 (p-80) REVERT: qa 97 ARG cc_start: 0.7087 (ptt180) cc_final: 0.6726 (mtm180) REVERT: ta 69 ARG cc_start: 0.3679 (OUTLIER) cc_final: 0.2130 (mtp180) REVERT: ua 27 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7840 (mmtp) REVERT: ua 69 GLU cc_start: 0.7348 (mt-10) cc_final: 0.7119 (mt-10) REVERT: va 67 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7442 (pmm-80) REVERT: va 79 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7832 (m-30) REVERT: va 86 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7644 (tm-30) REVERT: va 88 TYR cc_start: 0.7846 (OUTLIER) cc_final: 0.6841 (m-80) REVERT: xa 37 VAL cc_start: 0.7753 (OUTLIER) cc_final: 0.7429 (t) REVERT: xa 57 VAL cc_start: 0.7505 (m) cc_final: 0.7170 (p) REVERT: za 15 LYS cc_start: 0.8507 (tptm) cc_final: 0.7924 (ttpp) REVERT: za 16 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8079 (mt-10) REVERT: za 174 SER cc_start: 0.7961 (OUTLIER) cc_final: 0.7411 (t) REVERT: za 197 HIS cc_start: 0.5105 (OUTLIER) cc_final: 0.3235 (p90) REVERT: za 208 TYR cc_start: 0.8043 (OUTLIER) cc_final: 0.7041 (p90) REVERT: za 209 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6606 (mmm-85) REVERT: bb 28 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.7269 (mm110) REVERT: bb 31 ASP cc_start: 0.7851 (t0) cc_final: 0.7570 (t0) REVERT: bb 50 ARG cc_start: 0.6260 (mtt180) cc_final: 0.5725 (mtt180) REVERT: bb 111 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7817 (mmp80) REVERT: bb 146 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.7320 (mmt180) REVERT: bb 152 ARG cc_start: 0.7090 (OUTLIER) cc_final: 0.6822 (tmt-80) REVERT: bb 159 SER cc_start: 0.7801 (OUTLIER) cc_final: 0.7556 (p) REVERT: bb 175 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8370 (tt0) REVERT: bb 189 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7953 (mt) REVERT: bb 227 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7934 (mmtp) REVERT: cb 63 ASP cc_start: 0.6305 (t70) cc_final: 0.5974 (t0) REVERT: cb 71 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8598 (mp) REVERT: db 45 VAL cc_start: 0.7809 (OUTLIER) cc_final: 0.7545 (t) REVERT: eb 46 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.7642 (ptp-170) REVERT: fb 205 ASP cc_start: 0.7974 (m-30) cc_final: 0.7423 (m-30) REVERT: fb 211 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7768 (ttt180) REVERT: gb 56 CYS cc_start: 0.7198 (p) cc_final: 0.6909 (p) REVERT: gb 79 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7691 (ttp80) REVERT: gb 91 VAL cc_start: 0.8388 (OUTLIER) cc_final: 0.8064 (t) REVERT: hb 37 LEU cc_start: 0.4616 (OUTLIER) cc_final: 0.4217 (pt) REVERT: hb 117 ARG cc_start: 0.6512 (ptp90) cc_final: 0.5928 (mtm180) REVERT: hb 144 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.6412 (mtt-85) REVERT: hb 176 ARG cc_start: 0.5998 (ttm-80) cc_final: 0.5769 (ttm-80) REVERT: ib 37 LYS cc_start: 0.8278 (ptmt) cc_final: 0.7874 (pttt) REVERT: ib 89 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.7351 (mmm-85) REVERT: IB 11 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.5778 (ttm170) REVERT: IB 20 MET cc_start: 0.4737 (OUTLIER) cc_final: 0.4401 (mpt) outliers start: 391 outliers final: 176 residues processed: 1062 average time/residue: 1.5097 time to fit residues: 2122.1570 Evaluate side-chains 1004 residues out of total 3778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 773 time to evaluate : 4.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain ba residue 19 THR Chi-restraints excluded: chain ba residue 32 VAL Chi-restraints excluded: chain ba residue 51 LYS Chi-restraints excluded: chain ba residue 68 THR Chi-restraints excluded: chain ca residue 18 GLN Chi-restraints excluded: chain ca residue 43 THR Chi-restraints excluded: chain ca residue 44 VAL Chi-restraints excluded: chain ca residue 63 THR Chi-restraints excluded: chain ca residue 73 VAL Chi-restraints excluded: chain ca residue 83 VAL Chi-restraints excluded: chain ca residue 94 THR Chi-restraints excluded: chain ca residue 169 ARG Chi-restraints excluded: chain da residue 10 GLU Chi-restraints excluded: chain da residue 57 GLU Chi-restraints excluded: chain ga residue 35 GLU Chi-restraints excluded: chain ga residue 72 GLN Chi-restraints excluded: chain ga residue 90 LEU Chi-restraints excluded: chain ga residue 118 ARG Chi-restraints excluded: chain ga residue 128 SER Chi-restraints excluded: chain ha residue 20 VAL Chi-restraints excluded: chain ha residue 28 ILE Chi-restraints excluded: chain ha residue 102 LEU Chi-restraints excluded: chain ha residue 103 SER Chi-restraints excluded: chain ha residue 118 VAL Chi-restraints excluded: chain ha residue 120 SER Chi-restraints excluded: chain ha residue 132 SER Chi-restraints excluded: chain ha residue 155 ASP Chi-restraints excluded: chain ha residue 180 ILE Chi-restraints excluded: chain ha residue 189 VAL Chi-restraints excluded: chain ha residue 231 THR Chi-restraints excluded: chain ha residue 246 ASP Chi-restraints excluded: chain ha residue 272 LYS Chi-restraints excluded: chain ha residue 296 MET Chi-restraints excluded: chain ha residue 302 LEU Chi-restraints excluded: chain ha residue 303 SER Chi-restraints excluded: chain ha residue 305 SER Chi-restraints excluded: chain ia residue 5 ILE Chi-restraints excluded: chain ia residue 13 SER Chi-restraints excluded: chain ia residue 37 VAL Chi-restraints excluded: chain ia residue 42 THR Chi-restraints excluded: chain ia residue 55 THR Chi-restraints excluded: chain ia residue 58 VAL Chi-restraints excluded: chain ia residue 65 ARG Chi-restraints excluded: chain ia residue 66 ILE Chi-restraints excluded: chain ia residue 84 VAL Chi-restraints excluded: chain ia residue 89 GLU Chi-restraints excluded: chain ia residue 91 VAL Chi-restraints excluded: chain ia residue 101 GLN Chi-restraints excluded: chain ia residue 179 GLN Chi-restraints excluded: chain ia residue 202 THR Chi-restraints excluded: chain ia residue 207 LEU Chi-restraints excluded: chain ja residue 33 SER Chi-restraints excluded: chain ja residue 40 GLU Chi-restraints excluded: chain ja residue 57 THR Chi-restraints excluded: chain ja residue 71 MET Chi-restraints excluded: chain ja residue 116 ASP Chi-restraints excluded: chain ja residue 163 ASP Chi-restraints excluded: chain ja residue 192 VAL Chi-restraints excluded: chain ja residue 207 THR Chi-restraints excluded: chain ja residue 232 THR Chi-restraints excluded: chain ja residue 237 SER Chi-restraints excluded: chain ja residue 246 LEU Chi-restraints excluded: chain ka residue 19 THR Chi-restraints excluded: chain ka residue 36 VAL Chi-restraints excluded: chain ka residue 45 LEU Chi-restraints excluded: chain ka residue 74 MET Chi-restraints excluded: chain ka residue 92 THR Chi-restraints excluded: chain ka residue 98 LEU Chi-restraints excluded: chain ka residue 100 THR Chi-restraints excluded: chain ka residue 136 ASP Chi-restraints excluded: chain ka residue 156 GLU Chi-restraints excluded: chain ka residue 167 GLU Chi-restraints excluded: chain ka residue 180 SER Chi-restraints excluded: chain la residue 21 THR Chi-restraints excluded: chain la residue 23 VAL Chi-restraints excluded: chain la residue 32 ARG Chi-restraints excluded: chain la residue 49 MET Chi-restraints excluded: chain la residue 69 ILE Chi-restraints excluded: chain la residue 76 ARG Chi-restraints excluded: chain la residue 121 THR Chi-restraints excluded: chain la residue 123 LEU Chi-restraints excluded: chain ma residue 27 ARG Chi-restraints excluded: chain ma residue 30 ILE Chi-restraints excluded: chain ma residue 31 THR Chi-restraints excluded: chain ma residue 49 LYS Chi-restraints excluded: chain ma residue 52 LYS Chi-restraints excluded: chain ma residue 73 THR Chi-restraints excluded: chain ma residue 104 ASP Chi-restraints excluded: chain ma residue 109 ILE Chi-restraints excluded: chain ma residue 113 THR Chi-restraints excluded: chain ma residue 126 ASP Chi-restraints excluded: chain na residue 27 VAL Chi-restraints excluded: chain na residue 40 THR Chi-restraints excluded: chain na residue 47 LEU Chi-restraints excluded: chain na residue 54 VAL Chi-restraints excluded: chain na residue 56 ILE Chi-restraints excluded: chain na residue 57 THR Chi-restraints excluded: chain na residue 81 VAL Chi-restraints excluded: chain na residue 85 CYS Chi-restraints excluded: chain na residue 91 THR Chi-restraints excluded: chain na residue 107 THR Chi-restraints excluded: chain na residue 119 LEU Chi-restraints excluded: chain na residue 135 VAL Chi-restraints excluded: chain oa residue 32 SER Chi-restraints excluded: chain oa residue 43 ILE Chi-restraints excluded: chain oa residue 108 ARG Chi-restraints excluded: chain oa residue 112 GLU Chi-restraints excluded: chain oa residue 130 ARG Chi-restraints excluded: chain oa residue 136 THR Chi-restraints excluded: chain pa residue 33 VAL Chi-restraints excluded: chain pa residue 60 ILE Chi-restraints excluded: chain pa residue 87 ASP Chi-restraints excluded: chain pa residue 138 THR Chi-restraints excluded: chain qa residue 8 THR Chi-restraints excluded: chain qa residue 16 VAL Chi-restraints excluded: chain qa residue 24 MET Chi-restraints excluded: chain qa residue 25 THR Chi-restraints excluded: chain qa residue 40 ILE Chi-restraints excluded: chain qa residue 43 SER Chi-restraints excluded: chain qa residue 56 HIS Chi-restraints excluded: chain qa residue 66 VAL Chi-restraints excluded: chain qa residue 82 MET Chi-restraints excluded: chain qa residue 114 LEU Chi-restraints excluded: chain ra residue 57 GLU Chi-restraints excluded: chain sa residue 85 VAL Chi-restraints excluded: chain sa residue 88 HIS Chi-restraints excluded: chain ta residue 33 GLN Chi-restraints excluded: chain ta residue 45 GLN Chi-restraints excluded: chain ta residue 69 ARG Chi-restraints excluded: chain ta residue 97 SER Chi-restraints excluded: chain ua residue 27 LYS Chi-restraints excluded: chain ua residue 45 THR Chi-restraints excluded: chain ua residue 54 ASP Chi-restraints excluded: chain ua residue 67 VAL Chi-restraints excluded: chain va residue 8 ASP Chi-restraints excluded: chain va residue 17 GLU Chi-restraints excluded: chain va residue 23 THR Chi-restraints excluded: chain va residue 57 VAL Chi-restraints excluded: chain va residue 67 ARG Chi-restraints excluded: chain va residue 79 ASP Chi-restraints excluded: chain va residue 81 ARG Chi-restraints excluded: chain va residue 83 THR Chi-restraints excluded: chain va residue 88 TYR Chi-restraints excluded: chain va residue 89 ARG Chi-restraints excluded: chain va residue 116 ILE Chi-restraints excluded: chain wa residue 30 LEU Chi-restraints excluded: chain xa residue 37 VAL Chi-restraints excluded: chain xa residue 54 THR Chi-restraints excluded: chain xa residue 65 LEU Chi-restraints excluded: chain xa residue 77 GLU Chi-restraints excluded: chain ya residue 8 LEU Chi-restraints excluded: chain za residue 23 LEU Chi-restraints excluded: chain za residue 29 LEU Chi-restraints excluded: chain za residue 40 ARG Chi-restraints excluded: chain za residue 68 VAL Chi-restraints excluded: chain za residue 118 THR Chi-restraints excluded: chain za residue 141 SER Chi-restraints excluded: chain za residue 162 ASP Chi-restraints excluded: chain za residue 174 SER Chi-restraints excluded: chain za residue 177 CYS Chi-restraints excluded: chain za residue 197 HIS Chi-restraints excluded: chain za residue 208 TYR Chi-restraints excluded: chain za residue 209 ARG Chi-restraints excluded: chain bb residue 26 LYS Chi-restraints excluded: chain bb residue 28 GLN Chi-restraints excluded: chain bb residue 37 LEU Chi-restraints excluded: chain bb residue 40 SER Chi-restraints excluded: chain bb residue 47 LEU Chi-restraints excluded: chain bb residue 69 SER Chi-restraints excluded: chain bb residue 91 VAL Chi-restraints excluded: chain bb residue 98 THR Chi-restraints excluded: chain bb residue 108 ASP Chi-restraints excluded: chain bb residue 111 ARG Chi-restraints excluded: chain bb residue 122 GLU Chi-restraints excluded: chain bb residue 129 THR Chi-restraints excluded: chain bb residue 146 ARG Chi-restraints excluded: chain bb residue 148 ASN Chi-restraints excluded: chain bb residue 152 ARG Chi-restraints excluded: chain bb residue 159 SER Chi-restraints excluded: chain bb residue 175 GLN Chi-restraints excluded: chain bb residue 189 ILE Chi-restraints excluded: chain bb residue 201 THR Chi-restraints excluded: chain bb residue 227 LYS Chi-restraints excluded: chain cb residue 12 TYR Chi-restraints excluded: chain cb residue 36 ILE Chi-restraints excluded: chain cb residue 67 SER Chi-restraints excluded: chain cb residue 71 LEU Chi-restraints excluded: chain db residue 19 LYS Chi-restraints excluded: chain db residue 24 SER Chi-restraints excluded: chain db residue 41 VAL Chi-restraints excluded: chain db residue 45 VAL Chi-restraints excluded: chain db residue 76 SER Chi-restraints excluded: chain eb residue 46 ARG Chi-restraints excluded: chain eb residue 52 SER Chi-restraints excluded: chain eb residue 63 THR Chi-restraints excluded: chain eb residue 102 THR Chi-restraints excluded: chain eb residue 113 THR Chi-restraints excluded: chain eb residue 143 VAL Chi-restraints excluded: chain eb residue 152 VAL Chi-restraints excluded: chain eb residue 158 ILE Chi-restraints excluded: chain eb residue 163 THR Chi-restraints excluded: chain fb residue 133 THR Chi-restraints excluded: chain fb residue 149 VAL Chi-restraints excluded: chain fb residue 186 SER Chi-restraints excluded: chain fb residue 211 ARG Chi-restraints excluded: chain fb residue 213 SER Chi-restraints excluded: chain fb residue 226 ASP Chi-restraints excluded: chain fb residue 229 MET Chi-restraints excluded: chain fb residue 238 ASP Chi-restraints excluded: chain gb residue 52 ILE Chi-restraints excluded: chain gb residue 67 VAL Chi-restraints excluded: chain gb residue 68 LEU Chi-restraints excluded: chain gb residue 79 ARG Chi-restraints excluded: chain gb residue 91 VAL Chi-restraints excluded: chain gb residue 113 LEU Chi-restraints excluded: chain gb residue 205 LYS Chi-restraints excluded: chain hb residue 37 LEU Chi-restraints excluded: chain hb residue 84 LEU Chi-restraints excluded: chain hb residue 102 VAL Chi-restraints excluded: chain hb residue 118 THR Chi-restraints excluded: chain hb residue 130 VAL Chi-restraints excluded: chain hb residue 137 VAL Chi-restraints excluded: chain hb residue 144 ARG Chi-restraints excluded: chain hb residue 155 LEU Chi-restraints excluded: chain hb residue 182 VAL Chi-restraints excluded: chain ib residue 75 THR Chi-restraints excluded: chain ib residue 87 VAL Chi-restraints excluded: chain ib residue 89 ARG Chi-restraints excluded: chain ib residue 122 ASP Chi-restraints excluded: chain IB residue 11 ARG Chi-restraints excluded: chain IB residue 20 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 541 optimal weight: 7.9990 chunk 411 optimal weight: 5.9990 chunk 284 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 261 optimal weight: 6.9990 chunk 367 optimal weight: 4.9990 chunk 549 optimal weight: 9.9990 chunk 581 optimal weight: 4.9990 chunk 287 optimal weight: 10.0000 chunk 520 optimal weight: 0.8980 chunk 156 optimal weight: 10.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** ba 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ca 174 HIS ca 216 GLN da 7 ASN ** da 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ga 91 ASN ha 18 ASN ** ha 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ja 67 GLN ** ma 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ma 39 ASN ** na 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** oa 120 HIS ra 81 GLN ** ra 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** sa 113 GLN sa 137 HIS va 48 ASN va 65 GLN xa 67 GLN za 20 GLN za 76 GLN ** za 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** za 101 ASN za 173 ASN db 94 ASN eb 9 ASN eb 68 ASN ** eb 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** eb 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** eb 178 ASN ** gb 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** gb 7 ASN ** hb 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 78029 Z= 0.335 Angle : 0.756 14.251 113871 Z= 0.399 Chirality : 0.044 0.360 14101 Planarity : 0.007 0.127 7899 Dihedral : 23.752 179.509 32389 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.05 % Favored : 92.83 % Rotamer: Outliers : 10.46 % Allowed : 29.12 % Favored : 60.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.12), residues: 4325 helix: -0.24 (0.14), residues: 1334 sheet: -0.81 (0.17), residues: 861 loop : -1.54 (0.13), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRPva 98 HIS 0.008 0.002 HISoa 120 PHE 0.029 0.002 PHEoa 28 TYR 0.026 0.002 TYRpa 18 ARG 0.010 0.001 ARGua 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8650 Ramachandran restraints generated. 4325 Oldfield, 0 Emsley, 4325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8650 Ramachandran restraints generated. 4325 Oldfield, 0 Emsley, 4325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1205 residues out of total 3778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 395 poor density : 810 time to evaluate : 4.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: ba 51 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7379 (mptp) REVERT: ca 159 GLN cc_start: 0.6313 (mp10) cc_final: 0.5575 (pt0) REVERT: ca 164 LYS cc_start: 0.7501 (tptm) cc_final: 0.7281 (mppt) REVERT: ca 169 ARG cc_start: 0.5330 (OUTLIER) cc_final: 0.3718 (mtp-110) REVERT: da 10 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: da 49 PHE cc_start: 0.8413 (m-10) cc_final: 0.8190 (m-10) REVERT: da 53 GLU cc_start: 0.7373 (pm20) cc_final: 0.6803 (tm-30) REVERT: da 57 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6402 (tp30) REVERT: da 71 ASP cc_start: 0.7474 (t70) cc_final: 0.7098 (t0) REVERT: ga 53 LYS cc_start: 0.8356 (mtmt) cc_final: 0.8108 (mtmm) REVERT: ga 70 ARG cc_start: 0.7183 (ttp80) cc_final: 0.6923 (ttp80) REVERT: ga 104 PHE cc_start: 0.9191 (OUTLIER) cc_final: 0.8981 (t80) REVERT: ga 118 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.7786 (ptm160) REVERT: ha 102 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8212 (mt) REVERT: ha 103 SER cc_start: 0.8235 (OUTLIER) cc_final: 0.8024 (t) REVERT: ha 160 GLU cc_start: 0.5703 (OUTLIER) cc_final: 0.4700 (pm20) REVERT: ha 274 TRP cc_start: 0.6600 (OUTLIER) cc_final: 0.5015 (m-90) REVERT: ha 322 ILE cc_start: 0.7341 (pp) cc_final: 0.6922 (mt) REVERT: ia 32 ASP cc_start: 0.6203 (m-30) cc_final: 0.5573 (m-30) REVERT: ia 68 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7728 (mt-10) REVERT: ia 89 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.5789 (mp0) REVERT: ia 101 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7438 (mp10) REVERT: ja 40 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7389 (pp20) REVERT: ja 66 MET cc_start: 0.8521 (mmm) cc_final: 0.8221 (mmm) REVERT: ja 205 PHE cc_start: 0.7821 (p90) cc_final: 0.7409 (p90) REVERT: ja 240 LYS cc_start: 0.5933 (OUTLIER) cc_final: 0.5639 (mttt) REVERT: ka 51 ARG cc_start: 0.7689 (ttm110) cc_final: 0.7469 (mtp180) REVERT: ka 98 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7643 (tm) REVERT: ka 132 ARG cc_start: 0.5806 (OUTLIER) cc_final: 0.4813 (ptp90) REVERT: ka 156 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7317 (mt-10) REVERT: la 12 THR cc_start: 0.8190 (t) cc_final: 0.7806 (m) REVERT: la 58 ILE cc_start: 0.9120 (mt) cc_final: 0.8913 (mp) REVERT: la 76 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.7071 (ttt90) REVERT: la 138 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8147 (ptp90) REVERT: ma 27 ARG cc_start: 0.6159 (OUTLIER) cc_final: 0.5871 (mmt90) REVERT: na 47 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8417 (mm) REVERT: na 56 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8536 (mm) REVERT: oa 108 ARG cc_start: 0.6555 (OUTLIER) cc_final: 0.6111 (tmt170) REVERT: pa 45 GLN cc_start: 0.7558 (mm-40) cc_final: 0.7294 (mm-40) REVERT: pa 53 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7558 (tp) REVERT: pa 60 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8347 (mm) REVERT: qa 24 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7590 (mpt) REVERT: qa 56 HIS cc_start: 0.7438 (OUTLIER) cc_final: 0.6728 (p-80) REVERT: qa 97 ARG cc_start: 0.7175 (ptt180) cc_final: 0.6864 (mtm180) REVERT: qa 100 LYS cc_start: 0.7282 (OUTLIER) cc_final: 0.6994 (ttpm) REVERT: ta 35 GLU cc_start: 0.1848 (OUTLIER) cc_final: 0.1471 (mt-10) REVERT: ta 69 ARG cc_start: 0.3580 (OUTLIER) cc_final: 0.2025 (mtt180) REVERT: ua 27 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.8019 (mttp) REVERT: ua 68 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7797 (ptt180) REVERT: ua 69 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7116 (mt-10) REVERT: ua 80 ARG cc_start: 0.7217 (mtp-110) cc_final: 0.6753 (ptm160) REVERT: ua 81 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.6017 (pp20) REVERT: va 88 TYR cc_start: 0.7856 (OUTLIER) cc_final: 0.6913 (m-80) REVERT: xa 37 VAL cc_start: 0.7872 (OUTLIER) cc_final: 0.7604 (t) REVERT: za 15 LYS cc_start: 0.8496 (tptm) cc_final: 0.7914 (ttpp) REVERT: za 16 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7993 (mt-10) REVERT: za 39 GLU cc_start: 0.7285 (tp30) cc_final: 0.7023 (mm-30) REVERT: za 174 SER cc_start: 0.8020 (OUTLIER) cc_final: 0.7512 (t) REVERT: za 197 HIS cc_start: 0.5200 (OUTLIER) cc_final: 0.3365 (p90) REVERT: za 208 TYR cc_start: 0.8160 (OUTLIER) cc_final: 0.7116 (p90) REVERT: za 209 ARG cc_start: 0.6970 (OUTLIER) cc_final: 0.6583 (mmm-85) REVERT: bb 24 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.7303 (t80) REVERT: bb 26 LYS cc_start: 0.7188 (OUTLIER) cc_final: 0.6982 (mtmt) REVERT: bb 28 GLN cc_start: 0.7423 (OUTLIER) cc_final: 0.7167 (mm110) REVERT: bb 31 ASP cc_start: 0.7889 (t0) cc_final: 0.7629 (t0) REVERT: bb 50 ARG cc_start: 0.6297 (mtt180) cc_final: 0.5897 (mtt90) REVERT: bb 111 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7827 (mmp80) REVERT: bb 152 ARG cc_start: 0.7109 (OUTLIER) cc_final: 0.6830 (tmt-80) REVERT: bb 159 SER cc_start: 0.7794 (OUTLIER) cc_final: 0.7542 (p) REVERT: bb 189 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7962 (mt) REVERT: bb 208 GLN cc_start: 0.8167 (pp30) cc_final: 0.7903 (pt0) REVERT: bb 227 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7876 (mmtp) REVERT: cb 63 ASP cc_start: 0.6320 (t70) cc_final: 0.5915 (t0) REVERT: cb 71 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8581 (mp) REVERT: db 45 VAL cc_start: 0.7792 (OUTLIER) cc_final: 0.7497 (t) REVERT: eb 46 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.7666 (ptp-170) REVERT: eb 70 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7982 (ttm170) REVERT: fb 89 GLU cc_start: 0.8387 (tp30) cc_final: 0.8125 (tp30) REVERT: fb 211 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7765 (ttt180) REVERT: gb 56 CYS cc_start: 0.7151 (p) cc_final: 0.6876 (p) REVERT: gb 91 VAL cc_start: 0.8401 (OUTLIER) cc_final: 0.8110 (t) REVERT: hb 37 LEU cc_start: 0.4498 (OUTLIER) cc_final: 0.4152 (pt) REVERT: hb 91 LYS cc_start: 0.2869 (OUTLIER) cc_final: 0.2492 (mttp) REVERT: hb 112 GLN cc_start: 0.2142 (OUTLIER) cc_final: 0.1902 (tt0) REVERT: hb 144 ARG cc_start: 0.6895 (OUTLIER) cc_final: 0.6594 (mtt-85) REVERT: hb 176 ARG cc_start: 0.5918 (ttm-80) cc_final: 0.5648 (ttm-80) REVERT: ib 34 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7479 (ttm170) REVERT: ib 37 LYS cc_start: 0.8308 (ptmt) cc_final: 0.7923 (pttt) REVERT: ib 89 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.7349 (mmm-85) REVERT: ib 96 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8166 (tmmm) REVERT: IB 9 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.7629 (ttm170) REVERT: IB 20 MET cc_start: 0.4850 (OUTLIER) cc_final: 0.4572 (mpt) outliers start: 395 outliers final: 194 residues processed: 1068 average time/residue: 1.5229 time to fit residues: 2152.1776 Evaluate side-chains 1019 residues out of total 3778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 763 time to evaluate : 4.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain ba residue 19 THR Chi-restraints excluded: chain ba residue 32 VAL Chi-restraints excluded: chain ba residue 51 LYS Chi-restraints excluded: chain ba residue 68 THR Chi-restraints excluded: chain ba residue 110 ARG Chi-restraints excluded: chain ca residue 3 ILE Chi-restraints excluded: chain ca residue 43 THR Chi-restraints excluded: chain ca residue 44 VAL Chi-restraints excluded: chain ca residue 73 VAL Chi-restraints excluded: chain ca residue 83 VAL Chi-restraints excluded: chain ca residue 89 ASN Chi-restraints excluded: chain ca residue 94 THR Chi-restraints excluded: chain ca residue 162 LEU Chi-restraints excluded: chain ca residue 169 ARG Chi-restraints excluded: chain da residue 10 GLU Chi-restraints excluded: chain da residue 12 CYS Chi-restraints excluded: chain da residue 57 GLU Chi-restraints excluded: chain ga residue 35 GLU Chi-restraints excluded: chain ga residue 72 GLN Chi-restraints excluded: chain ga residue 90 LEU Chi-restraints excluded: chain ga residue 104 PHE Chi-restraints excluded: chain ga residue 118 ARG Chi-restraints excluded: chain ga residue 128 SER Chi-restraints excluded: chain ha residue 20 VAL Chi-restraints excluded: chain ha residue 28 ILE Chi-restraints excluded: chain ha residue 70 THR Chi-restraints excluded: chain ha residue 102 LEU Chi-restraints excluded: chain ha residue 103 SER Chi-restraints excluded: chain ha residue 120 SER Chi-restraints excluded: chain ha residue 126 ASP Chi-restraints excluded: chain ha residue 132 SER Chi-restraints excluded: chain ha residue 155 ASP Chi-restraints excluded: chain ha residue 160 GLU Chi-restraints excluded: chain ha residue 180 ILE Chi-restraints excluded: chain ha residue 189 VAL Chi-restraints excluded: chain ha residue 231 THR Chi-restraints excluded: chain ha residue 253 SER Chi-restraints excluded: chain ha residue 270 SER Chi-restraints excluded: chain ha residue 274 TRP Chi-restraints excluded: chain ha residue 282 VAL Chi-restraints excluded: chain ha residue 298 TYR Chi-restraints excluded: chain ha residue 300 THR Chi-restraints excluded: chain ha residue 302 LEU Chi-restraints excluded: chain ha residue 303 SER Chi-restraints excluded: chain ha residue 305 SER Chi-restraints excluded: chain ia residue 37 VAL Chi-restraints excluded: chain ia residue 42 THR Chi-restraints excluded: chain ia residue 58 VAL Chi-restraints excluded: chain ia residue 66 ILE Chi-restraints excluded: chain ia residue 84 VAL Chi-restraints excluded: chain ia residue 89 GLU Chi-restraints excluded: chain ia residue 91 VAL Chi-restraints excluded: chain ia residue 101 GLN Chi-restraints excluded: chain ia residue 179 GLN Chi-restraints excluded: chain ia residue 202 THR Chi-restraints excluded: chain ia residue 207 LEU Chi-restraints excluded: chain ja residue 33 SER Chi-restraints excluded: chain ja residue 40 GLU Chi-restraints excluded: chain ja residue 71 MET Chi-restraints excluded: chain ja residue 163 ASP Chi-restraints excluded: chain ja residue 192 VAL Chi-restraints excluded: chain ja residue 207 THR Chi-restraints excluded: chain ja residue 237 SER Chi-restraints excluded: chain ja residue 240 LYS Chi-restraints excluded: chain ja residue 246 LEU Chi-restraints excluded: chain ka residue 19 THR Chi-restraints excluded: chain ka residue 36 VAL Chi-restraints excluded: chain ka residue 45 LEU Chi-restraints excluded: chain ka residue 74 MET Chi-restraints excluded: chain ka residue 92 THR Chi-restraints excluded: chain ka residue 98 LEU Chi-restraints excluded: chain ka residue 132 ARG Chi-restraints excluded: chain ka residue 136 ASP Chi-restraints excluded: chain ka residue 156 GLU Chi-restraints excluded: chain ka residue 180 SER Chi-restraints excluded: chain la residue 21 THR Chi-restraints excluded: chain la residue 23 VAL Chi-restraints excluded: chain la residue 32 ARG Chi-restraints excluded: chain la residue 49 MET Chi-restraints excluded: chain la residue 69 ILE Chi-restraints excluded: chain la residue 76 ARG Chi-restraints excluded: chain la residue 121 THR Chi-restraints excluded: chain la residue 123 LEU Chi-restraints excluded: chain la residue 138 ARG Chi-restraints excluded: chain ma residue 27 ARG Chi-restraints excluded: chain ma residue 30 ILE Chi-restraints excluded: chain ma residue 31 THR Chi-restraints excluded: chain ma residue 49 LYS Chi-restraints excluded: chain ma residue 52 LYS Chi-restraints excluded: chain ma residue 73 THR Chi-restraints excluded: chain ma residue 104 ASP Chi-restraints excluded: chain ma residue 109 ILE Chi-restraints excluded: chain ma residue 113 THR Chi-restraints excluded: chain na residue 27 VAL Chi-restraints excluded: chain na residue 40 THR Chi-restraints excluded: chain na residue 47 LEU Chi-restraints excluded: chain na residue 54 VAL Chi-restraints excluded: chain na residue 56 ILE Chi-restraints excluded: chain na residue 57 THR Chi-restraints excluded: chain na residue 81 VAL Chi-restraints excluded: chain na residue 85 CYS Chi-restraints excluded: chain na residue 88 LEU Chi-restraints excluded: chain na residue 91 THR Chi-restraints excluded: chain na residue 107 THR Chi-restraints excluded: chain na residue 119 LEU Chi-restraints excluded: chain na residue 135 VAL Chi-restraints excluded: chain oa residue 32 SER Chi-restraints excluded: chain oa residue 104 ASP Chi-restraints excluded: chain oa residue 105 MET Chi-restraints excluded: chain oa residue 108 ARG Chi-restraints excluded: chain oa residue 114 LEU Chi-restraints excluded: chain oa residue 130 ARG Chi-restraints excluded: chain oa residue 136 THR Chi-restraints excluded: chain oa residue 139 THR Chi-restraints excluded: chain pa residue 33 VAL Chi-restraints excluded: chain pa residue 53 LEU Chi-restraints excluded: chain pa residue 60 ILE Chi-restraints excluded: chain pa residue 87 ASP Chi-restraints excluded: chain pa residue 102 LEU Chi-restraints excluded: chain pa residue 138 THR Chi-restraints excluded: chain qa residue 8 THR Chi-restraints excluded: chain qa residue 16 VAL Chi-restraints excluded: chain qa residue 24 MET Chi-restraints excluded: chain qa residue 25 THR Chi-restraints excluded: chain qa residue 40 ILE Chi-restraints excluded: chain qa residue 43 SER Chi-restraints excluded: chain qa residue 56 HIS Chi-restraints excluded: chain qa residue 66 VAL Chi-restraints excluded: chain qa residue 82 MET Chi-restraints excluded: chain qa residue 100 LYS Chi-restraints excluded: chain qa residue 114 LEU Chi-restraints excluded: chain ra residue 32 SER Chi-restraints excluded: chain ra residue 57 GLU Chi-restraints excluded: chain ra residue 128 VAL Chi-restraints excluded: chain sa residue 43 VAL Chi-restraints excluded: chain sa residue 85 VAL Chi-restraints excluded: chain sa residue 88 HIS Chi-restraints excluded: chain sa residue 127 GLU Chi-restraints excluded: chain ta residue 33 GLN Chi-restraints excluded: chain ta residue 35 GLU Chi-restraints excluded: chain ta residue 45 GLN Chi-restraints excluded: chain ta residue 69 ARG Chi-restraints excluded: chain ta residue 97 SER Chi-restraints excluded: chain ua residue 27 LYS Chi-restraints excluded: chain ua residue 45 THR Chi-restraints excluded: chain ua residue 54 ASP Chi-restraints excluded: chain ua residue 67 VAL Chi-restraints excluded: chain ua residue 68 ARG Chi-restraints excluded: chain ua residue 81 GLU Chi-restraints excluded: chain va residue 3 ARG Chi-restraints excluded: chain va residue 8 ASP Chi-restraints excluded: chain va residue 17 GLU Chi-restraints excluded: chain va residue 23 THR Chi-restraints excluded: chain va residue 57 VAL Chi-restraints excluded: chain va residue 81 ARG Chi-restraints excluded: chain va residue 83 THR Chi-restraints excluded: chain va residue 88 TYR Chi-restraints excluded: chain va residue 116 ILE Chi-restraints excluded: chain wa residue 20 VAL Chi-restraints excluded: chain wa residue 30 LEU Chi-restraints excluded: chain xa residue 37 VAL Chi-restraints excluded: chain xa residue 54 THR Chi-restraints excluded: chain xa residue 56 VAL Chi-restraints excluded: chain xa residue 77 GLU Chi-restraints excluded: chain xa residue 80 SER Chi-restraints excluded: chain ya residue 8 LEU Chi-restraints excluded: chain ya residue 45 VAL Chi-restraints excluded: chain za residue 23 LEU Chi-restraints excluded: chain za residue 29 LEU Chi-restraints excluded: chain za residue 40 ARG Chi-restraints excluded: chain za residue 68 VAL Chi-restraints excluded: chain za residue 118 THR Chi-restraints excluded: chain za residue 141 SER Chi-restraints excluded: chain za residue 162 ASP Chi-restraints excluded: chain za residue 174 SER Chi-restraints excluded: chain za residue 197 HIS Chi-restraints excluded: chain za residue 208 TYR Chi-restraints excluded: chain za residue 209 ARG Chi-restraints excluded: chain bb residue 24 PHE Chi-restraints excluded: chain bb residue 26 LYS Chi-restraints excluded: chain bb residue 28 GLN Chi-restraints excluded: chain bb residue 37 LEU Chi-restraints excluded: chain bb residue 47 LEU Chi-restraints excluded: chain bb residue 69 SER Chi-restraints excluded: chain bb residue 91 VAL Chi-restraints excluded: chain bb residue 98 THR Chi-restraints excluded: chain bb residue 108 ASP Chi-restraints excluded: chain bb residue 111 ARG Chi-restraints excluded: chain bb residue 120 LEU Chi-restraints excluded: chain bb residue 122 GLU Chi-restraints excluded: chain bb residue 129 THR Chi-restraints excluded: chain bb residue 148 ASN Chi-restraints excluded: chain bb residue 152 ARG Chi-restraints excluded: chain bb residue 159 SER Chi-restraints excluded: chain bb residue 189 ILE Chi-restraints excluded: chain bb residue 201 THR Chi-restraints excluded: chain bb residue 205 PHE Chi-restraints excluded: chain bb residue 227 LYS Chi-restraints excluded: chain cb residue 12 TYR Chi-restraints excluded: chain cb residue 36 ILE Chi-restraints excluded: chain cb residue 67 SER Chi-restraints excluded: chain cb residue 71 LEU Chi-restraints excluded: chain db residue 19 LYS Chi-restraints excluded: chain db residue 24 SER Chi-restraints excluded: chain db residue 41 VAL Chi-restraints excluded: chain db residue 45 VAL Chi-restraints excluded: chain db residue 60 ASP Chi-restraints excluded: chain db residue 76 SER Chi-restraints excluded: chain db residue 93 ARG Chi-restraints excluded: chain eb residue 23 LYS Chi-restraints excluded: chain eb residue 46 ARG Chi-restraints excluded: chain eb residue 63 THR Chi-restraints excluded: chain eb residue 70 ARG Chi-restraints excluded: chain eb residue 102 THR Chi-restraints excluded: chain eb residue 113 THR Chi-restraints excluded: chain eb residue 143 VAL Chi-restraints excluded: chain eb residue 152 VAL Chi-restraints excluded: chain eb residue 158 ILE Chi-restraints excluded: chain eb residue 163 THR Chi-restraints excluded: chain fb residue 133 THR Chi-restraints excluded: chain fb residue 149 VAL Chi-restraints excluded: chain fb residue 186 SER Chi-restraints excluded: chain fb residue 204 ASP Chi-restraints excluded: chain fb residue 211 ARG Chi-restraints excluded: chain fb residue 213 SER Chi-restraints excluded: chain fb residue 229 MET Chi-restraints excluded: chain fb residue 238 ASP Chi-restraints excluded: chain gb residue 52 ILE Chi-restraints excluded: chain gb residue 67 VAL Chi-restraints excluded: chain gb residue 68 LEU Chi-restraints excluded: chain gb residue 82 SER Chi-restraints excluded: chain gb residue 91 VAL Chi-restraints excluded: chain gb residue 113 LEU Chi-restraints excluded: chain gb residue 205 LYS Chi-restraints excluded: chain hb residue 37 LEU Chi-restraints excluded: chain hb residue 80 LEU Chi-restraints excluded: chain hb residue 84 LEU Chi-restraints excluded: chain hb residue 91 LYS Chi-restraints excluded: chain hb residue 102 VAL Chi-restraints excluded: chain hb residue 112 GLN Chi-restraints excluded: chain hb residue 118 THR Chi-restraints excluded: chain hb residue 130 VAL Chi-restraints excluded: chain hb residue 137 VAL Chi-restraints excluded: chain hb residue 144 ARG Chi-restraints excluded: chain hb residue 155 LEU Chi-restraints excluded: chain hb residue 182 VAL Chi-restraints excluded: chain ib residue 19 THR Chi-restraints excluded: chain ib residue 21 LYS Chi-restraints excluded: chain ib residue 34 ARG Chi-restraints excluded: chain ib residue 75 THR Chi-restraints excluded: chain ib residue 87 VAL Chi-restraints excluded: chain ib residue 89 ARG Chi-restraints excluded: chain ib residue 96 LYS Chi-restraints excluded: chain ib residue 122 ASP Chi-restraints excluded: chain IB residue 9 ARG Chi-restraints excluded: chain IB residue 20 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 484 optimal weight: 1.9990 chunk 330 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 433 optimal weight: 9.9990 chunk 240 optimal weight: 10.0000 chunk 496 optimal weight: 1.9990 chunk 402 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 297 optimal weight: 0.7980 chunk 522 optimal weight: 8.9990 chunk 146 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** ba 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** ca 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ca 216 GLN ga 91 ASN ha 18 ASN ha 283 GLN ja 67 GLN ja 188 ASN ma 26 HIS ma 39 ASN oa 19 ASN oa 120 HIS ra 81 GLN ** ra 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** sa 113 GLN ** ta 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** va 48 ASN va 65 GLN xa 67 GLN za 20 GLN ** za 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** za 101 ASN za 173 ASN bb 232 HIS db 94 ASN eb 68 ASN ** eb 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** eb 178 ASN gb 190 GLN ** hb 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ib 4 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 78029 Z= 0.255 Angle : 0.699 13.764 113871 Z= 0.372 Chirality : 0.041 0.331 14101 Planarity : 0.006 0.125 7899 Dihedral : 23.665 179.774 32388 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.50 % Favored : 93.41 % Rotamer: Outliers : 9.26 % Allowed : 30.73 % Favored : 60.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.12), residues: 4325 helix: -0.06 (0.14), residues: 1344 sheet: -0.74 (0.17), residues: 863 loop : -1.42 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRPva 98 HIS 0.006 0.001 HISoa 120 PHE 0.028 0.002 PHEoa 28 TYR 0.039 0.002 TYRpa 18 ARG 0.010 0.001 ARGya 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8650 Ramachandran restraints generated. 4325 Oldfield, 0 Emsley, 4325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8650 Ramachandran restraints generated. 4325 Oldfield, 0 Emsley, 4325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1154 residues out of total 3778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 350 poor density : 804 time to evaluate : 4.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: ca 18 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7671 (tt0) REVERT: ca 159 GLN cc_start: 0.6226 (mp10) cc_final: 0.5564 (pt0) REVERT: ca 164 LYS cc_start: 0.7483 (tptm) cc_final: 0.7275 (mppt) REVERT: ca 169 ARG cc_start: 0.5422 (OUTLIER) cc_final: 0.3779 (mtp-110) REVERT: da 10 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: da 49 PHE cc_start: 0.8448 (m-10) cc_final: 0.8233 (m-10) REVERT: da 53 GLU cc_start: 0.7316 (pm20) cc_final: 0.6839 (tm-30) REVERT: da 57 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6597 (tp30) REVERT: da 71 ASP cc_start: 0.7452 (t70) cc_final: 0.7105 (t0) REVERT: da 78 ASN cc_start: 0.7328 (p0) cc_final: 0.6538 (t0) REVERT: ga 53 LYS cc_start: 0.8332 (mtmt) cc_final: 0.8076 (mtmm) REVERT: ga 70 ARG cc_start: 0.7174 (ttp80) cc_final: 0.6906 (ttp80) REVERT: ga 118 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.7781 (ptm160) REVERT: ha 102 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8178 (mt) REVERT: ha 103 SER cc_start: 0.8257 (OUTLIER) cc_final: 0.8052 (t) REVERT: ha 322 ILE cc_start: 0.7274 (pp) cc_final: 0.6861 (mt) REVERT: ia 68 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7564 (mt-10) REVERT: ia 80 LEU cc_start: 0.7504 (mp) cc_final: 0.7256 (pt) REVERT: ia 89 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.5832 (mp0) REVERT: ia 101 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7442 (mp10) REVERT: ia 210 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7690 (mt) REVERT: ja 40 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7240 (pp20) REVERT: ja 205 PHE cc_start: 0.7808 (p90) cc_final: 0.7417 (p90) REVERT: ja 240 LYS cc_start: 0.5905 (OUTLIER) cc_final: 0.5619 (mttt) REVERT: ka 98 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7581 (tm) REVERT: ka 131 ARG cc_start: 0.2175 (OUTLIER) cc_final: -0.0164 (ptp90) REVERT: ka 132 ARG cc_start: 0.5738 (OUTLIER) cc_final: 0.4870 (ptp90) REVERT: ka 156 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7327 (mt-10) REVERT: la 12 THR cc_start: 0.8283 (t) cc_final: 0.7889 (m) REVERT: la 138 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.8156 (ptp90) REVERT: ma 27 ARG cc_start: 0.6155 (OUTLIER) cc_final: 0.5876 (mmt90) REVERT: na 47 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8393 (mm) REVERT: na 56 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8488 (mm) REVERT: oa 17 ASN cc_start: 0.6435 (m-40) cc_final: 0.6197 (m-40) REVERT: oa 108 ARG cc_start: 0.6543 (OUTLIER) cc_final: 0.6102 (tmt170) REVERT: oa 113 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7278 (ttm110) REVERT: qa 24 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7634 (mpt) REVERT: qa 56 HIS cc_start: 0.7401 (OUTLIER) cc_final: 0.6862 (p-80) REVERT: qa 97 ARG cc_start: 0.7166 (ptt180) cc_final: 0.6811 (mtm110) REVERT: sa 45 MET cc_start: 0.7038 (mmp) cc_final: 0.6749 (mpp) REVERT: ta 69 ARG cc_start: 0.3641 (OUTLIER) cc_final: 0.1955 (mtp180) REVERT: ua 27 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7864 (mmtp) REVERT: ua 68 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7728 (ptt180) REVERT: ua 69 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7121 (mt-10) REVERT: ua 80 ARG cc_start: 0.7229 (mtp-110) cc_final: 0.6778 (ptm160) REVERT: ua 81 GLU cc_start: 0.6530 (OUTLIER) cc_final: 0.5969 (pp20) REVERT: va 86 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7704 (tm-30) REVERT: va 88 TYR cc_start: 0.7727 (OUTLIER) cc_final: 0.6859 (m-80) REVERT: xa 45 ILE cc_start: 0.6841 (OUTLIER) cc_final: 0.6517 (tt) REVERT: za 15 LYS cc_start: 0.8454 (tptm) cc_final: 0.7919 (ttpp) REVERT: za 16 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7934 (mt-10) REVERT: za 39 GLU cc_start: 0.7301 (tp30) cc_final: 0.7090 (mm-30) REVERT: za 174 SER cc_start: 0.7975 (OUTLIER) cc_final: 0.7489 (t) REVERT: za 197 HIS cc_start: 0.5124 (OUTLIER) cc_final: 0.3288 (p90) REVERT: za 208 TYR cc_start: 0.8150 (OUTLIER) cc_final: 0.7145 (p90) REVERT: za 209 ARG cc_start: 0.6965 (OUTLIER) cc_final: 0.6584 (mmm-85) REVERT: bb 26 LYS cc_start: 0.7188 (OUTLIER) cc_final: 0.6956 (mtmt) REVERT: bb 28 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.7182 (mm110) REVERT: bb 31 ASP cc_start: 0.7873 (t0) cc_final: 0.7610 (t0) REVERT: bb 50 ARG cc_start: 0.6302 (mtt180) cc_final: 0.5827 (mtt90) REVERT: bb 111 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7778 (mmp80) REVERT: bb 170 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6385 (tp30) REVERT: bb 189 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7943 (mt) REVERT: cb 63 ASP cc_start: 0.6315 (t70) cc_final: 0.5897 (t0) REVERT: cb 71 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8574 (mp) REVERT: db 19 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8112 (mtpm) REVERT: db 45 VAL cc_start: 0.7754 (OUTLIER) cc_final: 0.7489 (t) REVERT: eb 46 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7532 (ptp-170) REVERT: eb 70 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7566 (ttm170) REVERT: gb 46 GLU cc_start: 0.3321 (OUTLIER) cc_final: 0.2498 (mm-30) REVERT: gb 56 CYS cc_start: 0.7065 (p) cc_final: 0.6798 (p) REVERT: hb 37 LEU cc_start: 0.4497 (OUTLIER) cc_final: 0.3740 (pt) REVERT: hb 176 ARG cc_start: 0.6035 (ttm-80) cc_final: 0.5780 (ttm-80) REVERT: ib 37 LYS cc_start: 0.8278 (ptmt) cc_final: 0.7916 (pttt) REVERT: ib 96 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8112 (tmmm) REVERT: IB 9 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.7658 (ttm170) REVERT: IB 20 MET cc_start: 0.4768 (OUTLIER) cc_final: 0.4521 (mpt) outliers start: 350 outliers final: 175 residues processed: 1031 average time/residue: 1.4852 time to fit residues: 2034.1541 Evaluate side-chains 990 residues out of total 3778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 765 time to evaluate : 4.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain ba residue 19 THR Chi-restraints excluded: chain ba residue 32 VAL Chi-restraints excluded: chain ba residue 68 THR Chi-restraints excluded: chain ca residue 3 ILE Chi-restraints excluded: chain ca residue 18 GLN Chi-restraints excluded: chain ca residue 43 THR Chi-restraints excluded: chain ca residue 44 VAL Chi-restraints excluded: chain ca residue 73 VAL Chi-restraints excluded: chain ca residue 83 VAL Chi-restraints excluded: chain ca residue 89 ASN Chi-restraints excluded: chain ca residue 94 THR Chi-restraints excluded: chain ca residue 169 ARG Chi-restraints excluded: chain da residue 10 GLU Chi-restraints excluded: chain da residue 57 GLU Chi-restraints excluded: chain ga residue 35 GLU Chi-restraints excluded: chain ga residue 72 GLN Chi-restraints excluded: chain ga residue 90 LEU Chi-restraints excluded: chain ga residue 118 ARG Chi-restraints excluded: chain ga residue 128 SER Chi-restraints excluded: chain ha residue 9 VAL Chi-restraints excluded: chain ha residue 20 VAL Chi-restraints excluded: chain ha residue 28 ILE Chi-restraints excluded: chain ha residue 50 ASN Chi-restraints excluded: chain ha residue 102 LEU Chi-restraints excluded: chain ha residue 103 SER Chi-restraints excluded: chain ha residue 120 SER Chi-restraints excluded: chain ha residue 126 ASP Chi-restraints excluded: chain ha residue 132 SER Chi-restraints excluded: chain ha residue 141 LEU Chi-restraints excluded: chain ha residue 155 ASP Chi-restraints excluded: chain ha residue 189 VAL Chi-restraints excluded: chain ha residue 231 THR Chi-restraints excluded: chain ha residue 246 ASP Chi-restraints excluded: chain ha residue 253 SER Chi-restraints excluded: chain ha residue 300 THR Chi-restraints excluded: chain ha residue 302 LEU Chi-restraints excluded: chain ha residue 303 SER Chi-restraints excluded: chain ha residue 305 SER Chi-restraints excluded: chain ia residue 5 ILE Chi-restraints excluded: chain ia residue 42 THR Chi-restraints excluded: chain ia residue 58 VAL Chi-restraints excluded: chain ia residue 84 VAL Chi-restraints excluded: chain ia residue 89 GLU Chi-restraints excluded: chain ia residue 91 VAL Chi-restraints excluded: chain ia residue 101 GLN Chi-restraints excluded: chain ia residue 179 GLN Chi-restraints excluded: chain ia residue 182 LEU Chi-restraints excluded: chain ia residue 202 THR Chi-restraints excluded: chain ia residue 207 LEU Chi-restraints excluded: chain ia residue 210 ILE Chi-restraints excluded: chain ja residue 33 SER Chi-restraints excluded: chain ja residue 40 GLU Chi-restraints excluded: chain ja residue 57 THR Chi-restraints excluded: chain ja residue 71 MET Chi-restraints excluded: chain ja residue 163 ASP Chi-restraints excluded: chain ja residue 189 THR Chi-restraints excluded: chain ja residue 192 VAL Chi-restraints excluded: chain ja residue 207 THR Chi-restraints excluded: chain ja residue 237 SER Chi-restraints excluded: chain ja residue 240 LYS Chi-restraints excluded: chain ja residue 246 LEU Chi-restraints excluded: chain ka residue 19 THR Chi-restraints excluded: chain ka residue 36 VAL Chi-restraints excluded: chain ka residue 45 LEU Chi-restraints excluded: chain ka residue 74 MET Chi-restraints excluded: chain ka residue 92 THR Chi-restraints excluded: chain ka residue 98 LEU Chi-restraints excluded: chain ka residue 119 GLU Chi-restraints excluded: chain ka residue 131 ARG Chi-restraints excluded: chain ka residue 132 ARG Chi-restraints excluded: chain ka residue 136 ASP Chi-restraints excluded: chain ka residue 156 GLU Chi-restraints excluded: chain ka residue 180 SER Chi-restraints excluded: chain la residue 21 THR Chi-restraints excluded: chain la residue 32 ARG Chi-restraints excluded: chain la residue 49 MET Chi-restraints excluded: chain la residue 69 ILE Chi-restraints excluded: chain la residue 121 THR Chi-restraints excluded: chain la residue 123 LEU Chi-restraints excluded: chain la residue 138 ARG Chi-restraints excluded: chain ma residue 27 ARG Chi-restraints excluded: chain ma residue 30 ILE Chi-restraints excluded: chain ma residue 31 THR Chi-restraints excluded: chain ma residue 49 LYS Chi-restraints excluded: chain ma residue 52 LYS Chi-restraints excluded: chain ma residue 73 THR Chi-restraints excluded: chain ma residue 86 ASP Chi-restraints excluded: chain ma residue 113 THR Chi-restraints excluded: chain na residue 27 VAL Chi-restraints excluded: chain na residue 40 THR Chi-restraints excluded: chain na residue 47 LEU Chi-restraints excluded: chain na residue 54 VAL Chi-restraints excluded: chain na residue 56 ILE Chi-restraints excluded: chain na residue 57 THR Chi-restraints excluded: chain na residue 81 VAL Chi-restraints excluded: chain na residue 85 CYS Chi-restraints excluded: chain na residue 88 LEU Chi-restraints excluded: chain na residue 107 THR Chi-restraints excluded: chain na residue 119 LEU Chi-restraints excluded: chain oa residue 16 LEU Chi-restraints excluded: chain oa residue 32 SER Chi-restraints excluded: chain oa residue 100 SER Chi-restraints excluded: chain oa residue 108 ARG Chi-restraints excluded: chain oa residue 113 ARG Chi-restraints excluded: chain oa residue 114 LEU Chi-restraints excluded: chain oa residue 136 THR Chi-restraints excluded: chain pa residue 34 ASP Chi-restraints excluded: chain pa residue 80 LEU Chi-restraints excluded: chain pa residue 87 ASP Chi-restraints excluded: chain pa residue 138 THR Chi-restraints excluded: chain qa residue 8 THR Chi-restraints excluded: chain qa residue 16 VAL Chi-restraints excluded: chain qa residue 24 MET Chi-restraints excluded: chain qa residue 25 THR Chi-restraints excluded: chain qa residue 40 ILE Chi-restraints excluded: chain qa residue 43 SER Chi-restraints excluded: chain qa residue 56 HIS Chi-restraints excluded: chain qa residue 66 VAL Chi-restraints excluded: chain qa residue 114 LEU Chi-restraints excluded: chain ra residue 32 SER Chi-restraints excluded: chain ra residue 57 GLU Chi-restraints excluded: chain sa residue 43 VAL Chi-restraints excluded: chain sa residue 85 VAL Chi-restraints excluded: chain ta residue 33 GLN Chi-restraints excluded: chain ta residue 61 ILE Chi-restraints excluded: chain ta residue 69 ARG Chi-restraints excluded: chain ta residue 93 VAL Chi-restraints excluded: chain ta residue 97 SER Chi-restraints excluded: chain ua residue 26 VAL Chi-restraints excluded: chain ua residue 27 LYS Chi-restraints excluded: chain ua residue 45 THR Chi-restraints excluded: chain ua residue 54 ASP Chi-restraints excluded: chain ua residue 67 VAL Chi-restraints excluded: chain ua residue 68 ARG Chi-restraints excluded: chain ua residue 81 GLU Chi-restraints excluded: chain va residue 3 ARG Chi-restraints excluded: chain va residue 8 ASP Chi-restraints excluded: chain va residue 17 GLU Chi-restraints excluded: chain va residue 23 THR Chi-restraints excluded: chain va residue 57 VAL Chi-restraints excluded: chain va residue 83 THR Chi-restraints excluded: chain va residue 86 GLU Chi-restraints excluded: chain va residue 88 TYR Chi-restraints excluded: chain va residue 89 ARG Chi-restraints excluded: chain va residue 116 ILE Chi-restraints excluded: chain wa residue 30 LEU Chi-restraints excluded: chain xa residue 38 LYS Chi-restraints excluded: chain xa residue 45 ILE Chi-restraints excluded: chain xa residue 54 THR Chi-restraints excluded: chain xa residue 65 LEU Chi-restraints excluded: chain xa residue 77 GLU Chi-restraints excluded: chain ya residue 8 LEU Chi-restraints excluded: chain za residue 23 LEU Chi-restraints excluded: chain za residue 29 LEU Chi-restraints excluded: chain za residue 40 ARG Chi-restraints excluded: chain za residue 68 VAL Chi-restraints excluded: chain za residue 118 THR Chi-restraints excluded: chain za residue 140 GLU Chi-restraints excluded: chain za residue 141 SER Chi-restraints excluded: chain za residue 162 ASP Chi-restraints excluded: chain za residue 174 SER Chi-restraints excluded: chain za residue 197 HIS Chi-restraints excluded: chain za residue 208 TYR Chi-restraints excluded: chain za residue 209 ARG Chi-restraints excluded: chain bb residue 26 LYS Chi-restraints excluded: chain bb residue 28 GLN Chi-restraints excluded: chain bb residue 37 LEU Chi-restraints excluded: chain bb residue 47 LEU Chi-restraints excluded: chain bb residue 98 THR Chi-restraints excluded: chain bb residue 108 ASP Chi-restraints excluded: chain bb residue 111 ARG Chi-restraints excluded: chain bb residue 120 LEU Chi-restraints excluded: chain bb residue 122 GLU Chi-restraints excluded: chain bb residue 129 THR Chi-restraints excluded: chain bb residue 148 ASN Chi-restraints excluded: chain bb residue 170 GLU Chi-restraints excluded: chain bb residue 189 ILE Chi-restraints excluded: chain bb residue 201 THR Chi-restraints excluded: chain bb residue 205 PHE Chi-restraints excluded: chain cb residue 12 TYR Chi-restraints excluded: chain cb residue 36 ILE Chi-restraints excluded: chain cb residue 67 SER Chi-restraints excluded: chain cb residue 71 LEU Chi-restraints excluded: chain db residue 19 LYS Chi-restraints excluded: chain db residue 24 SER Chi-restraints excluded: chain db residue 45 VAL Chi-restraints excluded: chain db residue 76 SER Chi-restraints excluded: chain eb residue 23 LYS Chi-restraints excluded: chain eb residue 46 ARG Chi-restraints excluded: chain eb residue 63 THR Chi-restraints excluded: chain eb residue 70 ARG Chi-restraints excluded: chain eb residue 102 THR Chi-restraints excluded: chain eb residue 113 THR Chi-restraints excluded: chain eb residue 143 VAL Chi-restraints excluded: chain eb residue 158 ILE Chi-restraints excluded: chain eb residue 163 THR Chi-restraints excluded: chain fb residue 133 THR Chi-restraints excluded: chain fb residue 149 VAL Chi-restraints excluded: chain fb residue 189 VAL Chi-restraints excluded: chain fb residue 213 SER Chi-restraints excluded: chain fb residue 229 MET Chi-restraints excluded: chain fb residue 238 ASP Chi-restraints excluded: chain gb residue 46 GLU Chi-restraints excluded: chain gb residue 52 ILE Chi-restraints excluded: chain gb residue 67 VAL Chi-restraints excluded: chain gb residue 68 LEU Chi-restraints excluded: chain gb residue 82 SER Chi-restraints excluded: chain gb residue 91 VAL Chi-restraints excluded: chain gb residue 113 LEU Chi-restraints excluded: chain gb residue 205 LYS Chi-restraints excluded: chain hb residue 21 ASP Chi-restraints excluded: chain hb residue 37 LEU Chi-restraints excluded: chain hb residue 84 LEU Chi-restraints excluded: chain hb residue 118 THR Chi-restraints excluded: chain hb residue 130 VAL Chi-restraints excluded: chain hb residue 137 VAL Chi-restraints excluded: chain hb residue 182 VAL Chi-restraints excluded: chain ib residue 21 LYS Chi-restraints excluded: chain ib residue 75 THR Chi-restraints excluded: chain ib residue 87 VAL Chi-restraints excluded: chain ib residue 96 LYS Chi-restraints excluded: chain ib residue 118 VAL Chi-restraints excluded: chain ib residue 122 ASP Chi-restraints excluded: chain IB residue 9 ARG Chi-restraints excluded: chain IB residue 20 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 195 optimal weight: 8.9990 chunk 524 optimal weight: 10.0000 chunk 115 optimal weight: 20.0000 chunk 341 optimal weight: 5.9990 chunk 143 optimal weight: 10.0000 chunk 582 optimal weight: 10.0000 chunk 483 optimal weight: 5.9990 chunk 269 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 192 optimal weight: 6.9990 chunk 305 optimal weight: 0.9980 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** ba 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ca 216 GLN ga 91 ASN ha 18 ASN ha 174 ASN ** ia 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ja 67 GLN ja 188 ASN ma 39 ASN oa 120 HIS ra 81 GLN ** ra 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** sa 113 GLN ** ta 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** va 48 ASN va 65 GLN za 76 GLN ** za 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** za 101 ASN za 173 ASN db 94 ASN eb 68 ASN ** eb 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** eb 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** eb 178 ASN fb 199 GLN gb 190 GLN hb 34 ASN ** hb 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ib 99 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 78029 Z= 0.397 Angle : 0.792 13.848 113871 Z= 0.416 Chirality : 0.046 0.391 14101 Planarity : 0.007 0.125 7899 Dihedral : 23.708 179.871 32388 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.68 % Favored : 92.23 % Rotamer: Outliers : 10.35 % Allowed : 30.07 % Favored : 59.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.12), residues: 4325 helix: -0.22 (0.14), residues: 1342 sheet: -0.74 (0.17), residues: 858 loop : -1.50 (0.13), residues: 2125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPha 165 HIS 0.008 0.002 HISoa 120 PHE 0.032 0.002 PHEoa 28 TYR 0.029 0.003 TYRpa 18 ARG 0.010 0.001 ARGya 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8650 Ramachandran restraints generated. 4325 Oldfield, 0 Emsley, 4325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8650 Ramachandran restraints generated. 4325 Oldfield, 0 Emsley, 4325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1183 residues out of total 3778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 391 poor density : 792 time to evaluate : 4.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: ca 18 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7721 (tt0) REVERT: ca 159 GLN cc_start: 0.6267 (OUTLIER) cc_final: 0.5824 (mt0) REVERT: ca 169 ARG cc_start: 0.5360 (OUTLIER) cc_final: 0.3809 (mtp-110) REVERT: da 1 MET cc_start: 0.6091 (OUTLIER) cc_final: 0.4560 (tpt) REVERT: da 10 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7228 (mp0) REVERT: da 49 PHE cc_start: 0.8450 (m-10) cc_final: 0.8184 (m-10) REVERT: da 53 GLU cc_start: 0.7365 (pm20) cc_final: 0.6856 (tm-30) REVERT: da 57 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6433 (tp30) REVERT: da 71 ASP cc_start: 0.7420 (t70) cc_final: 0.7092 (t0) REVERT: ga 53 LYS cc_start: 0.8373 (mtmt) cc_final: 0.8116 (mtmm) REVERT: ga 70 ARG cc_start: 0.7197 (ttp80) cc_final: 0.6881 (ttp80) REVERT: ga 118 ARG cc_start: 0.9154 (OUTLIER) cc_final: 0.7838 (ptm160) REVERT: ha 102 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8222 (mt) REVERT: ha 103 SER cc_start: 0.8304 (OUTLIER) cc_final: 0.8099 (t) REVERT: ha 160 GLU cc_start: 0.5825 (OUTLIER) cc_final: 0.4748 (pm20) REVERT: ha 279 LYS cc_start: 0.5725 (OUTLIER) cc_final: 0.5189 (mtmm) REVERT: ia 65 ARG cc_start: 0.7237 (OUTLIER) cc_final: 0.6541 (ttt180) REVERT: ia 68 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7730 (mt-10) REVERT: ia 80 LEU cc_start: 0.7584 (mp) cc_final: 0.7357 (pt) REVERT: ia 89 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.5863 (mp0) REVERT: ia 101 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7606 (mp10) REVERT: ia 127 MET cc_start: 0.7917 (OUTLIER) cc_final: 0.6388 (tpt) REVERT: ia 176 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8524 (mp) REVERT: ia 185 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8013 (mtmt) REVERT: ja 40 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7515 (pp20) REVERT: ja 66 MET cc_start: 0.8469 (mmm) cc_final: 0.8202 (mmm) REVERT: ja 205 PHE cc_start: 0.7867 (p90) cc_final: 0.7445 (p90) REVERT: ja 240 LYS cc_start: 0.6018 (OUTLIER) cc_final: 0.5682 (mttt) REVERT: ka 98 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7544 (tm) REVERT: ka 131 ARG cc_start: 0.2417 (OUTLIER) cc_final: 0.1937 (tpp-160) REVERT: ka 132 ARG cc_start: 0.5807 (OUTLIER) cc_final: 0.4632 (ptp90) REVERT: ka 156 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7286 (mt-10) REVERT: la 12 THR cc_start: 0.8337 (t) cc_final: 0.7934 (m) REVERT: la 76 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.7088 (ttt90) REVERT: la 100 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7452 (tp40) REVERT: la 123 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8216 (mt) REVERT: la 138 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8251 (ptp90) REVERT: ma 27 ARG cc_start: 0.6174 (OUTLIER) cc_final: 0.5850 (mmt90) REVERT: na 47 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8402 (mm) REVERT: na 56 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8502 (mm) REVERT: na 117 ARG cc_start: 0.7827 (tpp80) cc_final: 0.7402 (mmm-85) REVERT: oa 101 ASN cc_start: 0.8324 (OUTLIER) cc_final: 0.8107 (m110) REVERT: oa 108 ARG cc_start: 0.6538 (OUTLIER) cc_final: 0.5968 (tmt170) REVERT: oa 112 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6552 (mp0) REVERT: oa 113 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7235 (ttm110) REVERT: oa 130 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7073 (mmt-90) REVERT: pa 60 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8410 (mm) REVERT: qa 24 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7608 (mpt) REVERT: qa 56 HIS cc_start: 0.7394 (OUTLIER) cc_final: 0.6826 (p-80) REVERT: qa 97 ARG cc_start: 0.7152 (ptt180) cc_final: 0.6804 (mtm110) REVERT: qa 100 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.7094 (ttpm) REVERT: ta 69 ARG cc_start: 0.3740 (OUTLIER) cc_final: 0.2124 (mtt180) REVERT: ua 27 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7947 (mmtp) REVERT: ua 68 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7666 (ptt180) REVERT: ua 69 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7166 (mt-10) REVERT: ua 80 ARG cc_start: 0.7269 (mtp-110) cc_final: 0.6802 (ptm160) REVERT: ua 81 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.6037 (pp20) REVERT: va 76 TYR cc_start: 0.6374 (OUTLIER) cc_final: 0.5895 (t80) REVERT: va 86 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7683 (tm-30) REVERT: va 88 TYR cc_start: 0.7808 (OUTLIER) cc_final: 0.6897 (m-80) REVERT: xa 45 ILE cc_start: 0.6862 (OUTLIER) cc_final: 0.6476 (tt) REVERT: za 15 LYS cc_start: 0.8452 (tptm) cc_final: 0.7923 (ttpp) REVERT: za 16 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7930 (mt-10) REVERT: za 39 GLU cc_start: 0.7329 (tp30) cc_final: 0.7098 (mm-30) REVERT: za 174 SER cc_start: 0.8008 (OUTLIER) cc_final: 0.7529 (t) REVERT: za 197 HIS cc_start: 0.5234 (OUTLIER) cc_final: 0.3398 (p90) REVERT: za 208 TYR cc_start: 0.8245 (OUTLIER) cc_final: 0.7379 (p90) REVERT: za 209 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.6610 (mmm-85) REVERT: bb 26 LYS cc_start: 0.7245 (OUTLIER) cc_final: 0.6987 (mtmt) REVERT: bb 28 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.7164 (mm110) REVERT: bb 31 ASP cc_start: 0.7908 (t0) cc_final: 0.7658 (t0) REVERT: bb 50 ARG cc_start: 0.6284 (mtt180) cc_final: 0.5803 (mtt90) REVERT: bb 111 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7885 (mmp80) REVERT: bb 152 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6867 (tmt-80) REVERT: bb 189 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.8026 (mt) REVERT: bb 227 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7707 (mmtp) REVERT: cb 63 ASP cc_start: 0.6372 (t70) cc_final: 0.5909 (t0) REVERT: cb 71 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8600 (mp) REVERT: db 45 VAL cc_start: 0.7879 (OUTLIER) cc_final: 0.7586 (t) REVERT: eb 46 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7802 (ptp-170) REVERT: eb 70 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.8002 (ttm170) REVERT: fb 252 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.7111 (tt0) REVERT: gb 46 GLU cc_start: 0.3346 (OUTLIER) cc_final: 0.2630 (mm-30) REVERT: gb 56 CYS cc_start: 0.7317 (p) cc_final: 0.6905 (p) REVERT: gb 91 VAL cc_start: 0.8396 (OUTLIER) cc_final: 0.8138 (t) REVERT: hb 37 LEU cc_start: 0.4270 (OUTLIER) cc_final: 0.3900 (pt) REVERT: hb 112 GLN cc_start: 0.2123 (OUTLIER) cc_final: 0.1825 (tt0) REVERT: hb 176 ARG cc_start: 0.5961 (ttm-80) cc_final: 0.5682 (ttm-80) REVERT: ib 96 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8198 (tmmm) REVERT: IB 9 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7282 (ttt180) REVERT: IB 20 MET cc_start: 0.4854 (OUTLIER) cc_final: 0.4626 (mpt) outliers start: 391 outliers final: 209 residues processed: 1053 average time/residue: 1.5240 time to fit residues: 2142.7246 Evaluate side-chains 1047 residues out of total 3778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 769 time to evaluate : 4.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain ba residue 19 THR Chi-restraints excluded: chain ba residue 32 VAL Chi-restraints excluded: chain ba residue 68 THR Chi-restraints excluded: chain ca residue 3 ILE Chi-restraints excluded: chain ca residue 18 GLN Chi-restraints excluded: chain ca residue 43 THR Chi-restraints excluded: chain ca residue 44 VAL Chi-restraints excluded: chain ca residue 73 VAL Chi-restraints excluded: chain ca residue 77 THR Chi-restraints excluded: chain ca residue 83 VAL Chi-restraints excluded: chain ca residue 89 ASN Chi-restraints excluded: chain ca residue 94 THR Chi-restraints excluded: chain ca residue 105 VAL Chi-restraints excluded: chain ca residue 159 GLN Chi-restraints excluded: chain ca residue 169 ARG Chi-restraints excluded: chain da residue 1 MET Chi-restraints excluded: chain da residue 10 GLU Chi-restraints excluded: chain da residue 57 GLU Chi-restraints excluded: chain ga residue 35 GLU Chi-restraints excluded: chain ga residue 72 GLN Chi-restraints excluded: chain ga residue 90 LEU Chi-restraints excluded: chain ga residue 118 ARG Chi-restraints excluded: chain ga residue 128 SER Chi-restraints excluded: chain ha residue 9 VAL Chi-restraints excluded: chain ha residue 20 VAL Chi-restraints excluded: chain ha residue 28 ILE Chi-restraints excluded: chain ha residue 50 ASN Chi-restraints excluded: chain ha residue 70 THR Chi-restraints excluded: chain ha residue 102 LEU Chi-restraints excluded: chain ha residue 103 SER Chi-restraints excluded: chain ha residue 107 THR Chi-restraints excluded: chain ha residue 120 SER Chi-restraints excluded: chain ha residue 126 ASP Chi-restraints excluded: chain ha residue 132 SER Chi-restraints excluded: chain ha residue 141 LEU Chi-restraints excluded: chain ha residue 155 ASP Chi-restraints excluded: chain ha residue 160 GLU Chi-restraints excluded: chain ha residue 189 VAL Chi-restraints excluded: chain ha residue 231 THR Chi-restraints excluded: chain ha residue 250 ILE Chi-restraints excluded: chain ha residue 253 SER Chi-restraints excluded: chain ha residue 279 LYS Chi-restraints excluded: chain ha residue 282 VAL Chi-restraints excluded: chain ha residue 294 LYS Chi-restraints excluded: chain ha residue 300 THR Chi-restraints excluded: chain ha residue 302 LEU Chi-restraints excluded: chain ha residue 303 SER Chi-restraints excluded: chain ha residue 305 SER Chi-restraints excluded: chain ia residue 5 ILE Chi-restraints excluded: chain ia residue 42 THR Chi-restraints excluded: chain ia residue 58 VAL Chi-restraints excluded: chain ia residue 65 ARG Chi-restraints excluded: chain ia residue 84 VAL Chi-restraints excluded: chain ia residue 89 GLU Chi-restraints excluded: chain ia residue 91 VAL Chi-restraints excluded: chain ia residue 101 GLN Chi-restraints excluded: chain ia residue 127 MET Chi-restraints excluded: chain ia residue 176 LEU Chi-restraints excluded: chain ia residue 185 LYS Chi-restraints excluded: chain ia residue 202 THR Chi-restraints excluded: chain ia residue 207 LEU Chi-restraints excluded: chain ja residue 33 SER Chi-restraints excluded: chain ja residue 40 GLU Chi-restraints excluded: chain ja residue 57 THR Chi-restraints excluded: chain ja residue 59 ARG Chi-restraints excluded: chain ja residue 71 MET Chi-restraints excluded: chain ja residue 115 ARG Chi-restraints excluded: chain ja residue 124 CYS Chi-restraints excluded: chain ja residue 163 ASP Chi-restraints excluded: chain ja residue 189 THR Chi-restraints excluded: chain ja residue 192 VAL Chi-restraints excluded: chain ja residue 204 THR Chi-restraints excluded: chain ja residue 207 THR Chi-restraints excluded: chain ja residue 237 SER Chi-restraints excluded: chain ja residue 240 LYS Chi-restraints excluded: chain ja residue 246 LEU Chi-restraints excluded: chain ka residue 19 THR Chi-restraints excluded: chain ka residue 36 VAL Chi-restraints excluded: chain ka residue 38 SER Chi-restraints excluded: chain ka residue 45 LEU Chi-restraints excluded: chain ka residue 74 MET Chi-restraints excluded: chain ka residue 92 THR Chi-restraints excluded: chain ka residue 98 LEU Chi-restraints excluded: chain ka residue 119 GLU Chi-restraints excluded: chain ka residue 131 ARG Chi-restraints excluded: chain ka residue 132 ARG Chi-restraints excluded: chain ka residue 136 ASP Chi-restraints excluded: chain ka residue 156 GLU Chi-restraints excluded: chain ka residue 180 SER Chi-restraints excluded: chain la residue 21 THR Chi-restraints excluded: chain la residue 23 VAL Chi-restraints excluded: chain la residue 32 ARG Chi-restraints excluded: chain la residue 49 MET Chi-restraints excluded: chain la residue 69 ILE Chi-restraints excluded: chain la residue 76 ARG Chi-restraints excluded: chain la residue 100 GLN Chi-restraints excluded: chain la residue 121 THR Chi-restraints excluded: chain la residue 123 LEU Chi-restraints excluded: chain la residue 138 ARG Chi-restraints excluded: chain ma residue 27 ARG Chi-restraints excluded: chain ma residue 30 ILE Chi-restraints excluded: chain ma residue 31 THR Chi-restraints excluded: chain ma residue 49 LYS Chi-restraints excluded: chain ma residue 52 LYS Chi-restraints excluded: chain ma residue 68 VAL Chi-restraints excluded: chain ma residue 73 THR Chi-restraints excluded: chain ma residue 86 ASP Chi-restraints excluded: chain ma residue 113 THR Chi-restraints excluded: chain na residue 27 VAL Chi-restraints excluded: chain na residue 40 THR Chi-restraints excluded: chain na residue 47 LEU Chi-restraints excluded: chain na residue 54 VAL Chi-restraints excluded: chain na residue 56 ILE Chi-restraints excluded: chain na residue 57 THR Chi-restraints excluded: chain na residue 81 VAL Chi-restraints excluded: chain na residue 85 CYS Chi-restraints excluded: chain na residue 88 LEU Chi-restraints excluded: chain na residue 91 THR Chi-restraints excluded: chain na residue 107 THR Chi-restraints excluded: chain na residue 119 LEU Chi-restraints excluded: chain na residue 135 VAL Chi-restraints excluded: chain oa residue 16 LEU Chi-restraints excluded: chain oa residue 32 SER Chi-restraints excluded: chain oa residue 43 ILE Chi-restraints excluded: chain oa residue 100 SER Chi-restraints excluded: chain oa residue 101 ASN Chi-restraints excluded: chain oa residue 104 ASP Chi-restraints excluded: chain oa residue 108 ARG Chi-restraints excluded: chain oa residue 112 GLU Chi-restraints excluded: chain oa residue 113 ARG Chi-restraints excluded: chain oa residue 114 LEU Chi-restraints excluded: chain oa residue 130 ARG Chi-restraints excluded: chain oa residue 136 THR Chi-restraints excluded: chain oa residue 139 THR Chi-restraints excluded: chain pa residue 34 ASP Chi-restraints excluded: chain pa residue 60 ILE Chi-restraints excluded: chain pa residue 80 LEU Chi-restraints excluded: chain pa residue 87 ASP Chi-restraints excluded: chain pa residue 138 THR Chi-restraints excluded: chain qa residue 8 THR Chi-restraints excluded: chain qa residue 16 VAL Chi-restraints excluded: chain qa residue 24 MET Chi-restraints excluded: chain qa residue 25 THR Chi-restraints excluded: chain qa residue 40 ILE Chi-restraints excluded: chain qa residue 43 SER Chi-restraints excluded: chain qa residue 56 HIS Chi-restraints excluded: chain qa residue 66 VAL Chi-restraints excluded: chain qa residue 82 MET Chi-restraints excluded: chain qa residue 96 ILE Chi-restraints excluded: chain qa residue 100 LYS Chi-restraints excluded: chain qa residue 114 LEU Chi-restraints excluded: chain ra residue 32 SER Chi-restraints excluded: chain ra residue 47 VAL Chi-restraints excluded: chain ra residue 57 GLU Chi-restraints excluded: chain ra residue 77 ILE Chi-restraints excluded: chain sa residue 43 VAL Chi-restraints excluded: chain sa residue 85 VAL Chi-restraints excluded: chain sa residue 127 GLU Chi-restraints excluded: chain ta residue 33 GLN Chi-restraints excluded: chain ta residue 69 ARG Chi-restraints excluded: chain ta residue 93 VAL Chi-restraints excluded: chain ta residue 97 SER Chi-restraints excluded: chain ua residue 27 LYS Chi-restraints excluded: chain ua residue 45 THR Chi-restraints excluded: chain ua residue 54 ASP Chi-restraints excluded: chain ua residue 67 VAL Chi-restraints excluded: chain ua residue 68 ARG Chi-restraints excluded: chain ua residue 81 GLU Chi-restraints excluded: chain va residue 3 ARG Chi-restraints excluded: chain va residue 8 ASP Chi-restraints excluded: chain va residue 17 GLU Chi-restraints excluded: chain va residue 23 THR Chi-restraints excluded: chain va residue 48 ASN Chi-restraints excluded: chain va residue 57 VAL Chi-restraints excluded: chain va residue 76 TYR Chi-restraints excluded: chain va residue 81 ARG Chi-restraints excluded: chain va residue 83 THR Chi-restraints excluded: chain va residue 86 GLU Chi-restraints excluded: chain va residue 88 TYR Chi-restraints excluded: chain va residue 92 MET Chi-restraints excluded: chain va residue 116 ILE Chi-restraints excluded: chain wa residue 27 SER Chi-restraints excluded: chain wa residue 30 LEU Chi-restraints excluded: chain xa residue 45 ILE Chi-restraints excluded: chain xa residue 54 THR Chi-restraints excluded: chain xa residue 56 VAL Chi-restraints excluded: chain xa residue 65 LEU Chi-restraints excluded: chain xa residue 77 GLU Chi-restraints excluded: chain ya residue 8 LEU Chi-restraints excluded: chain ya residue 45 VAL Chi-restraints excluded: chain za residue 23 LEU Chi-restraints excluded: chain za residue 29 LEU Chi-restraints excluded: chain za residue 40 ARG Chi-restraints excluded: chain za residue 68 VAL Chi-restraints excluded: chain za residue 118 THR Chi-restraints excluded: chain za residue 140 GLU Chi-restraints excluded: chain za residue 141 SER Chi-restraints excluded: chain za residue 162 ASP Chi-restraints excluded: chain za residue 174 SER Chi-restraints excluded: chain za residue 197 HIS Chi-restraints excluded: chain za residue 208 TYR Chi-restraints excluded: chain za residue 209 ARG Chi-restraints excluded: chain bb residue 26 LYS Chi-restraints excluded: chain bb residue 28 GLN Chi-restraints excluded: chain bb residue 37 LEU Chi-restraints excluded: chain bb residue 47 LEU Chi-restraints excluded: chain bb residue 69 SER Chi-restraints excluded: chain bb residue 91 VAL Chi-restraints excluded: chain bb residue 98 THR Chi-restraints excluded: chain bb residue 108 ASP Chi-restraints excluded: chain bb residue 111 ARG Chi-restraints excluded: chain bb residue 120 LEU Chi-restraints excluded: chain bb residue 122 GLU Chi-restraints excluded: chain bb residue 128 LYS Chi-restraints excluded: chain bb residue 129 THR Chi-restraints excluded: chain bb residue 148 ASN Chi-restraints excluded: chain bb residue 152 ARG Chi-restraints excluded: chain bb residue 161 ILE Chi-restraints excluded: chain bb residue 172 MET Chi-restraints excluded: chain bb residue 189 ILE Chi-restraints excluded: chain bb residue 201 THR Chi-restraints excluded: chain bb residue 205 PHE Chi-restraints excluded: chain bb residue 227 LYS Chi-restraints excluded: chain cb residue 36 ILE Chi-restraints excluded: chain cb residue 67 SER Chi-restraints excluded: chain cb residue 71 LEU Chi-restraints excluded: chain db residue 19 LYS Chi-restraints excluded: chain db residue 24 SER Chi-restraints excluded: chain db residue 41 VAL Chi-restraints excluded: chain db residue 45 VAL Chi-restraints excluded: chain db residue 60 ASP Chi-restraints excluded: chain db residue 76 SER Chi-restraints excluded: chain eb residue 23 LYS Chi-restraints excluded: chain eb residue 46 ARG Chi-restraints excluded: chain eb residue 52 SER Chi-restraints excluded: chain eb residue 63 THR Chi-restraints excluded: chain eb residue 70 ARG Chi-restraints excluded: chain eb residue 102 THR Chi-restraints excluded: chain eb residue 113 THR Chi-restraints excluded: chain eb residue 143 VAL Chi-restraints excluded: chain eb residue 152 VAL Chi-restraints excluded: chain eb residue 158 ILE Chi-restraints excluded: chain eb residue 163 THR Chi-restraints excluded: chain fb residue 94 THR Chi-restraints excluded: chain fb residue 133 THR Chi-restraints excluded: chain fb residue 149 VAL Chi-restraints excluded: chain fb residue 186 SER Chi-restraints excluded: chain fb residue 213 SER Chi-restraints excluded: chain fb residue 229 MET Chi-restraints excluded: chain fb residue 238 ASP Chi-restraints excluded: chain fb residue 252 GLU Chi-restraints excluded: chain fb residue 254 THR Chi-restraints excluded: chain gb residue 4 ASN Chi-restraints excluded: chain gb residue 46 GLU Chi-restraints excluded: chain gb residue 52 ILE Chi-restraints excluded: chain gb residue 67 VAL Chi-restraints excluded: chain gb residue 68 LEU Chi-restraints excluded: chain gb residue 82 SER Chi-restraints excluded: chain gb residue 91 VAL Chi-restraints excluded: chain gb residue 115 ILE Chi-restraints excluded: chain gb residue 205 LYS Chi-restraints excluded: chain hb residue 21 ASP Chi-restraints excluded: chain hb residue 37 LEU Chi-restraints excluded: chain hb residue 84 LEU Chi-restraints excluded: chain hb residue 102 VAL Chi-restraints excluded: chain hb residue 112 GLN Chi-restraints excluded: chain hb residue 118 THR Chi-restraints excluded: chain hb residue 130 VAL Chi-restraints excluded: chain hb residue 137 VAL Chi-restraints excluded: chain hb residue 155 LEU Chi-restraints excluded: chain hb residue 182 VAL Chi-restraints excluded: chain ib residue 21 LYS Chi-restraints excluded: chain ib residue 75 THR Chi-restraints excluded: chain ib residue 87 VAL Chi-restraints excluded: chain ib residue 96 LYS Chi-restraints excluded: chain ib residue 122 ASP Chi-restraints excluded: chain IB residue 9 ARG Chi-restraints excluded: chain IB residue 20 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 561 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 331 optimal weight: 3.9990 chunk 425 optimal weight: 0.6980 chunk 329 optimal weight: 7.9990 chunk 490 optimal weight: 0.9980 chunk 325 optimal weight: 4.9990 chunk 580 optimal weight: 5.9990 chunk 363 optimal weight: 10.0000 chunk 353 optimal weight: 2.9990 chunk 267 optimal weight: 5.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** ba 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ca 85 ASN ca 216 GLN ** da 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ga 91 ASN ha 18 ASN ha 295 GLN ja 188 ASN ma 39 ASN oa 120 HIS ra 81 GLN ra 115 ASN ** ra 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** sa 113 GLN ** ta 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** va 48 ASN va 65 GLN za 76 GLN ** za 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** za 101 ASN za 173 ASN bb 232 HIS db 94 ASN eb 68 ASN ** eb 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** eb 178 ASN fb 199 GLN ** hb 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 78029 Z= 0.223 Angle : 0.686 13.429 113871 Z= 0.366 Chirality : 0.040 0.315 14101 Planarity : 0.006 0.123 7899 Dihedral : 23.607 179.553 32384 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.27 % Favored : 93.64 % Rotamer: Outliers : 8.23 % Allowed : 32.05 % Favored : 59.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.12), residues: 4325 helix: 0.03 (0.14), residues: 1350 sheet: -0.67 (0.17), residues: 838 loop : -1.38 (0.13), residues: 2137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRPva 98 HIS 0.006 0.001 HISeb 126 PHE 0.027 0.002 PHEoa 28 TYR 0.022 0.002 TYRpa 18 ARG 0.013 0.001 ARGya 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8650 Ramachandran restraints generated. 4325 Oldfield, 0 Emsley, 4325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8650 Ramachandran restraints generated. 4325 Oldfield, 0 Emsley, 4325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1125 residues out of total 3778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 311 poor density : 814 time to evaluate : 4.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: ca 18 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7727 (tt0) REVERT: ca 159 GLN cc_start: 0.5964 (OUTLIER) cc_final: 0.5398 (pt0) REVERT: ca 169 ARG cc_start: 0.5476 (OUTLIER) cc_final: 0.3885 (mtp-110) REVERT: da 10 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: da 49 PHE cc_start: 0.8447 (m-10) cc_final: 0.8226 (m-10) REVERT: da 53 GLU cc_start: 0.7275 (pm20) cc_final: 0.6923 (tm-30) REVERT: da 57 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6668 (tp30) REVERT: da 71 ASP cc_start: 0.7452 (t70) cc_final: 0.7133 (t0) REVERT: da 78 ASN cc_start: 0.7397 (p0) cc_final: 0.6565 (t0) REVERT: ga 53 LYS cc_start: 0.8330 (mtmt) cc_final: 0.8071 (mtmm) REVERT: ga 70 ARG cc_start: 0.7148 (ttp80) cc_final: 0.6851 (ttp80) REVERT: ga 118 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.7803 (ptm160) REVERT: ha 102 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8198 (mt) REVERT: ha 103 SER cc_start: 0.8265 (OUTLIER) cc_final: 0.8064 (t) REVERT: ha 160 GLU cc_start: 0.5858 (OUTLIER) cc_final: 0.4795 (pm20) REVERT: ha 322 ILE cc_start: 0.7319 (pp) cc_final: 0.7021 (mp) REVERT: ia 68 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7613 (mt-10) REVERT: ia 80 LEU cc_start: 0.7555 (mp) cc_final: 0.7326 (pt) REVERT: ia 89 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.5882 (mp0) REVERT: ia 101 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7451 (mp10) REVERT: ia 127 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.6324 (tpt) REVERT: ia 185 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7937 (mtmt) REVERT: ja 40 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7290 (pp20) REVERT: ja 205 PHE cc_start: 0.7813 (p90) cc_final: 0.7428 (p90) REVERT: ka 98 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7499 (tm) REVERT: ka 131 ARG cc_start: 0.2172 (OUTLIER) cc_final: 0.1700 (tpp-160) REVERT: ka 132 ARG cc_start: 0.5759 (OUTLIER) cc_final: 0.4909 (ptp90) REVERT: ka 156 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7331 (mt-10) REVERT: la 12 THR cc_start: 0.8240 (t) cc_final: 0.7989 (m) REVERT: la 46 ARG cc_start: 0.7025 (ptm160) cc_final: 0.6747 (ttp-110) REVERT: la 76 ARG cc_start: 0.7337 (OUTLIER) cc_final: 0.7050 (ttt90) REVERT: la 100 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7458 (tp40) REVERT: la 138 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.8201 (ptp90) REVERT: na 47 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8406 (mm) REVERT: na 56 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8483 (mm) REVERT: na 117 ARG cc_start: 0.7839 (tpp80) cc_final: 0.7481 (mmm-85) REVERT: oa 17 ASN cc_start: 0.6362 (m-40) cc_final: 0.6143 (m-40) REVERT: oa 108 ARG cc_start: 0.6503 (OUTLIER) cc_final: 0.5954 (tmt170) REVERT: oa 112 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6431 (mp0) REVERT: oa 113 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7214 (ttm170) REVERT: qa 24 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7670 (mpt) REVERT: qa 56 HIS cc_start: 0.7265 (OUTLIER) cc_final: 0.6766 (p-80) REVERT: qa 97 ARG cc_start: 0.7155 (ptt180) cc_final: 0.6877 (mtm180) REVERT: ra 90 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7911 (mtmp) REVERT: ta 69 ARG cc_start: 0.3698 (OUTLIER) cc_final: 0.1996 (mtp180) REVERT: ua 27 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7972 (mttp) REVERT: ua 68 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7709 (ptt180) REVERT: ua 69 GLU cc_start: 0.7375 (mt-10) cc_final: 0.7162 (mt-10) REVERT: ua 80 ARG cc_start: 0.7230 (mtp-110) cc_final: 0.6794 (ptm160) REVERT: ua 81 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.5973 (pp20) REVERT: va 86 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7677 (tm-30) REVERT: va 117 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7906 (ttp-170) REVERT: xa 45 ILE cc_start: 0.6732 (OUTLIER) cc_final: 0.6368 (tt) REVERT: za 15 LYS cc_start: 0.8459 (tptm) cc_final: 0.7891 (ttpp) REVERT: za 16 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7951 (mt-10) REVERT: za 156 SER cc_start: 0.8441 (m) cc_final: 0.7941 (p) REVERT: za 174 SER cc_start: 0.7951 (OUTLIER) cc_final: 0.7508 (t) REVERT: za 197 HIS cc_start: 0.5115 (OUTLIER) cc_final: 0.3274 (p90) REVERT: za 208 TYR cc_start: 0.8196 (OUTLIER) cc_final: 0.7338 (p90) REVERT: za 209 ARG cc_start: 0.6970 (mmm160) cc_final: 0.6605 (mmm-85) REVERT: bb 26 LYS cc_start: 0.7113 (OUTLIER) cc_final: 0.6842 (mtmt) REVERT: bb 28 GLN cc_start: 0.7497 (OUTLIER) cc_final: 0.7274 (mm110) REVERT: bb 50 ARG cc_start: 0.6276 (mtt180) cc_final: 0.5810 (mtt90) REVERT: bb 111 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7771 (mmp80) REVERT: bb 152 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6849 (tmt-80) REVERT: bb 189 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7995 (mt) REVERT: bb 198 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7506 (tm-30) REVERT: bb 205 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8232 (m-80) REVERT: cb 63 ASP cc_start: 0.6350 (t70) cc_final: 0.5907 (t0) REVERT: cb 71 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8561 (mp) REVERT: db 19 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8109 (mtpm) REVERT: db 45 VAL cc_start: 0.7826 (OUTLIER) cc_final: 0.7564 (t) REVERT: eb 46 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7515 (ptp-170) REVERT: eb 70 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7562 (ttm170) REVERT: eb 152 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8724 (t) REVERT: gb 46 GLU cc_start: 0.3221 (OUTLIER) cc_final: 0.2545 (mm-30) REVERT: gb 56 CYS cc_start: 0.7075 (p) cc_final: 0.6793 (p) REVERT: hb 37 LEU cc_start: 0.4115 (OUTLIER) cc_final: 0.3752 (pt) REVERT: hb 38 LYS cc_start: 0.3639 (mmtt) cc_final: 0.3221 (mmtt) REVERT: hb 68 ARG cc_start: 0.6102 (mmm160) cc_final: 0.5491 (mmm160) REVERT: hb 112 GLN cc_start: 0.2130 (OUTLIER) cc_final: 0.1829 (tt0) REVERT: hb 170 PHE cc_start: 0.6956 (m-10) cc_final: 0.6158 (m-10) REVERT: hb 176 ARG cc_start: 0.6120 (ttm-80) cc_final: 0.5845 (ttm-80) REVERT: ib 14 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8334 (tptt) REVERT: ib 37 LYS cc_start: 0.8286 (ptmt) cc_final: 0.7923 (pttt) REVERT: ib 96 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8070 (tmmm) REVERT: IB 9 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.7710 (ttm170) REVERT: IB 20 MET cc_start: 0.4786 (OUTLIER) cc_final: 0.4560 (mpt) outliers start: 311 outliers final: 170 residues processed: 1010 average time/residue: 1.4800 time to fit residues: 1984.0343 Evaluate side-chains 1000 residues out of total 3778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 772 time to evaluate : 4.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain ba residue 19 THR Chi-restraints excluded: chain ba residue 32 VAL Chi-restraints excluded: chain ba residue 68 THR Chi-restraints excluded: chain ca residue 3 ILE Chi-restraints excluded: chain ca residue 18 GLN Chi-restraints excluded: chain ca residue 44 VAL Chi-restraints excluded: chain ca residue 73 VAL Chi-restraints excluded: chain ca residue 83 VAL Chi-restraints excluded: chain ca residue 89 ASN Chi-restraints excluded: chain ca residue 94 THR Chi-restraints excluded: chain ca residue 105 VAL Chi-restraints excluded: chain ca residue 159 GLN Chi-restraints excluded: chain ca residue 169 ARG Chi-restraints excluded: chain da residue 10 GLU Chi-restraints excluded: chain da residue 57 GLU Chi-restraints excluded: chain ga residue 35 GLU Chi-restraints excluded: chain ga residue 72 GLN Chi-restraints excluded: chain ga residue 90 LEU Chi-restraints excluded: chain ga residue 118 ARG Chi-restraints excluded: chain ga residue 128 SER Chi-restraints excluded: chain ha residue 9 VAL Chi-restraints excluded: chain ha residue 20 VAL Chi-restraints excluded: chain ha residue 28 ILE Chi-restraints excluded: chain ha residue 50 ASN Chi-restraints excluded: chain ha residue 102 LEU Chi-restraints excluded: chain ha residue 103 SER Chi-restraints excluded: chain ha residue 107 THR Chi-restraints excluded: chain ha residue 120 SER Chi-restraints excluded: chain ha residue 126 ASP Chi-restraints excluded: chain ha residue 132 SER Chi-restraints excluded: chain ha residue 141 LEU Chi-restraints excluded: chain ha residue 143 ASN Chi-restraints excluded: chain ha residue 160 GLU Chi-restraints excluded: chain ha residue 189 VAL Chi-restraints excluded: chain ha residue 231 THR Chi-restraints excluded: chain ha residue 253 SER Chi-restraints excluded: chain ha residue 300 THR Chi-restraints excluded: chain ha residue 302 LEU Chi-restraints excluded: chain ha residue 303 SER Chi-restraints excluded: chain ha residue 305 SER Chi-restraints excluded: chain ia residue 5 ILE Chi-restraints excluded: chain ia residue 42 THR Chi-restraints excluded: chain ia residue 58 VAL Chi-restraints excluded: chain ia residue 84 VAL Chi-restraints excluded: chain ia residue 89 GLU Chi-restraints excluded: chain ia residue 91 VAL Chi-restraints excluded: chain ia residue 101 GLN Chi-restraints excluded: chain ia residue 127 MET Chi-restraints excluded: chain ia residue 179 GLN Chi-restraints excluded: chain ia residue 185 LYS Chi-restraints excluded: chain ia residue 202 THR Chi-restraints excluded: chain ia residue 207 LEU Chi-restraints excluded: chain ja residue 33 SER Chi-restraints excluded: chain ja residue 40 GLU Chi-restraints excluded: chain ja residue 57 THR Chi-restraints excluded: chain ja residue 71 MET Chi-restraints excluded: chain ja residue 115 ARG Chi-restraints excluded: chain ja residue 143 ASP Chi-restraints excluded: chain ja residue 163 ASP Chi-restraints excluded: chain ja residue 189 THR Chi-restraints excluded: chain ja residue 207 THR Chi-restraints excluded: chain ja residue 237 SER Chi-restraints excluded: chain ja residue 246 LEU Chi-restraints excluded: chain ka residue 19 THR Chi-restraints excluded: chain ka residue 36 VAL Chi-restraints excluded: chain ka residue 38 SER Chi-restraints excluded: chain ka residue 45 LEU Chi-restraints excluded: chain ka residue 74 MET Chi-restraints excluded: chain ka residue 92 THR Chi-restraints excluded: chain ka residue 98 LEU Chi-restraints excluded: chain ka residue 131 ARG Chi-restraints excluded: chain ka residue 132 ARG Chi-restraints excluded: chain ka residue 136 ASP Chi-restraints excluded: chain ka residue 156 GLU Chi-restraints excluded: chain ka residue 180 SER Chi-restraints excluded: chain la residue 23 VAL Chi-restraints excluded: chain la residue 32 ARG Chi-restraints excluded: chain la residue 49 MET Chi-restraints excluded: chain la residue 69 ILE Chi-restraints excluded: chain la residue 76 ARG Chi-restraints excluded: chain la residue 100 GLN Chi-restraints excluded: chain la residue 121 THR Chi-restraints excluded: chain la residue 123 LEU Chi-restraints excluded: chain la residue 138 ARG Chi-restraints excluded: chain ma residue 30 ILE Chi-restraints excluded: chain ma residue 31 THR Chi-restraints excluded: chain ma residue 52 LYS Chi-restraints excluded: chain ma residue 68 VAL Chi-restraints excluded: chain ma residue 73 THR Chi-restraints excluded: chain na residue 27 VAL Chi-restraints excluded: chain na residue 40 THR Chi-restraints excluded: chain na residue 47 LEU Chi-restraints excluded: chain na residue 54 VAL Chi-restraints excluded: chain na residue 56 ILE Chi-restraints excluded: chain na residue 57 THR Chi-restraints excluded: chain na residue 81 VAL Chi-restraints excluded: chain na residue 85 CYS Chi-restraints excluded: chain na residue 88 LEU Chi-restraints excluded: chain na residue 91 THR Chi-restraints excluded: chain na residue 107 THR Chi-restraints excluded: chain na residue 119 LEU Chi-restraints excluded: chain oa residue 100 SER Chi-restraints excluded: chain oa residue 104 ASP Chi-restraints excluded: chain oa residue 105 MET Chi-restraints excluded: chain oa residue 108 ARG Chi-restraints excluded: chain oa residue 112 GLU Chi-restraints excluded: chain oa residue 113 ARG Chi-restraints excluded: chain oa residue 136 THR Chi-restraints excluded: chain oa residue 139 THR Chi-restraints excluded: chain pa residue 34 ASP Chi-restraints excluded: chain pa residue 80 LEU Chi-restraints excluded: chain pa residue 87 ASP Chi-restraints excluded: chain pa residue 138 THR Chi-restraints excluded: chain qa residue 8 THR Chi-restraints excluded: chain qa residue 16 VAL Chi-restraints excluded: chain qa residue 24 MET Chi-restraints excluded: chain qa residue 25 THR Chi-restraints excluded: chain qa residue 40 ILE Chi-restraints excluded: chain qa residue 43 SER Chi-restraints excluded: chain qa residue 54 THR Chi-restraints excluded: chain qa residue 56 HIS Chi-restraints excluded: chain qa residue 66 VAL Chi-restraints excluded: chain qa residue 114 LEU Chi-restraints excluded: chain ra residue 32 SER Chi-restraints excluded: chain ra residue 57 GLU Chi-restraints excluded: chain ra residue 90 LYS Chi-restraints excluded: chain sa residue 43 VAL Chi-restraints excluded: chain sa residue 85 VAL Chi-restraints excluded: chain sa residue 127 GLU Chi-restraints excluded: chain ta residue 33 GLN Chi-restraints excluded: chain ta residue 61 ILE Chi-restraints excluded: chain ta residue 69 ARG Chi-restraints excluded: chain ta residue 93 VAL Chi-restraints excluded: chain ua residue 27 LYS Chi-restraints excluded: chain ua residue 45 THR Chi-restraints excluded: chain ua residue 67 VAL Chi-restraints excluded: chain ua residue 68 ARG Chi-restraints excluded: chain ua residue 81 GLU Chi-restraints excluded: chain va residue 3 ARG Chi-restraints excluded: chain va residue 8 ASP Chi-restraints excluded: chain va residue 17 GLU Chi-restraints excluded: chain va residue 23 THR Chi-restraints excluded: chain va residue 57 VAL Chi-restraints excluded: chain va residue 81 ARG Chi-restraints excluded: chain va residue 83 THR Chi-restraints excluded: chain va residue 86 GLU Chi-restraints excluded: chain va residue 89 ARG Chi-restraints excluded: chain va residue 117 ARG Chi-restraints excluded: chain wa residue 27 SER Chi-restraints excluded: chain xa residue 45 ILE Chi-restraints excluded: chain xa residue 54 THR Chi-restraints excluded: chain xa residue 65 LEU Chi-restraints excluded: chain xa residue 77 GLU Chi-restraints excluded: chain ya residue 8 LEU Chi-restraints excluded: chain za residue 23 LEU Chi-restraints excluded: chain za residue 29 LEU Chi-restraints excluded: chain za residue 40 ARG Chi-restraints excluded: chain za residue 68 VAL Chi-restraints excluded: chain za residue 118 THR Chi-restraints excluded: chain za residue 140 GLU Chi-restraints excluded: chain za residue 141 SER Chi-restraints excluded: chain za residue 162 ASP Chi-restraints excluded: chain za residue 174 SER Chi-restraints excluded: chain za residue 197 HIS Chi-restraints excluded: chain za residue 208 TYR Chi-restraints excluded: chain bb residue 26 LYS Chi-restraints excluded: chain bb residue 28 GLN Chi-restraints excluded: chain bb residue 37 LEU Chi-restraints excluded: chain bb residue 47 LEU Chi-restraints excluded: chain bb residue 108 ASP Chi-restraints excluded: chain bb residue 111 ARG Chi-restraints excluded: chain bb residue 120 LEU Chi-restraints excluded: chain bb residue 122 GLU Chi-restraints excluded: chain bb residue 128 LYS Chi-restraints excluded: chain bb residue 129 THR Chi-restraints excluded: chain bb residue 148 ASN Chi-restraints excluded: chain bb residue 152 ARG Chi-restraints excluded: chain bb residue 172 MET Chi-restraints excluded: chain bb residue 189 ILE Chi-restraints excluded: chain bb residue 201 THR Chi-restraints excluded: chain bb residue 205 PHE Chi-restraints excluded: chain cb residue 36 ILE Chi-restraints excluded: chain cb residue 67 SER Chi-restraints excluded: chain cb residue 71 LEU Chi-restraints excluded: chain db residue 19 LYS Chi-restraints excluded: chain db residue 24 SER Chi-restraints excluded: chain db residue 45 VAL Chi-restraints excluded: chain db residue 76 SER Chi-restraints excluded: chain eb residue 23 LYS Chi-restraints excluded: chain eb residue 46 ARG Chi-restraints excluded: chain eb residue 52 SER Chi-restraints excluded: chain eb residue 63 THR Chi-restraints excluded: chain eb residue 70 ARG Chi-restraints excluded: chain eb residue 113 THR Chi-restraints excluded: chain eb residue 143 VAL Chi-restraints excluded: chain eb residue 152 VAL Chi-restraints excluded: chain eb residue 163 THR Chi-restraints excluded: chain fb residue 133 THR Chi-restraints excluded: chain fb residue 149 VAL Chi-restraints excluded: chain fb residue 189 VAL Chi-restraints excluded: chain fb residue 213 SER Chi-restraints excluded: chain fb residue 229 MET Chi-restraints excluded: chain fb residue 238 ASP Chi-restraints excluded: chain gb residue 46 GLU Chi-restraints excluded: chain gb residue 67 VAL Chi-restraints excluded: chain gb residue 68 LEU Chi-restraints excluded: chain gb residue 82 SER Chi-restraints excluded: chain gb residue 91 VAL Chi-restraints excluded: chain gb residue 115 ILE Chi-restraints excluded: chain gb residue 205 LYS Chi-restraints excluded: chain hb residue 21 ASP Chi-restraints excluded: chain hb residue 37 LEU Chi-restraints excluded: chain hb residue 84 LEU Chi-restraints excluded: chain hb residue 112 GLN Chi-restraints excluded: chain hb residue 116 THR Chi-restraints excluded: chain hb residue 130 VAL Chi-restraints excluded: chain hb residue 137 VAL Chi-restraints excluded: chain hb residue 155 LEU Chi-restraints excluded: chain hb residue 182 VAL Chi-restraints excluded: chain ib residue 14 LYS Chi-restraints excluded: chain ib residue 19 THR Chi-restraints excluded: chain ib residue 21 LYS Chi-restraints excluded: chain ib residue 75 THR Chi-restraints excluded: chain ib residue 87 VAL Chi-restraints excluded: chain ib residue 96 LYS Chi-restraints excluded: chain ib residue 122 ASP Chi-restraints excluded: chain IB residue 9 ARG Chi-restraints excluded: chain IB residue 20 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 358 optimal weight: 3.9990 chunk 231 optimal weight: 8.9990 chunk 346 optimal weight: 9.9990 chunk 174 optimal weight: 3.9990 chunk 114 optimal weight: 20.0000 chunk 112 optimal weight: 20.0000 chunk 368 optimal weight: 8.9990 chunk 395 optimal weight: 7.9990 chunk 286 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 456 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** ba 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ca 216 GLN ga 91 ASN ha 18 ASN ha 174 ASN ia 211 HIS ja 188 ASN ka 16 ASN ma 39 ASN oa 19 ASN oa 120 HIS ra 81 GLN ** ra 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** sa 113 GLN ** ta 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** va 48 ASN va 65 GLN za 76 GLN ** za 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** za 101 ASN za 173 ASN db 94 ASN eb 68 ASN ** eb 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** eb 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** eb 178 ASN fb 199 GLN gb 190 GLN ** hb 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ib 99 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 78029 Z= 0.457 Angle : 0.836 13.489 113871 Z= 0.435 Chirality : 0.048 0.408 14101 Planarity : 0.007 0.124 7899 Dihedral : 23.704 179.684 32383 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.00 % Favored : 91.91 % Rotamer: Outliers : 9.66 % Allowed : 31.18 % Favored : 59.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.12), residues: 4325 helix: -0.24 (0.14), residues: 1336 sheet: -0.77 (0.17), residues: 844 loop : -1.51 (0.13), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRPib 36 HIS 0.011 0.002 HISoa 120 PHE 0.037 0.002 PHEoa 28 TYR 0.026 0.003 TYRha 261 ARG 0.013 0.001 ARGra 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8650 Ramachandran restraints generated. 4325 Oldfield, 0 Emsley, 4325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8650 Ramachandran restraints generated. 4325 Oldfield, 0 Emsley, 4325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1152 residues out of total 3778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 365 poor density : 787 time to evaluate : 4.196 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: ca 18 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7741 (tt0) REVERT: ca 159 GLN cc_start: 0.5898 (OUTLIER) cc_final: 0.5344 (pt0) REVERT: ca 169 ARG cc_start: 0.5421 (OUTLIER) cc_final: 0.3794 (mtp-110) REVERT: da 10 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: da 49 PHE cc_start: 0.8432 (m-10) cc_final: 0.8173 (m-10) REVERT: da 57 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6491 (tp30) REVERT: da 71 ASP cc_start: 0.7486 (t70) cc_final: 0.7238 (t0) REVERT: ga 53 LYS cc_start: 0.8396 (mtmt) cc_final: 0.8130 (mtmm) REVERT: ga 118 ARG cc_start: 0.9181 (OUTLIER) cc_final: 0.7812 (ptm160) REVERT: ha 102 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8233 (mt) REVERT: ha 160 GLU cc_start: 0.5855 (OUTLIER) cc_final: 0.4819 (pm20) REVERT: ha 262 TRP cc_start: 0.6327 (OUTLIER) cc_final: 0.5564 (m-10) REVERT: ha 322 ILE cc_start: 0.7471 (pp) cc_final: 0.7172 (mp) REVERT: ia 68 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7743 (mt-10) REVERT: ia 89 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.5923 (mp0) REVERT: ia 101 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7677 (mp10) REVERT: ia 127 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.6398 (tpt) REVERT: ia 185 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7987 (mtmt) REVERT: ja 40 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7586 (pp20) REVERT: ja 205 PHE cc_start: 0.7942 (p90) cc_final: 0.7463 (p90) REVERT: ja 240 LYS cc_start: 0.6161 (OUTLIER) cc_final: 0.5770 (mttt) REVERT: ka 98 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7568 (tm) REVERT: ka 132 ARG cc_start: 0.5864 (OUTLIER) cc_final: 0.4769 (ptp90) REVERT: ka 156 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7283 (mt-10) REVERT: la 12 THR cc_start: 0.8300 (t) cc_final: 0.8032 (m) REVERT: la 76 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.7065 (ttt90) REVERT: la 100 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7480 (tp40) REVERT: la 123 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8253 (mt) REVERT: la 138 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8314 (ptp90) REVERT: ma 27 ARG cc_start: 0.6154 (OUTLIER) cc_final: 0.5830 (mmt90) REVERT: ma 52 LYS cc_start: 0.6771 (OUTLIER) cc_final: 0.6336 (mptm) REVERT: na 47 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8421 (mm) REVERT: na 56 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8480 (mm) REVERT: na 128 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7054 (mtt-85) REVERT: oa 108 ARG cc_start: 0.6449 (OUTLIER) cc_final: 0.5912 (tmt170) REVERT: oa 112 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6481 (mp0) REVERT: oa 113 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7199 (ttm110) REVERT: oa 130 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7031 (mmt-90) REVERT: pa 60 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8390 (mm) REVERT: pa 71 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8114 (mt) REVERT: qa 24 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7594 (mpt) REVERT: qa 56 HIS cc_start: 0.7294 (OUTLIER) cc_final: 0.6728 (p-80) REVERT: qa 97 ARG cc_start: 0.7138 (ptt180) cc_final: 0.6868 (mtm180) REVERT: ra 54 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8552 (ttm170) REVERT: ra 90 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8055 (mttp) REVERT: ta 69 ARG cc_start: 0.3750 (OUTLIER) cc_final: 0.2181 (mtp180) REVERT: ua 27 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.8018 (mmtm) REVERT: ua 68 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7665 (ptt180) REVERT: ua 69 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7201 (mt-10) REVERT: ua 80 ARG cc_start: 0.7244 (mtp-110) cc_final: 0.6765 (ptm160) REVERT: ua 81 GLU cc_start: 0.6634 (OUTLIER) cc_final: 0.6063 (pp20) REVERT: va 76 TYR cc_start: 0.6529 (OUTLIER) cc_final: 0.5611 (t80) REVERT: va 78 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8300 (mm110) REVERT: va 86 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7694 (tm-30) REVERT: va 88 TYR cc_start: 0.7924 (OUTLIER) cc_final: 0.6873 (m-80) REVERT: va 117 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7928 (ttp-170) REVERT: xa 45 ILE cc_start: 0.6686 (OUTLIER) cc_final: 0.6329 (tt) REVERT: za 15 LYS cc_start: 0.8461 (tptm) cc_final: 0.7956 (ttpp) REVERT: za 16 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7889 (mt-10) REVERT: za 88 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7223 (mp10) REVERT: za 174 SER cc_start: 0.8043 (OUTLIER) cc_final: 0.7605 (t) REVERT: za 197 HIS cc_start: 0.5251 (OUTLIER) cc_final: 0.3427 (p90) REVERT: za 208 TYR cc_start: 0.8268 (OUTLIER) cc_final: 0.7403 (p90) REVERT: za 209 ARG cc_start: 0.7023 (OUTLIER) cc_final: 0.6607 (mmm-85) REVERT: bb 24 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7362 (t80) REVERT: bb 26 LYS cc_start: 0.7219 (OUTLIER) cc_final: 0.6947 (mtmt) REVERT: bb 28 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.7172 (mm110) REVERT: bb 50 ARG cc_start: 0.6276 (mtt180) cc_final: 0.5815 (mtt90) REVERT: bb 111 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7925 (mmp80) REVERT: bb 152 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.6874 (tmt-80) REVERT: bb 189 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8061 (mt) REVERT: cb 63 ASP cc_start: 0.6383 (t70) cc_final: 0.5876 (t0) REVERT: cb 71 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8606 (mp) REVERT: eb 46 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.7869 (ptp-170) REVERT: eb 70 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.8013 (ttm170) REVERT: fb 211 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7797 (ttt90) REVERT: gb 46 GLU cc_start: 0.3337 (OUTLIER) cc_final: 0.2808 (mm-30) REVERT: gb 56 CYS cc_start: 0.7382 (OUTLIER) cc_final: 0.6988 (p) REVERT: gb 91 VAL cc_start: 0.8424 (OUTLIER) cc_final: 0.8197 (t) REVERT: hb 37 LEU cc_start: 0.4204 (OUTLIER) cc_final: 0.3812 (pt) REVERT: hb 38 LYS cc_start: 0.3824 (mmtt) cc_final: 0.3473 (mmtt) REVERT: hb 73 PHE cc_start: 0.6974 (OUTLIER) cc_final: 0.6521 (m-80) REVERT: hb 76 ILE cc_start: 0.6136 (OUTLIER) cc_final: 0.5747 (tt) REVERT: hb 112 GLN cc_start: 0.2216 (OUTLIER) cc_final: 0.1910 (tt0) REVERT: hb 115 ARG cc_start: 0.4852 (OUTLIER) cc_final: 0.4546 (tpp-160) REVERT: hb 176 ARG cc_start: 0.6024 (ttm-80) cc_final: 0.5749 (ttm-80) REVERT: ib 14 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8338 (tptt) REVERT: ib 96 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8207 (tmmm) REVERT: IB 9 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.7378 (ttt180) REVERT: IB 20 MET cc_start: 0.4838 (OUTLIER) cc_final: 0.4611 (mpt) outliers start: 365 outliers final: 208 residues processed: 1030 average time/residue: 1.5024 time to fit residues: 2054.3363 Evaluate side-chains 1039 residues out of total 3778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 757 time to evaluate : 4.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain ba residue 19 THR Chi-restraints excluded: chain ba residue 32 VAL Chi-restraints excluded: chain ba residue 68 THR Chi-restraints excluded: chain ba residue 108 LYS Chi-restraints excluded: chain ca residue 3 ILE Chi-restraints excluded: chain ca residue 18 GLN Chi-restraints excluded: chain ca residue 43 THR Chi-restraints excluded: chain ca residue 44 VAL Chi-restraints excluded: chain ca residue 73 VAL Chi-restraints excluded: chain ca residue 83 VAL Chi-restraints excluded: chain ca residue 89 ASN Chi-restraints excluded: chain ca residue 94 THR Chi-restraints excluded: chain ca residue 105 VAL Chi-restraints excluded: chain ca residue 159 GLN Chi-restraints excluded: chain ca residue 167 GLN Chi-restraints excluded: chain ca residue 169 ARG Chi-restraints excluded: chain da residue 10 GLU Chi-restraints excluded: chain da residue 57 GLU Chi-restraints excluded: chain ga residue 35 GLU Chi-restraints excluded: chain ga residue 90 LEU Chi-restraints excluded: chain ga residue 118 ARG Chi-restraints excluded: chain ga residue 128 SER Chi-restraints excluded: chain ha residue 9 VAL Chi-restraints excluded: chain ha residue 20 VAL Chi-restraints excluded: chain ha residue 28 ILE Chi-restraints excluded: chain ha residue 50 ASN Chi-restraints excluded: chain ha residue 55 THR Chi-restraints excluded: chain ha residue 70 THR Chi-restraints excluded: chain ha residue 102 LEU Chi-restraints excluded: chain ha residue 107 THR Chi-restraints excluded: chain ha residue 120 SER Chi-restraints excluded: chain ha residue 126 ASP Chi-restraints excluded: chain ha residue 132 SER Chi-restraints excluded: chain ha residue 141 LEU Chi-restraints excluded: chain ha residue 151 THR Chi-restraints excluded: chain ha residue 160 GLU Chi-restraints excluded: chain ha residue 189 VAL Chi-restraints excluded: chain ha residue 231 THR Chi-restraints excluded: chain ha residue 253 SER Chi-restraints excluded: chain ha residue 262 TRP Chi-restraints excluded: chain ha residue 282 VAL Chi-restraints excluded: chain ha residue 294 LYS Chi-restraints excluded: chain ha residue 300 THR Chi-restraints excluded: chain ha residue 302 LEU Chi-restraints excluded: chain ha residue 303 SER Chi-restraints excluded: chain ha residue 305 SER Chi-restraints excluded: chain ia residue 5 ILE Chi-restraints excluded: chain ia residue 37 VAL Chi-restraints excluded: chain ia residue 42 THR Chi-restraints excluded: chain ia residue 58 VAL Chi-restraints excluded: chain ia residue 84 VAL Chi-restraints excluded: chain ia residue 89 GLU Chi-restraints excluded: chain ia residue 91 VAL Chi-restraints excluded: chain ia residue 101 GLN Chi-restraints excluded: chain ia residue 127 MET Chi-restraints excluded: chain ia residue 179 GLN Chi-restraints excluded: chain ia residue 185 LYS Chi-restraints excluded: chain ia residue 202 THR Chi-restraints excluded: chain ia residue 207 LEU Chi-restraints excluded: chain ja residue 33 SER Chi-restraints excluded: chain ja residue 40 GLU Chi-restraints excluded: chain ja residue 57 THR Chi-restraints excluded: chain ja residue 59 ARG Chi-restraints excluded: chain ja residue 71 MET Chi-restraints excluded: chain ja residue 115 ARG Chi-restraints excluded: chain ja residue 124 CYS Chi-restraints excluded: chain ja residue 163 ASP Chi-restraints excluded: chain ja residue 189 THR Chi-restraints excluded: chain ja residue 192 VAL Chi-restraints excluded: chain ja residue 204 THR Chi-restraints excluded: chain ja residue 207 THR Chi-restraints excluded: chain ja residue 237 SER Chi-restraints excluded: chain ja residue 240 LYS Chi-restraints excluded: chain ja residue 246 LEU Chi-restraints excluded: chain ka residue 19 THR Chi-restraints excluded: chain ka residue 36 VAL Chi-restraints excluded: chain ka residue 38 SER Chi-restraints excluded: chain ka residue 45 LEU Chi-restraints excluded: chain ka residue 69 THR Chi-restraints excluded: chain ka residue 74 MET Chi-restraints excluded: chain ka residue 92 THR Chi-restraints excluded: chain ka residue 98 LEU Chi-restraints excluded: chain ka residue 119 GLU Chi-restraints excluded: chain ka residue 132 ARG Chi-restraints excluded: chain ka residue 136 ASP Chi-restraints excluded: chain ka residue 156 GLU Chi-restraints excluded: chain ka residue 180 SER Chi-restraints excluded: chain la residue 21 THR Chi-restraints excluded: chain la residue 23 VAL Chi-restraints excluded: chain la residue 32 ARG Chi-restraints excluded: chain la residue 49 MET Chi-restraints excluded: chain la residue 69 ILE Chi-restraints excluded: chain la residue 76 ARG Chi-restraints excluded: chain la residue 100 GLN Chi-restraints excluded: chain la residue 121 THR Chi-restraints excluded: chain la residue 123 LEU Chi-restraints excluded: chain la residue 138 ARG Chi-restraints excluded: chain ma residue 27 ARG Chi-restraints excluded: chain ma residue 30 ILE Chi-restraints excluded: chain ma residue 31 THR Chi-restraints excluded: chain ma residue 52 LYS Chi-restraints excluded: chain ma residue 73 THR Chi-restraints excluded: chain ma residue 86 ASP Chi-restraints excluded: chain na residue 27 VAL Chi-restraints excluded: chain na residue 40 THR Chi-restraints excluded: chain na residue 47 LEU Chi-restraints excluded: chain na residue 54 VAL Chi-restraints excluded: chain na residue 56 ILE Chi-restraints excluded: chain na residue 57 THR Chi-restraints excluded: chain na residue 81 VAL Chi-restraints excluded: chain na residue 85 CYS Chi-restraints excluded: chain na residue 88 LEU Chi-restraints excluded: chain na residue 91 THR Chi-restraints excluded: chain na residue 107 THR Chi-restraints excluded: chain na residue 119 LEU Chi-restraints excluded: chain na residue 128 ARG Chi-restraints excluded: chain na residue 135 VAL Chi-restraints excluded: chain oa residue 16 LEU Chi-restraints excluded: chain oa residue 32 SER Chi-restraints excluded: chain oa residue 100 SER Chi-restraints excluded: chain oa residue 104 ASP Chi-restraints excluded: chain oa residue 108 ARG Chi-restraints excluded: chain oa residue 112 GLU Chi-restraints excluded: chain oa residue 113 ARG Chi-restraints excluded: chain oa residue 114 LEU Chi-restraints excluded: chain oa residue 130 ARG Chi-restraints excluded: chain oa residue 136 THR Chi-restraints excluded: chain oa residue 139 THR Chi-restraints excluded: chain pa residue 34 ASP Chi-restraints excluded: chain pa residue 60 ILE Chi-restraints excluded: chain pa residue 71 ILE Chi-restraints excluded: chain pa residue 80 LEU Chi-restraints excluded: chain pa residue 87 ASP Chi-restraints excluded: chain pa residue 138 THR Chi-restraints excluded: chain qa residue 8 THR Chi-restraints excluded: chain qa residue 16 VAL Chi-restraints excluded: chain qa residue 24 MET Chi-restraints excluded: chain qa residue 25 THR Chi-restraints excluded: chain qa residue 40 ILE Chi-restraints excluded: chain qa residue 43 SER Chi-restraints excluded: chain qa residue 54 THR Chi-restraints excluded: chain qa residue 56 HIS Chi-restraints excluded: chain qa residue 66 VAL Chi-restraints excluded: chain qa residue 82 MET Chi-restraints excluded: chain qa residue 109 LEU Chi-restraints excluded: chain qa residue 114 LEU Chi-restraints excluded: chain ra residue 32 SER Chi-restraints excluded: chain ra residue 47 VAL Chi-restraints excluded: chain ra residue 54 ARG Chi-restraints excluded: chain ra residue 57 GLU Chi-restraints excluded: chain ra residue 77 ILE Chi-restraints excluded: chain ra residue 90 LYS Chi-restraints excluded: chain sa residue 43 VAL Chi-restraints excluded: chain sa residue 85 VAL Chi-restraints excluded: chain sa residue 127 GLU Chi-restraints excluded: chain ta residue 33 GLN Chi-restraints excluded: chain ta residue 61 ILE Chi-restraints excluded: chain ta residue 62 THR Chi-restraints excluded: chain ta residue 69 ARG Chi-restraints excluded: chain ta residue 93 VAL Chi-restraints excluded: chain ta residue 97 SER Chi-restraints excluded: chain ua residue 27 LYS Chi-restraints excluded: chain ua residue 45 THR Chi-restraints excluded: chain ua residue 67 VAL Chi-restraints excluded: chain ua residue 68 ARG Chi-restraints excluded: chain ua residue 81 GLU Chi-restraints excluded: chain va residue 3 ARG Chi-restraints excluded: chain va residue 8 ASP Chi-restraints excluded: chain va residue 17 GLU Chi-restraints excluded: chain va residue 23 THR Chi-restraints excluded: chain va residue 42 HIS Chi-restraints excluded: chain va residue 48 ASN Chi-restraints excluded: chain va residue 57 VAL Chi-restraints excluded: chain va residue 76 TYR Chi-restraints excluded: chain va residue 78 GLN Chi-restraints excluded: chain va residue 81 ARG Chi-restraints excluded: chain va residue 83 THR Chi-restraints excluded: chain va residue 86 GLU Chi-restraints excluded: chain va residue 88 TYR Chi-restraints excluded: chain va residue 116 ILE Chi-restraints excluded: chain va residue 117 ARG Chi-restraints excluded: chain wa residue 20 VAL Chi-restraints excluded: chain wa residue 27 SER Chi-restraints excluded: chain xa residue 45 ILE Chi-restraints excluded: chain xa residue 54 THR Chi-restraints excluded: chain xa residue 56 VAL Chi-restraints excluded: chain xa residue 65 LEU Chi-restraints excluded: chain xa residue 77 GLU Chi-restraints excluded: chain ya residue 8 LEU Chi-restraints excluded: chain ya residue 38 ILE Chi-restraints excluded: chain za residue 23 LEU Chi-restraints excluded: chain za residue 29 LEU Chi-restraints excluded: chain za residue 40 ARG Chi-restraints excluded: chain za residue 48 ASP Chi-restraints excluded: chain za residue 68 VAL Chi-restraints excluded: chain za residue 88 GLN Chi-restraints excluded: chain za residue 118 THR Chi-restraints excluded: chain za residue 140 GLU Chi-restraints excluded: chain za residue 141 SER Chi-restraints excluded: chain za residue 162 ASP Chi-restraints excluded: chain za residue 174 SER Chi-restraints excluded: chain za residue 181 LEU Chi-restraints excluded: chain za residue 192 THR Chi-restraints excluded: chain za residue 197 HIS Chi-restraints excluded: chain za residue 208 TYR Chi-restraints excluded: chain za residue 209 ARG Chi-restraints excluded: chain bb residue 24 PHE Chi-restraints excluded: chain bb residue 26 LYS Chi-restraints excluded: chain bb residue 28 GLN Chi-restraints excluded: chain bb residue 37 LEU Chi-restraints excluded: chain bb residue 47 LEU Chi-restraints excluded: chain bb residue 98 THR Chi-restraints excluded: chain bb residue 108 ASP Chi-restraints excluded: chain bb residue 111 ARG Chi-restraints excluded: chain bb residue 120 LEU Chi-restraints excluded: chain bb residue 122 GLU Chi-restraints excluded: chain bb residue 128 LYS Chi-restraints excluded: chain bb residue 129 THR Chi-restraints excluded: chain bb residue 148 ASN Chi-restraints excluded: chain bb residue 152 ARG Chi-restraints excluded: chain bb residue 161 ILE Chi-restraints excluded: chain bb residue 172 MET Chi-restraints excluded: chain bb residue 179 CYS Chi-restraints excluded: chain bb residue 189 ILE Chi-restraints excluded: chain bb residue 201 THR Chi-restraints excluded: chain bb residue 205 PHE Chi-restraints excluded: chain cb residue 36 ILE Chi-restraints excluded: chain cb residue 67 SER Chi-restraints excluded: chain cb residue 71 LEU Chi-restraints excluded: chain db residue 19 LYS Chi-restraints excluded: chain db residue 24 SER Chi-restraints excluded: chain db residue 41 VAL Chi-restraints excluded: chain db residue 76 SER Chi-restraints excluded: chain eb residue 23 LYS Chi-restraints excluded: chain eb residue 46 ARG Chi-restraints excluded: chain eb residue 63 THR Chi-restraints excluded: chain eb residue 70 ARG Chi-restraints excluded: chain eb residue 102 THR Chi-restraints excluded: chain eb residue 113 THR Chi-restraints excluded: chain eb residue 143 VAL Chi-restraints excluded: chain eb residue 150 VAL Chi-restraints excluded: chain eb residue 152 VAL Chi-restraints excluded: chain eb residue 158 ILE Chi-restraints excluded: chain fb residue 51 LEU Chi-restraints excluded: chain fb residue 133 THR Chi-restraints excluded: chain fb residue 149 VAL Chi-restraints excluded: chain fb residue 186 SER Chi-restraints excluded: chain fb residue 211 ARG Chi-restraints excluded: chain fb residue 213 SER Chi-restraints excluded: chain fb residue 229 MET Chi-restraints excluded: chain fb residue 238 ASP Chi-restraints excluded: chain gb residue 4 ASN Chi-restraints excluded: chain gb residue 46 GLU Chi-restraints excluded: chain gb residue 52 ILE Chi-restraints excluded: chain gb residue 56 CYS Chi-restraints excluded: chain gb residue 67 VAL Chi-restraints excluded: chain gb residue 68 LEU Chi-restraints excluded: chain gb residue 82 SER Chi-restraints excluded: chain gb residue 91 VAL Chi-restraints excluded: chain gb residue 115 ILE Chi-restraints excluded: chain gb residue 205 LYS Chi-restraints excluded: chain hb residue 21 ASP Chi-restraints excluded: chain hb residue 37 LEU Chi-restraints excluded: chain hb residue 73 PHE Chi-restraints excluded: chain hb residue 76 ILE Chi-restraints excluded: chain hb residue 84 LEU Chi-restraints excluded: chain hb residue 112 GLN Chi-restraints excluded: chain hb residue 115 ARG Chi-restraints excluded: chain hb residue 118 THR Chi-restraints excluded: chain hb residue 130 VAL Chi-restraints excluded: chain hb residue 137 VAL Chi-restraints excluded: chain hb residue 155 LEU Chi-restraints excluded: chain hb residue 182 VAL Chi-restraints excluded: chain ib residue 14 LYS Chi-restraints excluded: chain ib residue 19 THR Chi-restraints excluded: chain ib residue 21 LYS Chi-restraints excluded: chain ib residue 75 THR Chi-restraints excluded: chain ib residue 87 VAL Chi-restraints excluded: chain ib residue 96 LYS Chi-restraints excluded: chain ib residue 122 ASP Chi-restraints excluded: chain IB residue 9 ARG Chi-restraints excluded: chain IB residue 20 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.1477 > 50: distance: 61 - 63: 12.751 distance: 63 - 64: 10.791 distance: 64 - 65: 22.945 distance: 64 - 67: 9.274 distance: 65 - 66: 6.773 distance: 65 - 75: 3.223 distance: 67 - 68: 9.574 distance: 68 - 69: 9.854 distance: 68 - 70: 16.792 distance: 69 - 71: 9.442 distance: 70 - 72: 13.399 distance: 71 - 73: 11.063 distance: 72 - 73: 8.132 distance: 73 - 74: 9.012 distance: 75 - 76: 17.846 distance: 76 - 77: 4.645 distance: 76 - 79: 28.711 distance: 77 - 78: 41.108 distance: 77 - 89: 17.712 distance: 79 - 80: 11.821 distance: 80 - 81: 20.551 distance: 80 - 82: 10.065 distance: 81 - 83: 7.394 distance: 82 - 84: 15.708 distance: 82 - 85: 15.508 distance: 83 - 84: 11.256 distance: 84 - 86: 14.479 distance: 85 - 87: 8.408 distance: 86 - 88: 14.056 distance: 87 - 88: 18.091 distance: 90 - 91: 15.734 distance: 91 - 92: 38.814 distance: 91 - 93: 11.262 distance: 93 - 94: 10.101 distance: 94 - 95: 17.726 distance: 94 - 97: 22.221 distance: 95 - 96: 26.389 distance: 95 - 101: 20.444 distance: 97 - 98: 7.482 distance: 98 - 99: 4.984 distance: 98 - 100: 26.754 distance: 101 - 102: 13.098 distance: 102 - 103: 6.510 distance: 102 - 105: 11.923 distance: 103 - 104: 13.321 distance: 103 - 110: 5.811 distance: 105 - 106: 20.205 distance: 106 - 107: 9.334 distance: 107 - 108: 16.429 distance: 108 - 109: 17.449 distance: 110 - 111: 8.099 distance: 111 - 112: 6.235 distance: 111 - 114: 12.680 distance: 112 - 113: 15.315 distance: 112 - 118: 14.417 distance: 114 - 115: 8.892 distance: 114 - 116: 8.419 distance: 115 - 117: 12.317 distance: 118 - 119: 15.036 distance: 119 - 120: 10.023 distance: 120 - 121: 16.394 distance: 120 - 122: 12.834 distance: 122 - 123: 18.060 distance: 123 - 124: 9.223 distance: 123 - 126: 16.250 distance: 124 - 125: 8.237 distance: 124 - 130: 16.048 distance: 126 - 127: 8.978 distance: 127 - 128: 8.719 distance: 127 - 129: 19.128 distance: 130 - 131: 14.561 distance: 130 - 136: 11.796 distance: 131 - 132: 4.886 distance: 131 - 134: 3.519 distance: 132 - 133: 7.522 distance: 132 - 137: 9.315 distance: 134 - 135: 15.294 distance: 135 - 136: 12.685 distance: 137 - 138: 14.828 distance: 138 - 139: 5.203 distance: 138 - 141: 12.824 distance: 139 - 140: 11.531 distance: 139 - 147: 5.556 distance: 141 - 142: 7.900 distance: 142 - 143: 13.362 distance: 142 - 144: 17.621 distance: 143 - 145: 3.232 distance: 145 - 146: 15.198