Starting phenix.real_space_refine on Sat Mar 16 13:16:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7br7_30158/03_2024/7br7_30158.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7br7_30158/03_2024/7br7_30158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7br7_30158/03_2024/7br7_30158.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7br7_30158/03_2024/7br7_30158.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7br7_30158/03_2024/7br7_30158.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7br7_30158/03_2024/7br7_30158.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.007 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: 4 Type Number sf(0) Gaussians S 401 5.16 5 C 46550 2.51 5 N 12724 2.21 5 O 13463 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K GLU 21": "OE1" <-> "OE2" Residue "K ARG 29": "NH1" <-> "NH2" Residue "K ARG 33": "NH1" <-> "NH2" Residue "K GLU 40": "OE1" <-> "OE2" Residue "K GLU 45": "OE1" <-> "OE2" Residue "K GLU 47": "OE1" <-> "OE2" Residue "K ARG 48": "NH1" <-> "NH2" Residue "K ARG 50": "NH1" <-> "NH2" Residue "K ARG 64": "NH1" <-> "NH2" Residue "K GLU 69": "OE1" <-> "OE2" Residue "K ARG 75": "NH1" <-> "NH2" Residue "K GLU 82": "OE1" <-> "OE2" Residue "K ARG 85": "NH1" <-> "NH2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "G GLU 43": "OE1" <-> "OE2" Residue "G ARG 44": "NH1" <-> "NH2" Residue "G GLU 45": "OE1" <-> "OE2" Residue "G ARG 50": "NH1" <-> "NH2" Residue "G ARG 64": "NH1" <-> "NH2" Residue "G GLU 69": "OE1" <-> "OE2" Residue "C ARG 35": "NH1" <-> "NH2" Residue "C ARG 51": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C GLU 111": "OE1" <-> "OE2" Residue "C ARG 125": "NH1" <-> "NH2" Residue "C GLU 304": "OE1" <-> "OE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C ARG 348": "NH1" <-> "NH2" Residue "C ARG 354": "NH1" <-> "NH2" Residue "C GLU 429": "OE1" <-> "OE2" Residue "C ARG 494": "NH1" <-> "NH2" Residue "B ARG 3128": "NH1" <-> "NH2" Residue "B ARG 3132": "NH1" <-> "NH2" Residue "O ARG 3132": "NH1" <-> "NH2" Residue "m ARG 4": "NH1" <-> "NH2" Residue "m GLU 42": "OE1" <-> "OE2" Residue "m ARG 45": "NH1" <-> "NH2" Residue "m ARG 63": "NH1" <-> "NH2" Residue "Y ARG 3": "NH1" <-> "NH2" Residue "Y GLU 42": "OE1" <-> "OE2" Residue "Y ARG 45": "NH1" <-> "NH2" Residue "Y GLU 58": "OE1" <-> "OE2" Residue "Y ARG 63": "NH1" <-> "NH2" Residue "Y ARG 70": "NH1" <-> "NH2" Residue "Z ARG 3": "NH1" <-> "NH2" Residue "Z GLU 15": "OE1" <-> "OE2" Residue "Z GLU 29": "OE1" <-> "OE2" Residue "Z ARG 45": "NH1" <-> "NH2" Residue "Z GLU 58": "OE1" <-> "OE2" Residue "Z ARG 63": "NH1" <-> "NH2" Residue "Z ARG 70": "NH1" <-> "NH2" Residue "Z ARG 72": "NH1" <-> "NH2" Residue "2 ARG 3": "NH1" <-> "NH2" Residue "2 GLU 29": "OE1" <-> "OE2" Residue "2 GLU 42": "OE1" <-> "OE2" Residue "2 ARG 45": "NH1" <-> "NH2" Residue "2 GLU 58": "OE1" <-> "OE2" Residue "2 ARG 63": "NH1" <-> "NH2" Residue "2 ARG 69": "NH1" <-> "NH2" Residue "2 ARG 70": "NH1" <-> "NH2" Residue "S ARG 10": "NH1" <-> "NH2" Residue "S ARG 26": "NH1" <-> "NH2" Residue "S ARG 46": "NH1" <-> "NH2" Residue "S GLU 53": "OE1" <-> "OE2" Residue "S ARG 67": "NH1" <-> "NH2" Residue "S ARG 87": "NH1" <-> "NH2" Residue "S ARG 96": "NH1" <-> "NH2" Residue "S ARG 109": "NH1" <-> "NH2" Residue "S GLU 132": "OE1" <-> "OE2" Residue "S GLU 146": "OE1" <-> "OE2" Residue "S GLU 173": "OE1" <-> "OE2" Residue "S GLU 234": "OE1" <-> "OE2" Residue "S GLU 258": "OE1" <-> "OE2" Residue "S ARG 326": "NH1" <-> "NH2" Residue "S ARG 481": "NH1" <-> "NH2" Residue "S ARG 483": "NH1" <-> "NH2" Residue "S ARG 493": "NH1" <-> "NH2" Residue "S ARG 552": "NH1" <-> "NH2" Residue "S ARG 557": "NH1" <-> "NH2" Residue "S ARG 559": "NH1" <-> "NH2" Residue "S GLU 582": "OE1" <-> "OE2" Residue "S GLU 589": "OE1" <-> "OE2" Residue "S ARG 650": "NH1" <-> "NH2" Residue "S GLU 689": "OE1" <-> "OE2" Residue "S GLU 709": "OE1" <-> "OE2" Residue "S ARG 742": "NH1" <-> "NH2" Residue "S GLU 764": "OE1" <-> "OE2" Residue "S GLU 802": "OE1" <-> "OE2" Residue "S ARG 852": "NH1" <-> "NH2" Residue "S GLU 854": "OE1" <-> "OE2" Residue "S GLU 861": "OE1" <-> "OE2" Residue "S ARG 866": "NH1" <-> "NH2" Residue "S ARG 875": "NH1" <-> "NH2" Residue "S ARG 882": "NH1" <-> "NH2" Residue "S ARG 896": "NH1" <-> "NH2" Residue "S ARG 936": "NH1" <-> "NH2" Residue "S ARG 938": "NH1" <-> "NH2" Residue "S ARG 958": "NH1" <-> "NH2" Residue "S GLU 981": "OE1" <-> "OE2" Residue "S GLU 987": "OE1" <-> "OE2" Residue "S GLU 995": "OE1" <-> "OE2" Residue "S GLU 1051": "OE1" <-> "OE2" Residue "S GLU 1213": "OE1" <-> "OE2" Residue "S GLU 1218": "OE1" <-> "OE2" Residue "S ARG 1272": "NH1" <-> "NH2" Residue "S GLU 1278": "OE1" <-> "OE2" Residue "S ARG 1297": "NH1" <-> "NH2" Residue "S ARG 1370": "NH1" <-> "NH2" Residue "T ARG 114": "NH1" <-> "NH2" Residue "T GLU 130": "OE1" <-> "OE2" Residue "T ARG 314": "NH1" <-> "NH2" Residue "T ARG 364": "NH1" <-> "NH2" Residue "T ARG 484": "NH1" <-> "NH2" Residue "T ARG 492": "NH1" <-> "NH2" Residue "T GLU 527": "OE1" <-> "OE2" Residue "T GLU 556": "OE1" <-> "OE2" Residue "T ARG 559": "NH1" <-> "NH2" Residue "T GLU 589": "OE1" <-> "OE2" Residue "T GLU 623": "OE1" <-> "OE2" Residue "T GLU 630": "OE1" <-> "OE2" Residue "T GLU 649": "OE1" <-> "OE2" Residue "T ARG 650": "NH1" <-> "NH2" Residue "T GLU 751": "OE1" <-> "OE2" Residue "T GLU 764": "OE1" <-> "OE2" Residue "T ARG 852": "NH1" <-> "NH2" Residue "T GLU 854": "OE1" <-> "OE2" Residue "T GLU 861": "OE1" <-> "OE2" Residue "T ARG 866": "NH1" <-> "NH2" Residue "T ARG 882": "NH1" <-> "NH2" Residue "T PHE 894": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 896": "NH1" <-> "NH2" Residue "T ARG 899": "NH1" <-> "NH2" Residue "T ARG 936": "NH1" <-> "NH2" Residue "T ARG 958": "NH1" <-> "NH2" Residue "T ARG 973": "NH1" <-> "NH2" Residue "T GLU 1007": "OE1" <-> "OE2" Residue "T GLU 1051": "OE1" <-> "OE2" Residue "T ARG 1077": "NH1" <-> "NH2" Residue "T GLU 1218": "OE1" <-> "OE2" Residue "T ARG 1260": "NH1" <-> "NH2" Residue "T ARG 1272": "NH1" <-> "NH2" Residue "T ARG 1297": "NH1" <-> "NH2" Residue "T ARG 1370": "NH1" <-> "NH2" Residue "W ARG 87": "NH1" <-> "NH2" Residue "W ARG 96": "NH1" <-> "NH2" Residue "W ARG 114": "NH1" <-> "NH2" Residue "W GLU 139": "OE1" <-> "OE2" Residue "W GLU 146": "OE1" <-> "OE2" Residue "W GLU 150": "OE1" <-> "OE2" Residue "W GLU 153": "OE1" <-> "OE2" Residue "W GLU 173": "OE1" <-> "OE2" Residue "W ARG 205": "NH1" <-> "NH2" Residue "W ARG 329": "NH1" <-> "NH2" Residue "W ARG 364": "NH1" <-> "NH2" Residue "W PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 481": "NH1" <-> "NH2" Residue "W ARG 483": "NH1" <-> "NH2" Residue "W ARG 557": "NH1" <-> "NH2" Residue "W GLU 631": "OE1" <-> "OE2" Residue "W GLU 649": "OE1" <-> "OE2" Residue "W ARG 650": "NH1" <-> "NH2" Residue "W ARG 653": "NH1" <-> "NH2" Residue "W GLU 678": "OE1" <-> "OE2" Residue "W GLU 689": "OE1" <-> "OE2" Residue "W ARG 783": "NH1" <-> "NH2" Residue "W ARG 852": "NH1" <-> "NH2" Residue "W GLU 861": "OE1" <-> "OE2" Residue "W ARG 866": "NH1" <-> "NH2" Residue "W ARG 882": "NH1" <-> "NH2" Residue "W ARG 899": "NH1" <-> "NH2" Residue "W ARG 918": "NH1" <-> "NH2" Residue "W ARG 936": "NH1" <-> "NH2" Residue "W ARG 938": "NH1" <-> "NH2" Residue "W GLU 992": "OE1" <-> "OE2" Residue "W ARG 1109": "NH1" <-> "NH2" Residue "W ARG 1260": "NH1" <-> "NH2" Residue "W ARG 1272": "NH1" <-> "NH2" Residue "W ARG 1370": "NH1" <-> "NH2" Residue "x ARG 67": "NH1" <-> "NH2" Residue "x ARG 96": "NH1" <-> "NH2" Residue "x ARG 108": "NH1" <-> "NH2" Residue "x ARG 109": "NH1" <-> "NH2" Residue "x ARG 114": "NH1" <-> "NH2" Residue "x GLU 130": "OE1" <-> "OE2" Residue "x ARG 186": "NH1" <-> "NH2" Residue "x ARG 205": "NH1" <-> "NH2" Residue "x GLU 234": "OE1" <-> "OE2" Residue "x ARG 326": "NH1" <-> "NH2" Residue "x ARG 329": "NH1" <-> "NH2" Residue "x GLU 437": "OE1" <-> "OE2" Residue "x ARG 463": "NH1" <-> "NH2" Residue "x ARG 481": "NH1" <-> "NH2" Residue "x ARG 483": "NH1" <-> "NH2" Residue "x ARG 484": "NH1" <-> "NH2" Residue "x GLU 505": "OE1" <-> "OE2" Residue "x TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 552": "NH1" <-> "NH2" Residue "x ARG 557": "NH1" <-> "NH2" Residue "x ARG 559": "NH1" <-> "NH2" Residue "x GLU 589": "OE1" <-> "OE2" Residue "x GLU 604": "OE1" <-> "OE2" Residue "x GLU 630": "OE1" <-> "OE2" Residue "x GLU 649": "OE1" <-> "OE2" Residue "x ARG 653": "NH1" <-> "NH2" Residue "x GLU 689": "OE1" <-> "OE2" Residue "x GLU 751": "OE1" <-> "OE2" Residue "x GLU 771": "OE1" <-> "OE2" Residue "x ARG 852": "NH1" <-> "NH2" Residue "x GLU 854": "OE1" <-> "OE2" Residue "x ARG 882": "NH1" <-> "NH2" Residue "x GLU 935": "OE1" <-> "OE2" Residue "x ARG 936": "NH1" <-> "NH2" Residue "x ARG 938": "NH1" <-> "NH2" Residue "x ARG 958": "NH1" <-> "NH2" Residue "x GLU 1051": "OE1" <-> "OE2" Residue "x ARG 1077": "NH1" <-> "NH2" Residue "x ARG 1080": "NH1" <-> "NH2" Residue "x GLU 1087": "OE1" <-> "OE2" Residue "x GLU 1183": "OE1" <-> "OE2" Residue "x TYR 1234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 1272": "NH1" <-> "NH2" Residue "x GLU 1278": "OE1" <-> "OE2" Residue "x TYR 1294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 1308": "OE1" <-> "OE2" Residue "x GLU 1330": "OE1" <-> "OE2" Residue "x ARG 1370": "NH1" <-> "NH2" Residue "y ARG 3": "NH1" <-> "NH2" Residue "y ARG 45": "NH1" <-> "NH2" Residue "y GLU 58": "OE1" <-> "OE2" Residue "y GLU 59": "OE1" <-> "OE2" Residue "y ARG 63": "NH1" <-> "NH2" Residue "y ARG 70": "NH1" <-> "NH2" Residue "e ARG 10": "NH1" <-> "NH2" Residue "e ARG 11": "NH1" <-> "NH2" Residue "e ARG 15": "NH1" <-> "NH2" Residue "e ARG 139": "NH1" <-> "NH2" Residue "e GLU 193": "OE1" <-> "OE2" Residue "e ARG 276": "NH1" <-> "NH2" Residue "e PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 12": "NH1" <-> "NH2" Residue "f GLU 52": "OE1" <-> "OE2" Residue "f GLU 74": "OE1" <-> "OE2" Residue "f ARG 118": "NH1" <-> "NH2" Residue "f GLU 126": "OE1" <-> "OE2" Residue "f ASP 129": "OD1" <-> "OD2" Residue "f GLU 144": "OE1" <-> "OE2" Residue "f ARG 158": "NH1" <-> "NH2" Residue "f ARG 225": "NH1" <-> "NH2" Residue "f ARG 265": "NH1" <-> "NH2" Residue "f GLU 292": "OE1" <-> "OE2" Residue "f ARG 301": "NH1" <-> "NH2" Residue "g GLU 74": "OE1" <-> "OE2" Residue "g ARG 118": "NH1" <-> "NH2" Residue "g GLU 119": "OE1" <-> "OE2" Residue "g ARG 158": "NH1" <-> "NH2" Residue "g ARG 218": "NH1" <-> "NH2" Residue "g ARG 225": "NH1" <-> "NH2" Residue "g ARG 229": "NH1" <-> "NH2" Residue "g GLU 231": "OE1" <-> "OE2" Residue "g GLU 246": "OE1" <-> "OE2" Residue "g ARG 249": "NH1" <-> "NH2" Residue "g ARG 265": "NH1" <-> "NH2" Residue "g ARG 283": "NH1" <-> "NH2" Residue "g GLU 292": "OE1" <-> "OE2" Residue "l ARG 46": "NH1" <-> "NH2" Residue "l GLU 70": "OE1" <-> "OE2" Residue "l ARG 87": "NH1" <-> "NH2" Residue "l ARG 96": "NH1" <-> "NH2" Residue "l ARG 108": "NH1" <-> "NH2" Residue "l ARG 109": "NH1" <-> "NH2" Residue "l GLU 150": "OE1" <-> "OE2" Residue "l GLU 204": "OE1" <-> "OE2" Residue "l ARG 205": "NH1" <-> "NH2" Residue "l ARG 221": "NH1" <-> "NH2" Residue "l ARG 288": "NH1" <-> "NH2" Residue "l GLU 296": "OE1" <-> "OE2" Residue "l ARG 329": "NH1" <-> "NH2" Residue "l ARG 364": "NH1" <-> "NH2" Residue "l ARG 481": "NH1" <-> "NH2" Residue "l ARG 483": "NH1" <-> "NH2" Residue "l ARG 484": "NH1" <-> "NH2" Residue "l ARG 539": "NH1" <-> "NH2" Residue "l ARG 552": "NH1" <-> "NH2" Residue "l ARG 557": "NH1" <-> "NH2" Residue "l ARG 559": "NH1" <-> "NH2" Residue "l GLU 589": "OE1" <-> "OE2" Residue "l GLU 604": "OE1" <-> "OE2" Residue "l ARG 653": "NH1" <-> "NH2" Residue "l GLU 694": "OE1" <-> "OE2" Residue "l GLU 709": "OE1" <-> "OE2" Residue "l GLU 771": "OE1" <-> "OE2" Residue "l GLU 809": "OE1" <-> "OE2" Residue "l ARG 852": "NH1" <-> "NH2" Residue "l GLU 861": "OE1" <-> "OE2" Residue "l ARG 882": "NH1" <-> "NH2" Residue "l GLU 920": "OE1" <-> "OE2" Residue "l ARG 936": "NH1" <-> "NH2" Residue "l ARG 938": "NH1" <-> "NH2" Residue "l ARG 958": "NH1" <-> "NH2" Residue "l GLU 981": "OE1" <-> "OE2" Residue "l ARG 985": "NH1" <-> "NH2" Residue "l ARG 998": "NH1" <-> "NH2" Residue "l ARG 1048": "NH1" <-> "NH2" Residue "l ARG 1076": "NH1" <-> "NH2" Residue "l GLU 1078": "OE1" <-> "OE2" Residue "l GLU 1087": "OE1" <-> "OE2" Residue "l ARG 1109": "NH1" <-> "NH2" Residue "l GLU 1183": "OE1" <-> "OE2" Residue "l ARG 1203": "NH1" <-> "NH2" Residue "l GLU 1213": "OE1" <-> "OE2" Residue "l GLU 1218": "OE1" <-> "OE2" Residue "l GLU 1221": "OE1" <-> "OE2" Residue "l ARG 1282": "NH1" <-> "NH2" Residue "l GLU 1293": "OE1" <-> "OE2" Residue "l ARG 1297": "NH1" <-> "NH2" Residue "l GLU 1322": "OE1" <-> "OE2" Residue "5 ARG 10": "NH1" <-> "NH2" Residue "5 ARG 11": "NH1" <-> "NH2" Residue "5 ARG 25": "NH1" <-> "NH2" Residue "5 ARG 40": "NH1" <-> "NH2" Residue "5 GLU 44": "OE1" <-> "OE2" Residue "5 ARG 86": "NH1" <-> "NH2" Residue "5 GLU 104": "OE1" <-> "OE2" Residue "5 PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 139": "NH1" <-> "NH2" Residue "5 ARG 153": "NH1" <-> "NH2" Residue "5 GLU 193": "OE1" <-> "OE2" Residue "5 ARG 218": "NH1" <-> "NH2" Residue "5 ARG 276": "NH1" <-> "NH2" Residue "5 ARG 284": "NH1" <-> "NH2" Residue "5 ARG 304": "NH1" <-> "NH2" Residue "5 GLU 361": "OE1" <-> "OE2" Residue "6 ARG 12": "NH1" <-> "NH2" Residue "6 ARG 24": "NH1" <-> "NH2" Residue "6 GLU 52": "OE1" <-> "OE2" Residue "6 ARG 118": "NH1" <-> "NH2" Residue "6 GLU 126": "OE1" <-> "OE2" Residue "6 GLU 187": "OE1" <-> "OE2" Residue "6 ARG 265": "NH1" <-> "NH2" Residue "6 ARG 301": "NH1" <-> "NH2" Residue "7 ARG 158": "NH1" <-> "NH2" Residue "7 GLU 187": "OE1" <-> "OE2" Residue "7 ARG 218": "NH1" <-> "NH2" Residue "7 ARG 222": "NH1" <-> "NH2" Residue "7 ARG 225": "NH1" <-> "NH2" Residue "7 ARG 229": "NH1" <-> "NH2" Residue "7 GLU 246": "OE1" <-> "OE2" Residue "7 ARG 265": "NH1" <-> "NH2" Residue "7 ARG 283": "NH1" <-> "NH2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 73138 Number of models: 1 Model: "" Number of chains: 21 Chain: "K" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 563 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "G" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 675 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 78} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2705 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 21, 'TRANS': 324} Chain breaks: 5 Chain: "B" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 301 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain: "O" Number of atoms: 252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 252 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "m" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 600 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 7, 'TRANS': 63} Chain: "Y" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 621 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 7, 'TRANS': 66} Chain: "Z" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 621 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 7, 'TRANS': 66} Chain: "2" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 621 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 7, 'TRANS': 66} Chain: "S" Number of atoms: 10455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1327, 10455 Classifications: {'peptide': 1327} Link IDs: {'PTRANS': 68, 'TRANS': 1258} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "T" Number of atoms: 10257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1305, 10257 Classifications: {'peptide': 1305} Link IDs: {'PTRANS': 68, 'TRANS': 1236} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "W" Number of atoms: 10463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1331, 10463 Classifications: {'peptide': 1331} Link IDs: {'PTRANS': 68, 'TRANS': 1262} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "x" Number of atoms: 10404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1325, 10404 Classifications: {'peptide': 1325} Link IDs: {'PTRANS': 68, 'TRANS': 1256} Chain breaks: 1 Chain: "y" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 621 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 7, 'TRANS': 66} Chain: "e" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2505 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 22, 'TRANS': 296} Chain breaks: 3 Chain: "f" Number of atoms: 2279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2279 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 15, 'TRANS': 274} Chain breaks: 1 Chain: "g" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2272 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 16, 'TRANS': 273} Chain breaks: 3 Chain: "l" Number of atoms: 9872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1250, 9872 Classifications: {'peptide': 1250} Link IDs: {'PTRANS': 64, 'TRANS': 1185} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "5" Number of atoms: 2460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2460 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 20, 'TRANS': 292} Chain breaks: 3 Chain: "6" Number of atoms: 2329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2329 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 16, 'TRANS': 280} Chain breaks: 1 Chain: "7" Number of atoms: 2262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2262 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 13, 'TRANS': 273} Chain breaks: 2 Time building chain proxies: 27.34, per 1000 atoms: 0.37 Number of scatterers: 73138 At special positions: 0 Unit cell: (212.22, 203.05, 212.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 401 16.00 O 13463 8.00 N 12724 7.00 C 46550 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: 20.85 Conformation dependent library (CDL) restraints added in 9.6 seconds 18310 Ramachandran restraints generated. 9155 Oldfield, 0 Emsley, 9155 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17570 Finding SS restraints... Secondary structure from input PDB file: 372 helices and 91 sheets defined 41.6% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.30 Creating SS restraints... Processing helix chain 'K' and resid 39 through 87 removed outlier: 3.990A pdb=" N ARG K 44 " --> pdb=" O GLU K 40 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU K 52 " --> pdb=" O ARG K 48 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP K 71 " --> pdb=" O ARG K 67 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY K 72 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE K 73 " --> pdb=" O GLU K 69 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU K 82 " --> pdb=" O LEU K 78 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLU K 83 " --> pdb=" O ALA K 79 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE K 84 " --> pdb=" O ARG K 80 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG K 85 " --> pdb=" O ALA K 81 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN K 86 " --> pdb=" O GLU K 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 55 removed outlier: 4.041A pdb=" N ASP G 55 " --> pdb=" O SER G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 88 removed outlier: 3.760A pdb=" N HIS G 77 " --> pdb=" O ILE G 73 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU G 78 " --> pdb=" O MET G 74 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU G 83 " --> pdb=" O ALA G 79 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE G 84 " --> pdb=" O ARG G 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 25 through 29 Processing helix chain 'C' and resid 32 through 36 removed outlier: 4.063A pdb=" N ARG C 35 " --> pdb=" O CYS C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 126 removed outlier: 4.009A pdb=" N GLY C 122 " --> pdb=" O SER C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 278 removed outlier: 4.021A pdb=" N ILE C 278 " --> pdb=" O THR C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 Processing helix chain 'C' and resid 311 through 314 Processing helix chain 'C' and resid 335 through 360 removed outlier: 3.714A pdb=" N PHE C 339 " --> pdb=" O PRO C 335 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG C 340 " --> pdb=" O GLU C 336 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN C 360 " --> pdb=" O LYS C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 380 Processing helix chain 'C' and resid 385 through 395 removed outlier: 5.152A pdb=" N THR C 392 " --> pdb=" O GLU C 388 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N VAL C 393 " --> pdb=" O ALA C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 Processing helix chain 'C' and resid 444 through 458 Processing helix chain 'C' and resid 490 through 502 removed outlier: 3.531A pdb=" N ARG C 494 " --> pdb=" O THR C 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 3119 through 3134 removed outlier: 3.885A pdb=" N GLN B3125 " --> pdb=" O ARG B3121 " (cutoff:3.500A) Processing helix chain 'B' and resid 3134 through 3149 removed outlier: 3.856A pdb=" N ILE B3138 " --> pdb=" O THR B3134 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU B3141 " --> pdb=" O LEU B3137 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU B3142 " --> pdb=" O ILE B3138 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG B3143 " --> pdb=" O ALA B3139 " (cutoff:3.500A) Processing helix chain 'O' and resid 3122 through 3149 removed outlier: 4.324A pdb=" N LEU O3126 " --> pdb=" O PHE O3122 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG O3127 " --> pdb=" O VAL O3123 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ARG O3128 " --> pdb=" O SER O3124 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA O3139 " --> pdb=" O HIS O3135 " (cutoff:3.500A) Processing helix chain 'm' and resid 23 through 28 Processing helix chain 'm' and resid 36 through 64 Processing helix chain 'Y' and resid 13 through 18 Processing helix chain 'Y' and resid 23 through 28 removed outlier: 3.810A pdb=" N GLN Y 28 " --> pdb=" O LEU Y 24 " (cutoff:3.500A) Processing helix chain 'Y' and resid 38 through 66 Processing helix chain 'Z' and resid 13 through 18 removed outlier: 3.847A pdb=" N ASP Z 17 " --> pdb=" O ARG Z 13 " (cutoff:3.500A) Processing helix chain 'Z' and resid 36 through 64 removed outlier: 3.657A pdb=" N ARG Z 63 " --> pdb=" O GLU Z 59 " (cutoff:3.500A) Processing helix chain 'Z' and resid 70 through 74 removed outlier: 3.577A pdb=" N ALA Z 73 " --> pdb=" O ARG Z 70 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE Z 74 " --> pdb=" O GLN Z 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 70 through 74' Processing helix chain '2' and resid 36 through 64 removed outlier: 4.279A pdb=" N GLU 2 42 " --> pdb=" O ASP 2 38 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR 2 47 " --> pdb=" O ALA 2 43 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL 2 49 " --> pdb=" O ARG 2 45 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE 2 50 " --> pdb=" O SER 2 46 " (cutoff:3.500A) Processing helix chain '2' and resid 70 through 74 Processing helix chain 'S' and resid 25 through 30 Processing helix chain 'S' and resid 71 through 75 removed outlier: 3.776A pdb=" N ALA S 74 " --> pdb=" O THR S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 135 through 143 removed outlier: 3.577A pdb=" N SER S 143 " --> pdb=" O GLU S 139 " (cutoff:3.500A) Processing helix chain 'S' and resid 147 through 185 removed outlier: 3.876A pdb=" N ILE S 177 " --> pdb=" O GLU S 173 " (cutoff:3.500A) Processing helix chain 'S' and resid 190 through 198 removed outlier: 5.340A pdb=" N THR S 196 " --> pdb=" O PHE S 192 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA S 198 " --> pdb=" O LEU S 194 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 226 removed outlier: 3.925A pdb=" N LYS S 212 " --> pdb=" O SER S 208 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA S 217 " --> pdb=" O SER S 213 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU S 224 " --> pdb=" O LYS S 220 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU S 225 " --> pdb=" O ARG S 221 " (cutoff:3.500A) Processing helix chain 'S' and resid 228 through 235 removed outlier: 3.713A pdb=" N ASN S 235 " --> pdb=" O ASP S 231 " (cutoff:3.500A) Processing helix chain 'S' and resid 240 through 256 Processing helix chain 'S' and resid 283 through 294 removed outlier: 3.554A pdb=" N THR S 292 " --> pdb=" O ARG S 288 " (cutoff:3.500A) Processing helix chain 'S' and resid 310 through 315 removed outlier: 3.907A pdb=" N ARG S 314 " --> pdb=" O SER S 310 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY S 315 " --> pdb=" O PHE S 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 310 through 315' Processing helix chain 'S' and resid 315 through 320 removed outlier: 3.873A pdb=" N VAL S 319 " --> pdb=" O GLY S 315 " (cutoff:3.500A) Processing helix chain 'S' and resid 321 through 323 No H-bonds generated for 'chain 'S' and resid 321 through 323' Processing helix chain 'S' and resid 326 through 341 Processing helix chain 'S' and resid 384 through 390 removed outlier: 3.845A pdb=" N ASP S 390 " --> pdb=" O LYS S 386 " (cutoff:3.500A) Processing helix chain 'S' and resid 451 through 460 removed outlier: 3.821A pdb=" N ALA S 455 " --> pdb=" O ASN S 451 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LYS S 457 " --> pdb=" O GLN S 453 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N VAL S 458 " --> pdb=" O ASN S 454 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS S 460 " --> pdb=" O LEU S 456 " (cutoff:3.500A) Processing helix chain 'S' and resid 461 through 466 removed outlier: 3.649A pdb=" N HIS S 465 " --> pdb=" O HIS S 461 " (cutoff:3.500A) Processing helix chain 'S' and resid 467 through 476 Processing helix chain 'S' and resid 498 through 506 removed outlier: 3.761A pdb=" N ILE S 502 " --> pdb=" O ASN S 498 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE S 506 " --> pdb=" O ILE S 502 " (cutoff:3.500A) Processing helix chain 'S' and resid 516 through 521 Processing helix chain 'S' and resid 525 through 530 removed outlier: 3.876A pdb=" N LEU S 530 " --> pdb=" O THR S 526 " (cutoff:3.500A) Processing helix chain 'S' and resid 531 through 533 No H-bonds generated for 'chain 'S' and resid 531 through 533' Processing helix chain 'S' and resid 534 through 539 Processing helix chain 'S' and resid 567 through 571 Processing helix chain 'S' and resid 577 through 593 Processing helix chain 'S' and resid 599 through 611 removed outlier: 3.611A pdb=" N ILE S 603 " --> pdb=" O ASP S 599 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR S 609 " --> pdb=" O THR S 605 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA S 610 " --> pdb=" O VAL S 606 " (cutoff:3.500A) Processing helix chain 'S' and resid 616 through 626 removed outlier: 4.026A pdb=" N TYR S 620 " --> pdb=" O PRO S 616 " (cutoff:3.500A) Processing helix chain 'S' and resid 629 through 634 Processing helix chain 'S' and resid 636 through 652 removed outlier: 3.566A pdb=" N ASN S 645 " --> pdb=" O SER S 641 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG S 650 " --> pdb=" O THR S 646 " (cutoff:3.500A) Processing helix chain 'S' and resid 659 through 670 removed outlier: 3.584A pdb=" N ILE S 663 " --> pdb=" O SER S 659 " (cutoff:3.500A) Processing helix chain 'S' and resid 676 through 702 removed outlier: 3.865A pdb=" N TYR S 683 " --> pdb=" O ALA S 679 " (cutoff:3.500A) Processing helix chain 'S' and resid 711 through 716 removed outlier: 3.591A pdb=" N CYS S 716 " --> pdb=" O GLY S 712 " (cutoff:3.500A) Processing helix chain 'S' and resid 733 through 740 Processing helix chain 'S' and resid 758 through 763 Processing helix chain 'S' and resid 772 through 774 No H-bonds generated for 'chain 'S' and resid 772 through 774' Processing helix chain 'S' and resid 775 through 785 Processing helix chain 'S' and resid 806 through 815 Processing helix chain 'S' and resid 816 through 821 Processing helix chain 'S' and resid 831 through 839 Processing helix chain 'S' and resid 855 through 860 removed outlier: 3.742A pdb=" N ASP S 858 " --> pdb=" O ASP S 855 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU S 860 " --> pdb=" O LEU S 857 " (cutoff:3.500A) Processing helix chain 'S' and resid 864 through 873 removed outlier: 3.714A pdb=" N ILE S 871 " --> pdb=" O ASP S 867 " (cutoff:3.500A) Processing helix chain 'S' and resid 877 through 886 removed outlier: 3.654A pdb=" N ILE S 881 " --> pdb=" O THR S 877 " (cutoff:3.500A) Processing helix chain 'S' and resid 905 through 909 removed outlier: 3.925A pdb=" N GLN S 909 " --> pdb=" O VAL S 906 " (cutoff:3.500A) Processing helix chain 'S' and resid 934 through 942 removed outlier: 3.687A pdb=" N VAL S 940 " --> pdb=" O ARG S 936 " (cutoff:3.500A) Processing helix chain 'S' and resid 956 through 961 Processing helix chain 'S' and resid 964 through 969 Processing helix chain 'S' and resid 969 through 974 removed outlier: 3.744A pdb=" N ARG S 973 " --> pdb=" O THR S 969 " (cutoff:3.500A) Processing helix chain 'S' and resid 975 through 979 removed outlier: 3.588A pdb=" N ARG S 978 " --> pdb=" O PRO S 975 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA S 979 " --> pdb=" O GLN S 976 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 975 through 979' Processing helix chain 'S' and resid 998 through 1008 Processing helix chain 'S' and resid 1011 through 1021 Processing helix chain 'S' and resid 1026 through 1035 Processing helix chain 'S' and resid 1123 through 1128 Processing helix chain 'S' and resid 1135 through 1146 Processing helix chain 'S' and resid 1193 through 1198 removed outlier: 4.188A pdb=" N LYS S1198 " --> pdb=" O ALA S1194 " (cutoff:3.500A) Processing helix chain 'S' and resid 1216 through 1225 removed outlier: 3.637A pdb=" N ALA S1220 " --> pdb=" O ASN S1216 " (cutoff:3.500A) Processing helix chain 'S' and resid 1249 through 1254 Processing helix chain 'S' and resid 1271 through 1276 removed outlier: 3.745A pdb=" N ASN S1276 " --> pdb=" O ARG S1272 " (cutoff:3.500A) Processing helix chain 'S' and resid 1276 through 1283 Processing helix chain 'S' and resid 1286 through 1291 Processing helix chain 'S' and resid 1323 through 1329 Processing helix chain 'S' and resid 1339 through 1347 removed outlier: 3.723A pdb=" N ILE S1343 " --> pdb=" O SER S1339 " (cutoff:3.500A) Processing helix chain 'T' and resid 71 through 75 removed outlier: 3.844A pdb=" N ALA T 74 " --> pdb=" O THR T 71 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 86 No H-bonds generated for 'chain 'T' and resid 84 through 86' Processing helix chain 'T' and resid 135 through 140 removed outlier: 4.211A pdb=" N ILE T 140 " --> pdb=" O LEU T 136 " (cutoff:3.500A) Processing helix chain 'T' and resid 147 through 187 removed outlier: 3.572A pdb=" N ILE T 177 " --> pdb=" O GLU T 173 " (cutoff:3.500A) Processing helix chain 'T' and resid 190 through 198 removed outlier: 4.060A pdb=" N THR T 196 " --> pdb=" O PHE T 192 " (cutoff:3.500A) Processing helix chain 'T' and resid 199 through 203 Processing helix chain 'T' and resid 210 through 225 removed outlier: 4.619A pdb=" N ILE T 216 " --> pdb=" O LYS T 212 " (cutoff:3.500A) Processing helix chain 'T' and resid 230 through 236 removed outlier: 3.955A pdb=" N ASN T 235 " --> pdb=" O ARG T 232 " (cutoff:3.500A) Processing helix chain 'T' and resid 239 through 255 removed outlier: 3.688A pdb=" N GLU T 250 " --> pdb=" O SER T 246 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA T 253 " --> pdb=" O SER T 249 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL T 255 " --> pdb=" O MET T 251 " (cutoff:3.500A) Processing helix chain 'T' and resid 283 through 290 Processing helix chain 'T' and resid 314 through 323 removed outlier: 3.638A pdb=" N VAL T 319 " --> pdb=" O GLY T 315 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR T 320 " --> pdb=" O GLU T 316 " (cutoff:3.500A) Processing helix chain 'T' and resid 330 through 339 Processing helix chain 'T' and resid 351 through 356 Processing helix chain 'T' and resid 384 through 390 removed outlier: 4.094A pdb=" N ASP T 390 " --> pdb=" O LYS T 386 " (cutoff:3.500A) Processing helix chain 'T' and resid 455 through 460 removed outlier: 3.693A pdb=" N CYS T 460 " --> pdb=" O LEU T 456 " (cutoff:3.500A) Processing helix chain 'T' and resid 467 through 476 Processing helix chain 'T' and resid 498 through 505 removed outlier: 3.661A pdb=" N ILE T 502 " --> pdb=" O ASN T 498 " (cutoff:3.500A) Processing helix chain 'T' and resid 516 through 524 removed outlier: 3.560A pdb=" N LEU T 520 " --> pdb=" O THR T 516 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU T 524 " --> pdb=" O LEU T 520 " (cutoff:3.500A) Processing helix chain 'T' and resid 525 through 530 removed outlier: 4.024A pdb=" N LEU T 530 " --> pdb=" O THR T 526 " (cutoff:3.500A) Processing helix chain 'T' and resid 531 through 533 No H-bonds generated for 'chain 'T' and resid 531 through 533' Processing helix chain 'T' and resid 534 through 539 Processing helix chain 'T' and resid 577 through 592 Processing helix chain 'T' and resid 599 through 611 removed outlier: 4.456A pdb=" N ILE T 603 " --> pdb=" O ASP T 599 " (cutoff:3.500A) Processing helix chain 'T' and resid 616 through 627 removed outlier: 3.903A pdb=" N TYR T 620 " --> pdb=" O PRO T 616 " (cutoff:3.500A) Processing helix chain 'T' and resid 629 through 635 Processing helix chain 'T' and resid 636 through 651 Processing helix chain 'T' and resid 659 through 669 Processing helix chain 'T' and resid 680 through 701 removed outlier: 4.481A pdb=" N ILE T 686 " --> pdb=" O MET T 682 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA T 701 " --> pdb=" O LEU T 697 " (cutoff:3.500A) Processing helix chain 'T' and resid 711 through 716 removed outlier: 3.527A pdb=" N CYS T 716 " --> pdb=" O GLY T 712 " (cutoff:3.500A) Processing helix chain 'T' and resid 717 through 720 Processing helix chain 'T' and resid 731 through 740 removed outlier: 3.520A pdb=" N HIS T 735 " --> pdb=" O ASP T 731 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR T 738 " --> pdb=" O THR T 734 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL T 739 " --> pdb=" O HIS T 735 " (cutoff:3.500A) Processing helix chain 'T' and resid 775 through 785 Processing helix chain 'T' and resid 807 through 815 Processing helix chain 'T' and resid 831 through 840 removed outlier: 3.607A pdb=" N ALA T 836 " --> pdb=" O PHE T 832 " (cutoff:3.500A) Processing helix chain 'T' and resid 842 through 847 Processing helix chain 'T' and resid 856 through 860 removed outlier: 3.652A pdb=" N LEU T 860 " --> pdb=" O LEU T 857 " (cutoff:3.500A) Processing helix chain 'T' and resid 877 through 887 removed outlier: 3.572A pdb=" N LEU T 884 " --> pdb=" O MET T 880 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER T 887 " --> pdb=" O ASP T 883 " (cutoff:3.500A) Processing helix chain 'T' and resid 905 through 909 removed outlier: 3.513A pdb=" N GLN T 908 " --> pdb=" O ASP T 905 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN T 909 " --> pdb=" O VAL T 906 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 905 through 909' Processing helix chain 'T' and resid 934 through 941 removed outlier: 3.551A pdb=" N VAL T 940 " --> pdb=" O ARG T 936 " (cutoff:3.500A) Processing helix chain 'T' and resid 956 through 961 Processing helix chain 'T' and resid 965 through 974 removed outlier: 3.862A pdb=" N THR T 969 " --> pdb=" O GLN T 965 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG T 973 " --> pdb=" O THR T 969 " (cutoff:3.500A) Processing helix chain 'T' and resid 975 through 979 removed outlier: 3.979A pdb=" N ALA T 979 " --> pdb=" O GLN T 976 " (cutoff:3.500A) Processing helix chain 'T' and resid 991 through 995 removed outlier: 3.859A pdb=" N GLU T 995 " --> pdb=" O GLU T 992 " (cutoff:3.500A) Processing helix chain 'T' and resid 998 through 1008 removed outlier: 3.783A pdb=" N TYR T1004 " --> pdb=" O PRO T1000 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA T1005 " --> pdb=" O MET T1001 " (cutoff:3.500A) Processing helix chain 'T' and resid 1011 through 1022 removed outlier: 3.647A pdb=" N HIS T1022 " --> pdb=" O MET T1018 " (cutoff:3.500A) Processing helix chain 'T' and resid 1026 through 1037 Processing helix chain 'T' and resid 1123 through 1128 Processing helix chain 'T' and resid 1135 through 1146 Processing helix chain 'T' and resid 1192 through 1196 Processing helix chain 'T' and resid 1219 through 1225 Processing helix chain 'T' and resid 1249 through 1254 Processing helix chain 'T' and resid 1269 through 1275 removed outlier: 4.112A pdb=" N ALA T1273 " --> pdb=" O PRO T1270 " (cutoff:3.500A) Processing helix chain 'T' and resid 1276 through 1281 Processing helix chain 'T' and resid 1287 through 1297 removed outlier: 4.041A pdb=" N GLU T1293 " --> pdb=" O ASN T1289 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG T1297 " --> pdb=" O GLU T1293 " (cutoff:3.500A) Processing helix chain 'T' and resid 1324 through 1329 Processing helix chain 'T' and resid 1339 through 1349 removed outlier: 3.709A pdb=" N ILE T1343 " --> pdb=" O SER T1339 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET T1347 " --> pdb=" O ILE T1343 " (cutoff:3.500A) Processing helix chain 'W' and resid 25 through 32 removed outlier: 3.721A pdb=" N GLU W 31 " --> pdb=" O GLN W 27 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY W 32 " --> pdb=" O SER W 28 " (cutoff:3.500A) Processing helix chain 'W' and resid 67 through 75 removed outlier: 3.753A pdb=" N THR W 71 " --> pdb=" O PHE W 68 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ALA W 72 " --> pdb=" O LEU W 69 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU W 73 " --> pdb=" O GLU W 70 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA W 74 " --> pdb=" O THR W 71 " (cutoff:3.500A) Processing helix chain 'W' and resid 84 through 88 Processing helix chain 'W' and resid 135 through 143 removed outlier: 4.200A pdb=" N LEU W 141 " --> pdb=" O ASP W 137 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER W 143 " --> pdb=" O GLU W 139 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 187 removed outlier: 3.596A pdb=" N GLY W 156 " --> pdb=" O ALA W 152 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE W 177 " --> pdb=" O GLU W 173 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS W 187 " --> pdb=" O VAL W 183 " (cutoff:3.500A) Processing helix chain 'W' and resid 190 through 198 removed outlier: 3.516A pdb=" N LEU W 194 " --> pdb=" O PRO W 190 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR W 196 " --> pdb=" O PHE W 192 " (cutoff:3.500A) Processing helix chain 'W' and resid 208 through 227 removed outlier: 3.743A pdb=" N LYS W 220 " --> pdb=" O ILE W 216 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU W 224 " --> pdb=" O LYS W 220 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU W 225 " --> pdb=" O ARG W 221 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER W 227 " --> pdb=" O LEU W 223 " (cutoff:3.500A) Processing helix chain 'W' and resid 228 through 233 Processing helix chain 'W' and resid 240 through 254 removed outlier: 4.038A pdb=" N GLU W 250 " --> pdb=" O SER W 246 " (cutoff:3.500A) Processing helix chain 'W' and resid 283 through 294 removed outlier: 4.049A pdb=" N THR W 292 " --> pdb=" O ARG W 288 " (cutoff:3.500A) Processing helix chain 'W' and resid 314 through 325 removed outlier: 4.463A pdb=" N THR W 320 " --> pdb=" O GLU W 316 " (cutoff:3.500A) Processing helix chain 'W' and resid 330 through 337 Processing helix chain 'W' and resid 351 through 356 Processing helix chain 'W' and resid 384 through 389 Processing helix chain 'W' and resid 390 through 392 No H-bonds generated for 'chain 'W' and resid 390 through 392' Processing helix chain 'W' and resid 429 through 433 removed outlier: 3.871A pdb=" N GLN W 433 " --> pdb=" O PRO W 430 " (cutoff:3.500A) Processing helix chain 'W' and resid 455 through 460 Processing helix chain 'W' and resid 461 through 465 Processing helix chain 'W' and resid 467 through 476 Processing helix chain 'W' and resid 498 through 509 removed outlier: 3.708A pdb=" N ILE W 502 " --> pdb=" O ASN W 498 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N TYR W 507 " --> pdb=" O VAL W 503 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ASN W 509 " --> pdb=" O GLU W 505 " (cutoff:3.500A) Processing helix chain 'W' and resid 516 through 522 Processing helix chain 'W' and resid 525 through 530 Processing helix chain 'W' and resid 534 through 540 removed outlier: 3.807A pdb=" N LEU W 538 " --> pdb=" O ASN W 534 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU W 540 " --> pdb=" O ASP W 536 " (cutoff:3.500A) Processing helix chain 'W' and resid 567 through 571 removed outlier: 3.563A pdb=" N ASN W 570 " --> pdb=" O MET W 567 " (cutoff:3.500A) Processing helix chain 'W' and resid 577 through 593 Processing helix chain 'W' and resid 599 through 611 Processing helix chain 'W' and resid 617 through 626 Processing helix chain 'W' and resid 636 through 646 Processing helix chain 'W' and resid 646 through 651 removed outlier: 3.580A pdb=" N SER W 651 " --> pdb=" O TYR W 647 " (cutoff:3.500A) Processing helix chain 'W' and resid 659 through 669 removed outlier: 3.967A pdb=" N ILE W 663 " --> pdb=" O SER W 659 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG W 668 " --> pdb=" O LYS W 664 " (cutoff:3.500A) Processing helix chain 'W' and resid 676 through 702 removed outlier: 4.090A pdb=" N MET W 682 " --> pdb=" O GLU W 678 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR W 683 " --> pdb=" O ALA W 679 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE W 691 " --> pdb=" O TYR W 687 " (cutoff:3.500A) Processing helix chain 'W' and resid 711 through 716 Processing helix chain 'W' and resid 717 through 720 Processing helix chain 'W' and resid 731 through 740 removed outlier: 3.607A pdb=" N HIS W 735 " --> pdb=" O ASP W 731 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR W 738 " --> pdb=" O THR W 734 " (cutoff:3.500A) Processing helix chain 'W' and resid 758 through 763 removed outlier: 4.414A pdb=" N PHE W 762 " --> pdb=" O ALA W 758 " (cutoff:3.500A) Processing helix chain 'W' and resid 775 through 785 Processing helix chain 'W' and resid 806 through 815 Processing helix chain 'W' and resid 815 through 821 Processing helix chain 'W' and resid 831 through 841 Processing helix chain 'W' and resid 842 through 847 removed outlier: 3.511A pdb=" N SER W 847 " --> pdb=" O GLY W 843 " (cutoff:3.500A) Processing helix chain 'W' and resid 863 through 872 Processing helix chain 'W' and resid 877 through 887 removed outlier: 4.594A pdb=" N ASP W 883 " --> pdb=" O GLY W 879 " (cutoff:3.500A) Processing helix chain 'W' and resid 914 through 916 No H-bonds generated for 'chain 'W' and resid 914 through 916' Processing helix chain 'W' and resid 934 through 942 Processing helix chain 'W' and resid 956 through 964 Processing helix chain 'W' and resid 964 through 974 Processing helix chain 'W' and resid 975 through 979 removed outlier: 3.838A pdb=" N ALA W 979 " --> pdb=" O GLN W 976 " (cutoff:3.500A) Processing helix chain 'W' and resid 998 through 1007 Processing helix chain 'W' and resid 1011 through 1021 Processing helix chain 'W' and resid 1026 through 1037 Processing helix chain 'W' and resid 1123 through 1128 removed outlier: 3.654A pdb=" N VAL W1127 " --> pdb=" O ASP W1123 " (cutoff:3.500A) Processing helix chain 'W' and resid 1135 through 1146 Processing helix chain 'W' and resid 1192 through 1198 removed outlier: 3.639A pdb=" N PHE W1196 " --> pdb=" O ASP W1192 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS W1198 " --> pdb=" O ALA W1194 " (cutoff:3.500A) Processing helix chain 'W' and resid 1217 through 1225 Processing helix chain 'W' and resid 1249 through 1256 removed outlier: 3.511A pdb=" N ILE W1253 " --> pdb=" O SER W1249 " (cutoff:3.500A) Processing helix chain 'W' and resid 1271 through 1276 removed outlier: 3.703A pdb=" N PHE W1275 " --> pdb=" O CYS W1271 " (cutoff:3.500A) Processing helix chain 'W' and resid 1276 through 1284 removed outlier: 3.714A pdb=" N LEU W1280 " --> pdb=" O ASN W1276 " (cutoff:3.500A) Processing helix chain 'W' and resid 1286 through 1297 Processing helix chain 'W' and resid 1324 through 1329 Processing helix chain 'W' and resid 1339 through 1347 removed outlier: 3.961A pdb=" N ILE W1343 " --> pdb=" O SER W1339 " (cutoff:3.500A) Processing helix chain 'x' and resid 71 through 77 removed outlier: 3.778A pdb=" N ALA x 74 " --> pdb=" O THR x 71 " (cutoff:3.500A) Processing helix chain 'x' and resid 135 through 140 removed outlier: 4.160A pdb=" N ILE x 140 " --> pdb=" O LEU x 136 " (cutoff:3.500A) Processing helix chain 'x' and resid 147 through 187 removed outlier: 3.503A pdb=" N GLY x 168 " --> pdb=" O ALA x 164 " (cutoff:3.500A) Processing helix chain 'x' and resid 190 through 198 removed outlier: 4.545A pdb=" N THR x 196 " --> pdb=" O PHE x 192 " (cutoff:3.500A) Processing helix chain 'x' and resid 208 through 226 removed outlier: 3.660A pdb=" N LYS x 212 " --> pdb=" O SER x 208 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER x 213 " --> pdb=" O LYS x 209 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP x 214 " --> pdb=" O THR x 210 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA x 217 " --> pdb=" O SER x 213 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU x 225 " --> pdb=" O ARG x 221 " (cutoff:3.500A) Processing helix chain 'x' and resid 239 through 254 removed outlier: 3.674A pdb=" N TYR x 243 " --> pdb=" O GLY x 239 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER x 249 " --> pdb=" O ARG x 245 " (cutoff:3.500A) Processing helix chain 'x' and resid 283 through 294 removed outlier: 3.988A pdb=" N ARG x 288 " --> pdb=" O ASP x 284 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN x 289 " --> pdb=" O ASN x 285 " (cutoff:3.500A) Processing helix chain 'x' and resid 314 through 323 Processing helix chain 'x' and resid 330 through 339 Processing helix chain 'x' and resid 351 through 356 removed outlier: 3.544A pdb=" N ALA x 356 " --> pdb=" O LEU x 352 " (cutoff:3.500A) Processing helix chain 'x' and resid 358 through 362 removed outlier: 3.805A pdb=" N GLN x 362 " --> pdb=" O VAL x 359 " (cutoff:3.500A) Processing helix chain 'x' and resid 385 through 390 removed outlier: 4.080A pdb=" N ASP x 390 " --> pdb=" O LYS x 386 " (cutoff:3.500A) Processing helix chain 'x' and resid 452 through 454 No H-bonds generated for 'chain 'x' and resid 452 through 454' Processing helix chain 'x' and resid 455 through 460 removed outlier: 3.534A pdb=" N CYS x 460 " --> pdb=" O LEU x 456 " (cutoff:3.500A) Processing helix chain 'x' and resid 461 through 465 Processing helix chain 'x' and resid 467 through 476 Processing helix chain 'x' and resid 498 through 508 removed outlier: 4.233A pdb=" N ILE x 502 " --> pdb=" O ASN x 498 " (cutoff:3.500A) Processing helix chain 'x' and resid 516 through 522 removed outlier: 3.560A pdb=" N CYS x 522 " --> pdb=" O ILE x 518 " (cutoff:3.500A) Processing helix chain 'x' and resid 525 through 530 Processing helix chain 'x' and resid 531 through 533 No H-bonds generated for 'chain 'x' and resid 531 through 533' Processing helix chain 'x' and resid 534 through 539 Processing helix chain 'x' and resid 567 through 571 Processing helix chain 'x' and resid 577 through 592 removed outlier: 3.529A pdb=" N THR x 590 " --> pdb=" O GLN x 586 " (cutoff:3.500A) Processing helix chain 'x' and resid 599 through 610 removed outlier: 4.089A pdb=" N ILE x 603 " --> pdb=" O ASP x 599 " (cutoff:3.500A) Processing helix chain 'x' and resid 617 through 627 Processing helix chain 'x' and resid 629 through 634 Processing helix chain 'x' and resid 636 through 651 removed outlier: 3.678A pdb=" N LEU x 642 " --> pdb=" O PRO x 638 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN x 645 " --> pdb=" O SER x 641 " (cutoff:3.500A) Processing helix chain 'x' and resid 659 through 669 removed outlier: 3.613A pdb=" N ILE x 663 " --> pdb=" O SER x 659 " (cutoff:3.500A) Processing helix chain 'x' and resid 676 through 702 removed outlier: 3.774A pdb=" N MET x 682 " --> pdb=" O GLU x 678 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR x 683 " --> pdb=" O ALA x 679 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU x 690 " --> pdb=" O ILE x 686 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE x 691 " --> pdb=" O TYR x 687 " (cutoff:3.500A) Processing helix chain 'x' and resid 711 through 716 removed outlier: 3.641A pdb=" N CYS x 716 " --> pdb=" O GLY x 712 " (cutoff:3.500A) Processing helix chain 'x' and resid 732 through 740 removed outlier: 3.833A pdb=" N LEU x 737 " --> pdb=" O PHE x 733 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR x 738 " --> pdb=" O THR x 734 " (cutoff:3.500A) Processing helix chain 'x' and resid 758 through 762 removed outlier: 3.968A pdb=" N PHE x 762 " --> pdb=" O ALA x 758 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 758 through 762' Processing helix chain 'x' and resid 772 through 774 No H-bonds generated for 'chain 'x' and resid 772 through 774' Processing helix chain 'x' and resid 775 through 785 Processing helix chain 'x' and resid 806 through 815 removed outlier: 4.081A pdb=" N LYS x 810 " --> pdb=" O ASP x 806 " (cutoff:3.500A) Processing helix chain 'x' and resid 816 through 821 Processing helix chain 'x' and resid 831 through 841 removed outlier: 3.504A pdb=" N VAL x 835 " --> pdb=" O ASP x 831 " (cutoff:3.500A) Processing helix chain 'x' and resid 843 through 848 removed outlier: 3.878A pdb=" N HIS x 848 " --> pdb=" O PRO x 844 " (cutoff:3.500A) Processing helix chain 'x' and resid 863 through 871 removed outlier: 3.557A pdb=" N ASP x 867 " --> pdb=" O GLY x 863 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE x 871 " --> pdb=" O ASP x 867 " (cutoff:3.500A) Processing helix chain 'x' and resid 881 through 887 Processing helix chain 'x' and resid 888 through 890 No H-bonds generated for 'chain 'x' and resid 888 through 890' Processing helix chain 'x' and resid 934 through 942 removed outlier: 3.626A pdb=" N VAL x 940 " --> pdb=" O ARG x 936 " (cutoff:3.500A) Processing helix chain 'x' and resid 956 through 961 Processing helix chain 'x' and resid 966 through 974 removed outlier: 3.668A pdb=" N MET x 972 " --> pdb=" O ALA x 968 " (cutoff:3.500A) Processing helix chain 'x' and resid 975 through 979 removed outlier: 3.845A pdb=" N ALA x 979 " --> pdb=" O GLN x 976 " (cutoff:3.500A) Processing helix chain 'x' and resid 998 through 1008 removed outlier: 3.636A pdb=" N GLY x1002 " --> pdb=" O ARG x 998 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU x1007 " --> pdb=" O LYS x1003 " (cutoff:3.500A) Processing helix chain 'x' and resid 1011 through 1021 Processing helix chain 'x' and resid 1026 through 1036 removed outlier: 3.885A pdb=" N LEU x1036 " --> pdb=" O ALA x1032 " (cutoff:3.500A) Processing helix chain 'x' and resid 1123 through 1128 Processing helix chain 'x' and resid 1135 through 1147 Processing helix chain 'x' and resid 1192 through 1197 removed outlier: 3.947A pdb=" N PHE x1196 " --> pdb=" O ASP x1192 " (cutoff:3.500A) Processing helix chain 'x' and resid 1218 through 1223 Processing helix chain 'x' and resid 1249 through 1254 removed outlier: 3.671A pdb=" N MET x1254 " --> pdb=" O LEU x1250 " (cutoff:3.500A) Processing helix chain 'x' and resid 1271 through 1276 Processing helix chain 'x' and resid 1276 through 1281 Processing helix chain 'x' and resid 1287 through 1296 Processing helix chain 'x' and resid 1324 through 1329 Processing helix chain 'x' and resid 1339 through 1349 removed outlier: 3.785A pdb=" N ILE x1343 " --> pdb=" O SER x1339 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER x1348 " --> pdb=" O ASP x1344 " (cutoff:3.500A) Processing helix chain 'y' and resid 31 through 35 removed outlier: 4.258A pdb=" N ASN y 34 " --> pdb=" O ASN y 31 " (cutoff:3.500A) Processing helix chain 'y' and resid 36 through 67 removed outlier: 3.656A pdb=" N GLN y 62 " --> pdb=" O GLU y 58 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG y 63 " --> pdb=" O GLU y 59 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE y 65 " --> pdb=" O VAL y 61 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY y 66 " --> pdb=" O GLN y 62 " (cutoff:3.500A) Processing helix chain 'y' and resid 69 through 75 removed outlier: 3.861A pdb=" N ALA y 73 " --> pdb=" O ARG y 69 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP y 75 " --> pdb=" O GLN y 71 " (cutoff:3.500A) Processing helix chain 'e' and resid 10 through 20 removed outlier: 3.551A pdb=" N ARG e 14 " --> pdb=" O ARG e 10 " (cutoff:3.500A) Processing helix chain 'e' and resid 36 through 44 Processing helix chain 'e' and resid 53 through 61 Processing helix chain 'e' and resid 127 through 137 removed outlier: 3.700A pdb=" N ILE e 133 " --> pdb=" O LEU e 129 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU e 134 " --> pdb=" O SER e 130 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N MET e 135 " --> pdb=" O LEU e 131 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS e 137 " --> pdb=" O ILE e 133 " (cutoff:3.500A) Processing helix chain 'e' and resid 151 through 159 Processing helix chain 'e' and resid 171 through 178 Processing helix chain 'e' and resid 233 through 238 removed outlier: 3.791A pdb=" N LEU e 237 " --> pdb=" O LEU e 233 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER e 238 " --> pdb=" O ASP e 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 233 through 238' Processing helix chain 'e' and resid 285 through 308 removed outlier: 3.833A pdb=" N ASN e 291 " --> pdb=" O CYS e 287 " (cutoff:3.500A) Proline residue: e 299 - end of helix removed outlier: 4.011A pdb=" N MET e 302 " --> pdb=" O SER e 298 " (cutoff:3.500A) Processing helix chain 'e' and resid 313 through 317 removed outlier: 4.081A pdb=" N LEU e 316 " --> pdb=" O ILE e 313 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR e 317 " --> pdb=" O GLU e 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 313 through 317' Processing helix chain 'f' and resid 14 through 24 removed outlier: 3.625A pdb=" N GLN f 23 " --> pdb=" O ALA f 19 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG f 24 " --> pdb=" O LYS f 20 " (cutoff:3.500A) Processing helix chain 'f' and resid 56 through 67 Processing helix chain 'f' and resid 140 through 156 Processing helix chain 'f' and resid 157 through 159 No H-bonds generated for 'chain 'f' and resid 157 through 159' Processing helix chain 'f' and resid 194 through 216 removed outlier: 3.707A pdb=" N GLY f 198 " --> pdb=" O PRO f 194 " (cutoff:3.500A) Processing helix chain 'f' and resid 218 through 231 removed outlier: 3.661A pdb=" N GLY f 226 " --> pdb=" O ARG f 222 " (cutoff:3.500A) Processing helix chain 'f' and resid 236 through 240 Processing helix chain 'f' and resid 244 through 251 Processing helix chain 'f' and resid 256 through 276 removed outlier: 3.844A pdb=" N VAL f 266 " --> pdb=" O SER f 262 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR f 269 " --> pdb=" O ARG f 265 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN f 272 " --> pdb=" O MET f 268 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER f 273 " --> pdb=" O THR f 269 " (cutoff:3.500A) Processing helix chain 'f' and resid 277 through 279 No H-bonds generated for 'chain 'f' and resid 277 through 279' Processing helix chain 'g' and resid 14 through 23 Processing helix chain 'g' and resid 56 through 67 Processing helix chain 'g' and resid 140 through 163 removed outlier: 3.647A pdb=" N PHE g 153 " --> pdb=" O LYS g 149 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL g 160 " --> pdb=" O TYR g 156 " (cutoff:3.500A) Processing helix chain 'g' and resid 204 through 229 removed outlier: 3.842A pdb=" N ILE g 211 " --> pdb=" O LEU g 207 " (cutoff:3.500A) Proline residue: g 217 - end of helix removed outlier: 3.669A pdb=" N ARG g 222 " --> pdb=" O ARG g 218 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG g 229 " --> pdb=" O ARG g 225 " (cutoff:3.500A) Processing helix chain 'g' and resid 235 through 240 removed outlier: 3.731A pdb=" N GLN g 240 " --> pdb=" O LEU g 236 " (cutoff:3.500A) Processing helix chain 'g' and resid 256 through 279 Processing helix chain 'l' and resid 71 through 76 removed outlier: 4.027A pdb=" N ALA l 74 " --> pdb=" O THR l 71 " (cutoff:3.500A) Processing helix chain 'l' and resid 135 through 143 removed outlier: 3.789A pdb=" N SER l 143 " --> pdb=" O GLU l 139 " (cutoff:3.500A) Processing helix chain 'l' and resid 147 through 186 removed outlier: 4.403A pdb=" N GLU l 153 " --> pdb=" O VAL l 149 " (cutoff:3.500A) Processing helix chain 'l' and resid 190 through 198 removed outlier: 5.301A pdb=" N THR l 196 " --> pdb=" O PHE l 192 " (cutoff:3.500A) Processing helix chain 'l' and resid 200 through 205 removed outlier: 3.607A pdb=" N GLU l 204 " --> pdb=" O PRO l 200 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ARG l 205 " --> pdb=" O THR l 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 200 through 205' Processing helix chain 'l' and resid 210 through 224 removed outlier: 3.840A pdb=" N ASP l 214 " --> pdb=" O THR l 210 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS l 220 " --> pdb=" O ILE l 216 " (cutoff:3.500A) Processing helix chain 'l' and resid 228 through 236 removed outlier: 3.659A pdb=" N ARG l 232 " --> pdb=" O PHE l 228 " (cutoff:3.500A) Processing helix chain 'l' and resid 239 through 254 Processing helix chain 'l' and resid 283 through 294 removed outlier: 3.961A pdb=" N ARG l 288 " --> pdb=" O ASP l 284 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN l 289 " --> pdb=" O ASN l 285 " (cutoff:3.500A) Processing helix chain 'l' and resid 323 through 337 removed outlier: 3.685A pdb=" N VAL l 327 " --> pdb=" O SER l 323 " (cutoff:3.500A) Processing helix chain 'l' and resid 384 through 390 Processing helix chain 'l' and resid 451 through 460 removed outlier: 4.061A pdb=" N ALA l 455 " --> pdb=" O ASN l 451 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS l 457 " --> pdb=" O GLN l 453 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL l 458 " --> pdb=" O ASN l 454 " (cutoff:3.500A) Processing helix chain 'l' and resid 461 through 465 Processing helix chain 'l' and resid 467 through 476 removed outlier: 3.856A pdb=" N SER l 473 " --> pdb=" O HIS l 469 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU l 474 " --> pdb=" O THR l 470 " (cutoff:3.500A) Processing helix chain 'l' and resid 499 through 505 Processing helix chain 'l' and resid 516 through 524 removed outlier: 3.904A pdb=" N LEU l 520 " --> pdb=" O THR l 516 " (cutoff:3.500A) Processing helix chain 'l' and resid 525 through 530 Processing helix chain 'l' and resid 531 through 533 No H-bonds generated for 'chain 'l' and resid 531 through 533' Processing helix chain 'l' and resid 534 through 540 removed outlier: 3.528A pdb=" N LEU l 538 " --> pdb=" O ASN l 534 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU l 540 " --> pdb=" O ASP l 536 " (cutoff:3.500A) Processing helix chain 'l' and resid 567 through 571 Processing helix chain 'l' and resid 577 through 593 Processing helix chain 'l' and resid 599 through 612 removed outlier: 3.916A pdb=" N ILE l 603 " --> pdb=" O ASP l 599 " (cutoff:3.500A) Processing helix chain 'l' and resid 617 through 627 Processing helix chain 'l' and resid 629 through 635 removed outlier: 3.825A pdb=" N MET l 635 " --> pdb=" O GLU l 631 " (cutoff:3.500A) Processing helix chain 'l' and resid 639 through 652 removed outlier: 4.254A pdb=" N ASN l 645 " --> pdb=" O SER l 641 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR l 647 " --> pdb=" O CYS l 643 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TRP l 648 " --> pdb=" O ILE l 644 " (cutoff:3.500A) Processing helix chain 'l' and resid 659 through 669 removed outlier: 3.658A pdb=" N ILE l 663 " --> pdb=" O SER l 659 " (cutoff:3.500A) Processing helix chain 'l' and resid 676 through 702 removed outlier: 4.867A pdb=" N MET l 682 " --> pdb=" O GLU l 678 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR l 683 " --> pdb=" O ALA l 679 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY l 702 " --> pdb=" O MET l 698 " (cutoff:3.500A) Processing helix chain 'l' and resid 711 through 716 Processing helix chain 'l' and resid 732 through 740 removed outlier: 4.057A pdb=" N THR l 738 " --> pdb=" O THR l 734 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL l 739 " --> pdb=" O HIS l 735 " (cutoff:3.500A) Processing helix chain 'l' and resid 768 through 773 removed outlier: 3.740A pdb=" N MET l 772 " --> pdb=" O MET l 769 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA l 773 " --> pdb=" O ASP l 770 " (cutoff:3.500A) Processing helix chain 'l' and resid 775 through 785 Processing helix chain 'l' and resid 807 through 816 Processing helix chain 'l' and resid 816 through 821 removed outlier: 3.879A pdb=" N CYS l 820 " --> pdb=" O PHE l 816 " (cutoff:3.500A) Processing helix chain 'l' and resid 835 through 840 removed outlier: 3.549A pdb=" N LEU l 839 " --> pdb=" O VAL l 835 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA l 840 " --> pdb=" O ALA l 836 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 835 through 840' Processing helix chain 'l' and resid 843 through 848 removed outlier: 3.722A pdb=" N SER l 847 " --> pdb=" O GLY l 843 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS l 848 " --> pdb=" O PRO l 844 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 843 through 848' Processing helix chain 'l' and resid 863 through 873 removed outlier: 3.645A pdb=" N ASP l 867 " --> pdb=" O GLY l 863 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE l 871 " --> pdb=" O ASP l 867 " (cutoff:3.500A) Processing helix chain 'l' and resid 881 through 887 Processing helix chain 'l' and resid 888 through 890 No H-bonds generated for 'chain 'l' and resid 888 through 890' Processing helix chain 'l' and resid 914 through 918 removed outlier: 3.844A pdb=" N ARG l 918 " --> pdb=" O ALA l 915 " (cutoff:3.500A) Processing helix chain 'l' and resid 934 through 942 removed outlier: 3.702A pdb=" N VAL l 940 " --> pdb=" O ARG l 936 " (cutoff:3.500A) Processing helix chain 'l' and resid 964 through 974 removed outlier: 3.517A pdb=" N ALA l 968 " --> pdb=" O HIS l 964 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN l 974 " --> pdb=" O PHE l 970 " (cutoff:3.500A) Processing helix chain 'l' and resid 975 through 979 removed outlier: 4.068A pdb=" N ALA l 979 " --> pdb=" O GLN l 976 " (cutoff:3.500A) Processing helix chain 'l' and resid 998 through 1007 removed outlier: 3.554A pdb=" N GLU l1007 " --> pdb=" O LYS l1003 " (cutoff:3.500A) Processing helix chain 'l' and resid 1011 through 1022 removed outlier: 3.784A pdb=" N ILE l1015 " --> pdb=" O SER l1011 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER l1016 " --> pdb=" O LEU l1012 " (cutoff:3.500A) Processing helix chain 'l' and resid 1026 through 1036 removed outlier: 3.588A pdb=" N TYR l1030 " --> pdb=" O SER l1026 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE l1031 " --> pdb=" O PRO l1027 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA l1032 " --> pdb=" O MET l1028 " (cutoff:3.500A) Processing helix chain 'l' and resid 1123 through 1128 Processing helix chain 'l' and resid 1135 through 1146 removed outlier: 3.754A pdb=" N ASN l1139 " --> pdb=" O ASN l1135 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TYR l1141 " --> pdb=" O GLN l1137 " (cutoff:3.500A) Processing helix chain 'l' and resid 1192 through 1198 removed outlier: 3.914A pdb=" N PHE l1196 " --> pdb=" O ASP l1192 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS l1198 " --> pdb=" O ALA l1194 " (cutoff:3.500A) Processing helix chain 'l' and resid 1208 through 1212 removed outlier: 4.138A pdb=" N SER l1211 " --> pdb=" O CYS l1208 " (cutoff:3.500A) Processing helix chain 'l' and resid 1219 through 1226 Processing helix chain 'l' and resid 1249 through 1256 removed outlier: 3.681A pdb=" N TYR l1255 " --> pdb=" O GLY l1251 " (cutoff:3.500A) Processing helix chain 'l' and resid 1271 through 1276 Processing helix chain 'l' and resid 1276 through 1298 removed outlier: 4.170A pdb=" N LEU l1298 " --> pdb=" O TYR l1294 " (cutoff:3.500A) Processing helix chain 'l' and resid 1340 through 1347 removed outlier: 3.771A pdb=" N PHE l1346 " --> pdb=" O LEU l1342 " (cutoff:3.500A) Processing helix chain '5' and resid 8 through 19 Processing helix chain '5' and resid 31 through 51 removed outlier: 4.048A pdb=" N ARG 5 37 " --> pdb=" O SER 5 33 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASP 5 38 " --> pdb=" O GLU 5 34 " (cutoff:3.500A) Processing helix chain '5' and resid 53 through 63 removed outlier: 4.111A pdb=" N VAL 5 57 " --> pdb=" O SER 5 53 " (cutoff:3.500A) Processing helix chain '5' and resid 127 through 139 Processing helix chain '5' and resid 149 through 159 removed outlier: 4.403A pdb=" N ARG 5 153 " --> pdb=" O GLY 5 149 " (cutoff:3.500A) Processing helix chain '5' and resid 161 through 169 removed outlier: 4.405A pdb=" N LEU 5 165 " --> pdb=" O SER 5 161 " (cutoff:3.500A) Processing helix chain '5' and resid 172 through 178 Processing helix chain '5' and resid 233 through 238 Processing helix chain '5' and resid 289 through 306 Proline residue: 5 299 - end of helix removed outlier: 4.362A pdb=" N MET 5 302 " --> pdb=" O SER 5 298 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N HIS 5 303 " --> pdb=" O PRO 5 299 " (cutoff:3.500A) Processing helix chain '6' and resid 14 through 24 removed outlier: 3.727A pdb=" N ALA 6 19 " --> pdb=" O THR 6 15 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LYS 6 20 " --> pdb=" O ASP 6 16 " (cutoff:3.500A) Processing helix chain '6' and resid 58 through 67 Processing helix chain '6' and resid 140 through 162 removed outlier: 4.993A pdb=" N ARG 6 158 " --> pdb=" O ASN 6 154 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL 6 159 " --> pdb=" O VAL 6 155 " (cutoff:3.500A) Processing helix chain '6' and resid 169 through 176 removed outlier: 4.258A pdb=" N HIS 6 173 " --> pdb=" O MET 6 169 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET 6 174 " --> pdb=" O LEU 6 170 " (cutoff:3.500A) Processing helix chain '6' and resid 194 through 213 removed outlier: 4.087A pdb=" N GLY 6 198 " --> pdb=" O PRO 6 194 " (cutoff:3.500A) Processing helix chain '6' and resid 218 through 230 removed outlier: 3.667A pdb=" N ARG 6 222 " --> pdb=" O ARG 6 218 " (cutoff:3.500A) Processing helix chain '6' and resid 233 through 237 removed outlier: 3.544A pdb=" N ASN 6 237 " --> pdb=" O ASP 6 234 " (cutoff:3.500A) Processing helix chain '6' and resid 244 through 250 Processing helix chain '6' and resid 257 through 277 removed outlier: 4.283A pdb=" N LEU 6 261 " --> pdb=" O VAL 6 257 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER 6 262 " --> pdb=" O ALA 6 258 " (cutoff:3.500A) Processing helix chain '7' and resid 14 through 24 Processing helix chain '7' and resid 44 through 48 removed outlier: 4.292A pdb=" N GLN 7 47 " --> pdb=" O GLY 7 44 " (cutoff:3.500A) Processing helix chain '7' and resid 56 through 67 removed outlier: 3.770A pdb=" N MET 7 60 " --> pdb=" O ASP 7 56 " (cutoff:3.500A) Processing helix chain '7' and resid 117 through 122 removed outlier: 3.885A pdb=" N ALA 7 121 " --> pdb=" O GLY 7 117 " (cutoff:3.500A) Processing helix chain '7' and resid 140 through 163 removed outlier: 4.034A pdb=" N PHE 7 153 " --> pdb=" O LYS 7 149 " (cutoff:3.500A) Processing helix chain '7' and resid 169 through 176 removed outlier: 3.819A pdb=" N HIS 7 175 " --> pdb=" O ASP 7 171 " (cutoff:3.500A) Processing helix chain '7' and resid 201 through 227 Proline residue: 7 217 - end of helix Processing helix chain '7' and resid 234 through 243 removed outlier: 4.042A pdb=" N VAL 7 243 " --> pdb=" O PHE 7 239 " (cutoff:3.500A) Processing helix chain '7' and resid 256 through 279 Processing sheet with id=AA1, first strand: chain 'G' and resid 13 through 14 Processing sheet with id=AA2, first strand: chain 'C' and resid 17 through 24 removed outlier: 3.999A pdb=" N LEU C 17 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 59 Processing sheet with id=AA4, first strand: chain 'C' and resid 285 through 289 Processing sheet with id=AA5, first strand: chain 'C' and resid 436 through 438 removed outlier: 3.553A pdb=" N LEU C 419 " --> pdb=" O ILE C 438 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN C 472 " --> pdb=" O THR C 468 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S' and resid 15 through 17 removed outlier: 4.113A pdb=" N ASN W 61 " --> pdb=" O ARG x 96 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N SER x 98 " --> pdb=" O ASN W 61 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'S' and resid 15 through 17 removed outlier: 4.113A pdb=" N ASN W 61 " --> pdb=" O ARG x 96 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N SER x 98 " --> pdb=" O ASN W 61 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE W 52 " --> pdb=" O MET x 88 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASP x 90 " --> pdb=" O PHE W 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'T' and resid 326 through 328 Processing sheet with id=AA9, first strand: chain 'T' and resid 326 through 328 removed outlier: 6.301A pdb=" N PHE S 52 " --> pdb=" O MET T 88 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP T 90 " --> pdb=" O PHE S 52 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLN T 94 " --> pdb=" O LEU S 56 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL S 58 " --> pdb=" O GLN T 94 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ARG T 96 " --> pdb=" O VAL S 58 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N THR S 60 " --> pdb=" O ARG T 96 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N SER T 98 " --> pdb=" O THR S 60 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG T 114 " --> pdb=" O VAL T 99 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE T 117 " --> pdb=" O ASP W 38 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL T 119 " --> pdb=" O SER W 36 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N SER W 36 " --> pdb=" O VAL T 119 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 77 through 79 removed outlier: 3.559A pdb=" N ALA S1093 " --> pdb=" O PHE S1068 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 94 through 96 Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'S' and resid 133 through 134 Processing sheet with id=AB5, first strand: chain 'S' and resid 370 through 374 removed outlier: 6.020A pdb=" N GLY S 278 " --> pdb=" O ALA S 380 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N GLU S 382 " --> pdb=" O GLY S 278 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N PHE S 280 " --> pdb=" O GLU S 382 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ARG S 400 " --> pdb=" O GLU S1322 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 1321 through 1322 removed outlier: 6.217A pdb=" N ARG S 400 " --> pdb=" O GLU S1322 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 1103 through 1112 removed outlier: 6.885A pdb=" N GLU S1055 " --> pdb=" O ALA S1108 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N VAL S1110 " --> pdb=" O LEU S1053 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LEU S1053 " --> pdb=" O VAL S1110 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N ALA S1112 " --> pdb=" O GLU S1051 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N GLU S1051 " --> pdb=" O ALA S1112 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N PHE S1332 " --> pdb=" O GLN S 402 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER S 404 " --> pdb=" O PHE S1332 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 425 through 426 Processing sheet with id=AB9, first strand: chain 'S' and resid 438 through 441 Processing sheet with id=AC1, first strand: chain 'S' and resid 546 through 549 Processing sheet with id=AC2, first strand: chain 'S' and resid 727 through 728 removed outlier: 3.533A pdb=" N ILE S 746 " --> pdb=" O TYR S 753 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE S 748 " --> pdb=" O GLU S 751 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'S' and resid 727 through 728 Processing sheet with id=AC4, first strand: chain 'S' and resid 928 through 930 removed outlier: 3.508A pdb=" N CYS S 826 " --> pdb=" O ALA S 930 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'S' and resid 1373 through 1375 removed outlier: 3.575A pdb=" N VAL S1380 " --> pdb=" O LEU S1373 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS S1378 " --> pdb=" O PHE S1375 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'T' and resid 77 through 81 removed outlier: 6.453A pdb=" N VAL T 78 " --> pdb=" O MET T1067 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE T1069 " --> pdb=" O VAL T 78 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR T 80 " --> pdb=" O ILE T1069 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE T1095 " --> pdb=" O SER T1066 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR T 129 " --> pdb=" O VAL T1088 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'T' and resid 132 through 134 Processing sheet with id=AC8, first strand: chain 'T' and resid 268 through 269 removed outlier: 4.725A pdb=" N ASN T 300 " --> pdb=" O ALA T 369 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N PHE T 280 " --> pdb=" O GLU T 382 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR T1049 " --> pdb=" O THR T1181 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N THR T1181 " --> pdb=" O THR T1049 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N GLU T1051 " --> pdb=" O GLN T1179 " (cutoff:3.500A) removed outlier: 10.634A pdb=" N GLN T1179 " --> pdb=" O GLU T1051 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA T1180 " --> pdb=" O ASP T1116 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N GLY T1118 " --> pdb=" O ALA T1180 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N CYS T1182 " --> pdb=" O GLY T1118 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N HIS T1120 " --> pdb=" O CYS T1182 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N ILE T1184 " --> pdb=" O HIS T1120 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'T' and resid 1103 through 1113 removed outlier: 6.687A pdb=" N GLU T1055 " --> pdb=" O ALA T1108 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N VAL T1110 " --> pdb=" O LEU T1053 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LEU T1053 " --> pdb=" O VAL T1110 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA T1112 " --> pdb=" O GLU T1051 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLU T1051 " --> pdb=" O ALA T1112 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N PHE T1332 " --> pdb=" O GLN T 402 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N SER T 404 " --> pdb=" O PHE T1332 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'T' and resid 438 through 441 Processing sheet with id=AD2, first strand: chain 'T' and resid 546 through 550 removed outlier: 3.693A pdb=" N VAL T 563 " --> pdb=" O ASP T 547 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'T' and resid 727 through 728 Processing sheet with id=AD4, first strand: chain 'T' and resid 763 through 765 removed outlier: 5.861A pdb=" N GLU T 764 " --> pdb=" O LEU T 796 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'T' and resid 928 through 930 removed outlier: 3.519A pdb=" N LEU T 928 " --> pdb=" O LEU T 828 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS T 826 " --> pdb=" O ALA T 930 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY T 827 " --> pdb=" O ILE T 948 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'T' and resid 1373 through 1375 removed outlier: 3.943A pdb=" N LEU T1373 " --> pdb=" O VAL T1380 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'W' and resid 123 through 129 removed outlier: 3.703A pdb=" N SER W1094 " --> pdb=" O HIS W 123 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR W 129 " --> pdb=" O VAL W1088 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL W1088 " --> pdb=" O THR W 129 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL W 78 " --> pdb=" O MET W1067 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE W1069 " --> pdb=" O VAL W 78 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR W 80 " --> pdb=" O ILE W1069 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'W' and resid 132 through 134 removed outlier: 6.571A pdb=" N ALA W1083 " --> pdb=" O ALA W1079 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ALA W1079 " --> pdb=" O ALA W1083 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N THR W1085 " --> pdb=" O ARG W1077 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'W' and resid 92 through 95 Processing sheet with id=AE1, first strand: chain 'W' and resid 98 through 99 removed outlier: 3.864A pdb=" N ARG W 114 " --> pdb=" O VAL W 99 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'W' and resid 370 through 371 removed outlier: 3.710A pdb=" N ALA W 370 " --> pdb=" O VAL W 381 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N PHE W 280 " --> pdb=" O GLU W 382 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'W' and resid 1103 through 1112 removed outlier: 5.444A pdb=" N MET W1105 " --> pdb=" O PHE W1059 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N PHE W1059 " --> pdb=" O MET W1105 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ILE W1057 " --> pdb=" O PRO W1107 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG W1109 " --> pdb=" O GLU W1055 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU W1053 " --> pdb=" O ALA W1111 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU W1322 " --> pdb=" O ARG W 400 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN W 402 " --> pdb=" O GLU W1322 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'W' and resid 302 through 304 Processing sheet with id=AE5, first strand: chain 'W' and resid 438 through 441 Processing sheet with id=AE6, first strand: chain 'W' and resid 546 through 550 Processing sheet with id=AE7, first strand: chain 'W' and resid 727 through 728 removed outlier: 3.512A pdb=" N ARG W 896 " --> pdb=" O VAL W 925 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE W 746 " --> pdb=" O TYR W 753 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR W 753 " --> pdb=" O ILE W 746 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'W' and resid 929 through 930 removed outlier: 3.575A pdb=" N CYS W 826 " --> pdb=" O ALA W 930 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY W 827 " --> pdb=" O ILE W 948 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'W' and resid 902 through 903 removed outlier: 4.000A pdb=" N VAL W 902 " --> pdb=" O THR W 919 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'x' and resid 52 through 56 removed outlier: 6.240A pdb=" N PHE x 52 " --> pdb=" O ASP x 38 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASP x 38 " --> pdb=" O PHE x 52 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL x 54 " --> pdb=" O SER x 36 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER x 36 " --> pdb=" O VAL x 54 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG l 314 " --> pdb=" O ASP x 38 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'x' and resid 123 through 129 Processing sheet with id=AF3, first strand: chain 'x' and resid 1103 through 1113 removed outlier: 7.810A pdb=" N THR x1106 " --> pdb=" O PHE x1059 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N PHE x1059 " --> pdb=" O THR x1106 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA x1108 " --> pdb=" O ILE x1057 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ILE x1057 " --> pdb=" O ALA x1108 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N VAL x1110 " --> pdb=" O GLU x1055 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLU x1055 " --> pdb=" O VAL x1110 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET x1044 " --> pdb=" O VAL x 409 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N PHE x1332 " --> pdb=" O GLN x 402 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N SER x 404 " --> pdb=" O PHE x1332 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'x' and resid 299 through 305 removed outlier: 4.898A pdb=" N ASN x 300 " --> pdb=" O ALA x 369 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA x 369 " --> pdb=" O ASN x 300 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA x 370 " --> pdb=" O VAL x 381 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL x 379 " --> pdb=" O ILE x 372 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET x1044 " --> pdb=" O VAL x 409 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'x' and resid 1184 through 1187 removed outlier: 3.620A pdb=" N MET x1044 " --> pdb=" O VAL x 409 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'x' and resid 438 through 439 Processing sheet with id=AF7, first strand: chain 'x' and resid 705 through 706 Processing sheet with id=AF8, first strand: chain 'x' and resid 745 through 747 removed outlier: 3.780A pdb=" N VAL x 902 " --> pdb=" O THR x 919 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'x' and resid 763 through 765 Processing sheet with id=AG1, first strand: chain 'x' and resid 929 through 930 removed outlier: 3.636A pdb=" N GLY x 827 " --> pdb=" O ILE x 948 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'x' and resid 1373 through 1375 removed outlier: 3.589A pdb=" N LEU x1373 " --> pdb=" O VAL x1380 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'e' and resid 89 through 96 removed outlier: 7.415A pdb=" N VAL e 89 " --> pdb=" O VAL e 207 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL e 207 " --> pdb=" O VAL e 89 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU e 324 " --> pdb=" O ASN e 356 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N VAL e 321 " --> pdb=" O LEU e 268 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU e 268 " --> pdb=" O VAL e 321 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N CYS e 323 " --> pdb=" O VAL e 266 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL e 266 " --> pdb=" O CYS e 323 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY e 325 " --> pdb=" O LEU e 264 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLN e 281 " --> pdb=" O VAL e 231 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'e' and resid 125 through 126 removed outlier: 6.117A pdb=" N LEU e 110 " --> pdb=" O VAL e 188 " (cutoff:3.500A) removed outlier: 9.197A pdb=" N GLY e 189 " --> pdb=" O HIS e 208 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N HIS e 208 " --> pdb=" O GLY e 189 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU e 191 " --> pdb=" O VAL e 206 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL e 206 " --> pdb=" O LEU e 191 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU e 324 " --> pdb=" O ASN e 356 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'e' and resid 222 through 226 Processing sheet with id=AG6, first strand: chain 'f' and resid 28 through 31 removed outlier: 3.610A pdb=" N LEU f 31 " --> pdb=" O THR f 68 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR f 68 " --> pdb=" O LEU f 31 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU f 72 " --> pdb=" O THR f 83 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR f 83 " --> pdb=" O LEU f 72 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU f 74 " --> pdb=" O ILE f 81 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL f 6 " --> pdb=" O GLN f 38 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'f' and resid 90 through 94 removed outlier: 4.077A pdb=" N ARG f 283 " --> pdb=" O ARG f 301 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'f' and resid 122 through 125 Processing sheet with id=AG9, first strand: chain 'f' and resid 178 through 180 Processing sheet with id=AH1, first strand: chain 'g' and resid 28 through 30 removed outlier: 4.939A pdb=" N LEU g 69 " --> pdb=" O ILE g 85 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN g 38 " --> pdb=" O VAL g 6 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'g' and resid 93 through 94 Processing sheet with id=AH3, first strand: chain 'g' and resid 136 through 139 Processing sheet with id=AH4, first strand: chain 'g' and resid 178 through 181 Processing sheet with id=AH5, first strand: chain 'l' and resid 80 through 81 removed outlier: 3.724A pdb=" N ILE l1069 " --> pdb=" O THR l 80 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE l1095 " --> pdb=" O SER l1066 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR l 129 " --> pdb=" O VAL l1088 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET l1092 " --> pdb=" O HIS l 125 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'l' and resid 80 through 81 removed outlier: 3.724A pdb=" N ILE l1069 " --> pdb=" O THR l 80 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE l1095 " --> pdb=" O SER l1066 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR l1085 " --> pdb=" O ARG l1077 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG 5 25 " --> pdb=" O VAL l1074 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'l' and resid 92 through 97 Processing sheet with id=AH8, first strand: chain 'l' and resid 268 through 269 removed outlier: 4.505A pdb=" N ASN l 300 " --> pdb=" O ALA l 369 " (cutoff:3.500A) removed outlier: 10.691A pdb=" N SER l 368 " --> pdb=" O SER l 383 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N SER l 383 " --> pdb=" O SER l 368 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA l 370 " --> pdb=" O VAL l 381 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N HIS l 377 " --> pdb=" O LEU l 374 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N PHE l 280 " --> pdb=" O GLU l 382 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N THR l1049 " --> pdb=" O THR l1181 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N THR l1181 " --> pdb=" O THR l1049 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N HIS l1120 " --> pdb=" O CYS l1182 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N ILE l1184 " --> pdb=" O HIS l1120 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'l' and resid 1103 through 1113 removed outlier: 6.737A pdb=" N GLU l1055 " --> pdb=" O ALA l1108 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N VAL l1110 " --> pdb=" O LEU l1053 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU l1053 " --> pdb=" O VAL l1110 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ALA l1112 " --> pdb=" O GLU l1051 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N GLU l1051 " --> pdb=" O ALA l1112 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR l 403 " --> pdb=" O ASP l1050 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'l' and resid 438 through 441 removed outlier: 3.507A pdb=" N ALA l 438 " --> pdb=" O PHE l 450 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'l' and resid 546 through 549 removed outlier: 3.558A pdb=" N ASP l 547 " --> pdb=" O VAL l 563 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL l 563 " --> pdb=" O ASP l 547 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'l' and resid 705 through 706 Processing sheet with id=AI4, first strand: chain 'l' and resid 727 through 728 removed outlier: 3.710A pdb=" N ALA l 728 " --> pdb=" O LEU l 924 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG l 899 " --> pdb=" O ILE l 747 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'l' and resid 763 through 765 removed outlier: 5.804A pdb=" N GLU l 764 " --> pdb=" O LEU l 796 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI5 Processing sheet with id=AI6, first strand: chain 'l' and resid 928 through 930 removed outlier: 3.727A pdb=" N LEU l 928 " --> pdb=" O LEU l 828 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY l 827 " --> pdb=" O ILE l 948 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'l' and resid 1336 through 1337 Processing sheet with id=AI8, first strand: chain '5' and resid 90 through 95 removed outlier: 6.457A pdb=" N VAL 5 206 " --> pdb=" O LEU 5 191 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEU 5 191 " --> pdb=" O VAL 5 206 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N LEU 5 110 " --> pdb=" O VAL 5 188 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain '5' and resid 208 through 210 removed outlier: 4.796A pdb=" N LEU 5 324 " --> pdb=" O ASN 5 356 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU 5 264 " --> pdb=" O LEU 5 324 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N THR 5 326 " --> pdb=" O ALA 5 262 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA 5 262 " --> pdb=" O THR 5 326 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN 5 281 " --> pdb=" O VAL 5 231 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain '5' and resid 208 through 210 removed outlier: 4.796A pdb=" N LEU 5 324 " --> pdb=" O ASN 5 356 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain '5' and resid 222 through 226 Processing sheet with id=AJ3, first strand: chain '6' and resid 4 through 8 removed outlier: 7.483A pdb=" N SER 6 79 " --> pdb=" O VAL 6 75 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N VAL 6 75 " --> pdb=" O SER 6 79 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE 6 81 " --> pdb=" O ASP 6 73 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP 6 73 " --> pdb=" O ILE 6 81 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain '6' and resid 91 through 94 Processing sheet with id=AJ5, first strand: chain '6' and resid 122 through 125 removed outlier: 3.786A pdb=" N LEU 6 125 " --> pdb=" O VAL 6 130 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL 6 130 " --> pdb=" O LEU 6 125 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain '6' and resid 178 through 179 removed outlier: 4.148A pdb=" N TYR 6 186 " --> pdb=" O VAL 6 179 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain '7' and resid 4 through 8 removed outlier: 6.512A pdb=" N SER 7 79 " --> pdb=" O VAL 7 75 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL 7 75 " --> pdb=" O SER 7 79 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE 7 81 " --> pdb=" O ASP 7 73 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain '7' and resid 91 through 94 removed outlier: 4.577A pdb=" N ALA 7 288 " --> pdb=" O THR 7 297 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N TRP 7 299 " --> pdb=" O THR 7 286 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N THR 7 286 " --> pdb=" O TRP 7 299 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain '7' and resid 109 through 112 Processing sheet with id=AK1, first strand: chain '7' and resid 180 through 181 2777 hydrogen bonds defined for protein. 7851 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 30.62 Time building geometry restraints manager: 23.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 19715 1.33 - 1.45: 15258 1.45 - 1.58: 39165 1.58 - 1.70: 1 1.70 - 1.82: 681 Bond restraints: 74820 Sorted by residual: bond pdb=" N PRO C 425 " pdb=" CA PRO C 425 " ideal model delta sigma weight residual 1.466 1.695 -0.229 1.24e-02 6.50e+03 3.40e+02 bond pdb=" C GLN T1323 " pdb=" N PRO T1324 " ideal model delta sigma weight residual 1.336 1.507 -0.171 1.08e-02 8.57e+03 2.51e+02 bond pdb=" C GLN x 362 " pdb=" N PRO x 363 " ideal model delta sigma weight residual 1.332 1.508 -0.177 1.34e-02 5.57e+03 1.74e+02 bond pdb=" C HIS C 424 " pdb=" N PRO C 425 " ideal model delta sigma weight residual 1.332 1.450 -0.118 1.34e-02 5.57e+03 7.81e+01 bond pdb=" N SER T 393 " pdb=" CA SER T 393 " ideal model delta sigma weight residual 1.453 1.486 -0.033 8.30e-03 1.45e+04 1.61e+01 ... (remaining 74815 not shown) Histogram of bond angle deviations from ideal: 96.39 - 104.89: 1729 104.89 - 113.39: 41285 113.39 - 121.89: 43502 121.89 - 130.38: 14724 130.38 - 138.88: 405 Bond angle restraints: 101645 Sorted by residual: angle pdb=" C HIS C 424 " pdb=" N PRO C 425 " pdb=" CA PRO C 425 " ideal model delta sigma weight residual 119.78 138.88 -19.10 1.03e+00 9.43e-01 3.44e+02 angle pdb=" C GLN x 362 " pdb=" N PRO x 363 " pdb=" CA PRO x 363 " ideal model delta sigma weight residual 119.78 132.98 -13.20 1.03e+00 9.43e-01 1.64e+02 angle pdb=" C GLN T1323 " pdb=" N PRO T1324 " pdb=" CA PRO T1324 " ideal model delta sigma weight residual 119.82 130.74 -10.92 9.80e-01 1.04e+00 1.24e+02 angle pdb=" CA PRO C 425 " pdb=" N PRO C 425 " pdb=" CD PRO C 425 " ideal model delta sigma weight residual 112.00 100.32 11.68 1.40e+00 5.10e-01 6.97e+01 angle pdb=" CA GLN T1323 " pdb=" C GLN T1323 " pdb=" N PRO T1324 " ideal model delta sigma weight residual 119.06 125.50 -6.44 1.05e+00 9.07e-01 3.76e+01 ... (remaining 101640 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 39729 17.96 - 35.91: 4369 35.91 - 53.87: 681 53.87 - 71.83: 150 71.83 - 89.78: 68 Dihedral angle restraints: 44997 sinusoidal: 17849 harmonic: 27148 Sorted by residual: dihedral pdb=" CA HIS 5 312 " pdb=" C HIS 5 312 " pdb=" N ILE 5 313 " pdb=" CA ILE 5 313 " ideal model delta harmonic sigma weight residual -180.00 -127.12 -52.88 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CA LEU T 817 " pdb=" C LEU T 817 " pdb=" N PRO T 818 " pdb=" CA PRO T 818 " ideal model delta harmonic sigma weight residual 180.00 135.14 44.86 0 5.00e+00 4.00e-02 8.05e+01 dihedral pdb=" CA GLY 2 66 " pdb=" C GLY 2 66 " pdb=" N VAL 2 67 " pdb=" CA VAL 2 67 " ideal model delta harmonic sigma weight residual -180.00 -139.85 -40.15 0 5.00e+00 4.00e-02 6.45e+01 ... (remaining 44994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 11079 0.128 - 0.255: 359 0.255 - 0.383: 11 0.383 - 0.510: 1 0.510 - 0.638: 1 Chirality restraints: 11451 Sorted by residual: chirality pdb=" CA PRO C 425 " pdb=" N PRO C 425 " pdb=" C PRO C 425 " pdb=" CB PRO C 425 " both_signs ideal model delta sigma weight residual False 2.72 3.36 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" CB ILE 5 216 " pdb=" CA ILE 5 216 " pdb=" CG1 ILE 5 216 " pdb=" CG2 ILE 5 216 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.62e+00 chirality pdb=" CB ILE S 748 " pdb=" CA ILE S 748 " pdb=" CG1 ILE S 748 " pdb=" CG2 ILE S 748 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 11448 not shown) Planarity restraints: 13225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP x 361 " -0.026 2.00e-02 2.50e+03 4.99e-02 2.49e+01 pdb=" C ASP x 361 " 0.086 2.00e-02 2.50e+03 pdb=" O ASP x 361 " -0.032 2.00e-02 2.50e+03 pdb=" N GLN x 362 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU T1322 " 0.021 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" C GLU T1322 " -0.071 2.00e-02 2.50e+03 pdb=" O GLU T1322 " 0.026 2.00e-02 2.50e+03 pdb=" N GLN T1323 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU T 817 " 0.061 5.00e-02 4.00e+02 9.15e-02 1.34e+01 pdb=" N PRO T 818 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO T 818 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO T 818 " 0.051 5.00e-02 4.00e+02 ... (remaining 13222 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.24: 6 2.24 - 2.90: 29200 2.90 - 3.57: 106675 3.57 - 4.23: 174047 4.23 - 4.90: 288808 Nonbonded interactions: 598736 Sorted by model distance: nonbonded pdb=" CE1 PHE 7 209 " pdb=" CD1 LEU 7 274 " model vdw 1.573 3.760 nonbonded pdb=" O ASN 7 204 " pdb=" CD1 TYR 7 208 " model vdw 1.852 3.340 nonbonded pdb=" OE1 GLN C 45 " pdb=" OG1 THR C 55 " model vdw 2.012 2.440 nonbonded pdb=" CE2 TYR x 507 " pdb=" CG1 VAL x 967 " model vdw 2.194 3.760 nonbonded pdb=" OH TYR 6 61 " pdb=" O LEU 6 280 " model vdw 2.209 2.440 ... (remaining 598731 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '2' and resid 3 through 73) selection = (chain 'Y' and resid 3 through 73) selection = (chain 'Z' and resid 3 through 73) selection = chain 'm' selection = (chain 'y' and resid 3 through 73) } ncs_group { reference = (chain '5' and (resid 9 through 148 or resid 151 through 363)) selection = (chain 'e' and (resid 9 through 65 or resid 85 through 238 or resid 261 through \ 363)) } ncs_group { reference = (chain '6' and (resid 1 through 9 or resid 13 through 32 or resid 38 through 50 \ or resid 54 through 125 or resid 131 through 160 or resid 172 through 190 or res \ id 200 through 301)) selection = (chain '7' and (resid 1 through 9 or resid 13 through 50 or resid 54 through 125 \ or resid 131 through 160 or resid 172 through 301)) selection = (chain 'f' and (resid 1 through 9 or resid 13 through 32 or resid 38 through 50 \ or resid 54 through 125 or resid 131 through 190 or resid 200 through 301)) selection = (chain 'g' and (resid 1 through 32 or resid 38 through 160 or resid 172 through \ 190 or resid 200 through 301)) } ncs_group { reference = (chain 'S' and (resid 51 through 104 or resid 113 through 256 or resid 264 throu \ gh 337 or resid 340 or resid 342 or resid 364 through 417 or resid 431 through 7 \ 85 or resid 788 through 1298 or resid 1321 through 1348 or resid 1357 through 13 \ 75)) selection = (chain 'T' and (resid 51 through 104 or resid 113 through 256 or resid 264 throu \ gh 337 or resid 340 or resid 342 or resid 364 through 417 or resid 431 through 7 \ 85 or resid 788 through 1149 or resid 1179 through 1298 or resid 1321 through 13 \ 48 or resid 1357 through 1375)) selection = (chain 'W' and (resid 51 through 256 or resid 264 through 337 or resid 351 or re \ sid 353 or resid 364 through 417 or resid 431 through 1298 or resid 1321 through \ 1348 or resid 1357 through 1375)) selection = (chain 'l' and (resid 51 through 104 or resid 113 through 337 or resid 340 or re \ sid 342 or resid 364 through 785 or resid 788 through 1149 or resid 1179 through \ 1375)) selection = (chain 'x' and (resid 51 through 104 or resid 113 through 256 or resid 264 throu \ gh 337 or resid 340 or resid 342 or resid 364 through 417 or resid 431 through 7 \ 85 or resid 788 through 952 or (resid 953 and (name N or name CA or name C or na \ me CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) o \ r resid 954 through 1298 or resid 1321 through 1348 or resid 1357 through 1375)) \ } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.550 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: 8.770 Check model and map are aligned: 0.790 Set scattering table: 0.490 Process input model: 145.940 Find NCS groups from input model: 4.520 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 164.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.229 74820 Z= 0.418 Angle : 0.942 19.103 101645 Z= 0.527 Chirality : 0.057 0.638 11451 Planarity : 0.007 0.091 13225 Dihedral : 15.203 89.782 27427 Min Nonbonded Distance : 1.573 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.77 % Favored : 93.22 % Rotamer: Outliers : 0.70 % Allowed : 11.04 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.20 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.57 (0.07), residues: 9155 helix: -3.28 (0.06), residues: 3427 sheet: -2.62 (0.13), residues: 1184 loop : -2.91 (0.08), residues: 4544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 24 HIS 0.009 0.002 HIS x 333 PHE 0.034 0.002 PHE 5 277 TYR 0.023 0.002 TYR C 302 ARG 0.011 0.001 ARG S 899 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18310 Ramachandran restraints generated. 9155 Oldfield, 0 Emsley, 9155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18310 Ramachandran restraints generated. 9155 Oldfield, 0 Emsley, 9155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2158 residues out of total 7954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 2102 time to evaluate : 6.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE W 953 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 28 LEU cc_start: 0.7848 (pp) cc_final: 0.7609 (pp) REVERT: K 29 ARG cc_start: 0.7348 (mtm-85) cc_final: 0.6148 (mtm-85) REVERT: K 45 GLU cc_start: 0.7318 (pt0) cc_final: 0.7067 (tm-30) REVERT: K 53 ARG cc_start: 0.7984 (tmm-80) cc_final: 0.7781 (ttm-80) REVERT: K 62 LYS cc_start: 0.7937 (mmtt) cc_final: 0.7632 (mmmt) REVERT: K 70 LEU cc_start: 0.6787 (tt) cc_final: 0.6482 (tt) REVERT: G 41 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6803 (mp) REVERT: G 45 GLU cc_start: 0.6600 (tp30) cc_final: 0.6384 (tp30) REVERT: G 62 LYS cc_start: 0.7458 (mmmt) cc_final: 0.7007 (tttp) REVERT: C 1 MET cc_start: 0.4916 (mpp) cc_final: 0.4365 (mpp) REVERT: C 8 GLN cc_start: 0.7616 (tp-100) cc_final: 0.7383 (tp40) REVERT: C 9 VAL cc_start: 0.5041 (m) cc_final: 0.4718 (p) REVERT: C 81 PRO cc_start: 0.7216 (Cg_exo) cc_final: 0.6915 (Cg_endo) REVERT: C 340 ARG cc_start: 0.8046 (tpp80) cc_final: 0.7743 (mtp85) REVERT: C 362 TRP cc_start: 0.6763 (m100) cc_final: 0.6541 (m100) REVERT: C 384 ASP cc_start: 0.8060 (t70) cc_final: 0.6688 (p0) REVERT: C 400 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7619 (mt-10) REVERT: C 452 GLN cc_start: 0.7303 (mt0) cc_final: 0.6941 (mt0) REVERT: C 487 LEU cc_start: 0.7722 (tt) cc_final: 0.7243 (tt) REVERT: C 500 ARG cc_start: 0.7523 (tpt90) cc_final: 0.6873 (tpt-90) REVERT: m 4 ARG cc_start: 0.6488 (OUTLIER) cc_final: 0.5270 (ttm170) REVERT: m 44 GLN cc_start: 0.7786 (mm-40) cc_final: 0.7566 (tp40) REVERT: m 50 PHE cc_start: 0.7261 (t80) cc_final: 0.5931 (t80) REVERT: m 52 THR cc_start: 0.5804 (m) cc_final: 0.5603 (p) REVERT: Y 51 LEU cc_start: 0.8708 (mm) cc_final: 0.8249 (mt) REVERT: Y 62 GLN cc_start: 0.8436 (pp30) cc_final: 0.8038 (tp40) REVERT: Z 7 LYS cc_start: 0.8202 (mmtm) cc_final: 0.7709 (mmmm) REVERT: Z 41 ARG cc_start: 0.8562 (ttm-80) cc_final: 0.8350 (ttm-80) REVERT: Z 42 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7926 (mm-30) REVERT: Z 47 TYR cc_start: 0.8484 (t80) cc_final: 0.8279 (t80) REVERT: Z 51 LEU cc_start: 0.8627 (mm) cc_final: 0.8382 (mm) REVERT: Z 58 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8300 (mt-10) REVERT: 2 57 TYR cc_start: 0.7315 (t80) cc_final: 0.6994 (t80) REVERT: 2 59 GLU cc_start: 0.8270 (pt0) cc_final: 0.7962 (pt0) REVERT: S 8 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7482 (tt0) REVERT: S 109 ARG cc_start: 0.5565 (mmp-170) cc_final: 0.5255 (mtm-85) REVERT: S 135 MET cc_start: 0.5235 (ttt) cc_final: 0.4598 (ttt) REVERT: S 150 GLU cc_start: 0.7393 (pt0) cc_final: 0.6699 (tp30) REVERT: S 170 ASP cc_start: 0.7154 (t70) cc_final: 0.6922 (t70) REVERT: S 199 ASP cc_start: 0.7191 (t0) cc_final: 0.6828 (t0) REVERT: S 207 PHE cc_start: 0.5437 (m-80) cc_final: 0.5213 (m-80) REVERT: S 218 MET cc_start: 0.8724 (mmm) cc_final: 0.8349 (mmm) REVERT: S 220 LYS cc_start: 0.7554 (mttt) cc_final: 0.7264 (ttmm) REVERT: S 284 ASP cc_start: 0.7141 (t0) cc_final: 0.6791 (t70) REVERT: S 314 ARG cc_start: 0.6745 (tpt-90) cc_final: 0.4963 (tpt90) REVERT: S 401 MET cc_start: 0.7135 (mmm) cc_final: 0.6507 (mmm) REVERT: S 425 LYS cc_start: 0.8617 (mppt) cc_final: 0.8128 (mptt) REVERT: S 493 ARG cc_start: 0.7891 (mmt90) cc_final: 0.7404 (mmt-90) REVERT: S 549 TYR cc_start: 0.8301 (p90) cc_final: 0.8057 (p90) REVERT: S 604 GLU cc_start: 0.8159 (pt0) cc_final: 0.7627 (pt0) REVERT: S 620 TYR cc_start: 0.8495 (m-10) cc_final: 0.8021 (m-80) REVERT: S 650 ARG cc_start: 0.8057 (tmm-80) cc_final: 0.6177 (tpt170) REVERT: S 682 MET cc_start: 0.7498 (mmp) cc_final: 0.7062 (mmm) REVERT: S 755 ASP cc_start: 0.8230 (t0) cc_final: 0.7875 (t0) REVERT: S 772 MET cc_start: 0.7720 (mmp) cc_final: 0.7427 (mmp) REVERT: S 790 HIS cc_start: 0.6560 (m-70) cc_final: 0.5990 (t70) REVERT: S 848 HIS cc_start: 0.7178 (t-90) cc_final: 0.6953 (t70) REVERT: S 866 ARG cc_start: 0.7571 (ttt-90) cc_final: 0.6865 (ttm-80) REVERT: S 882 ARG cc_start: 0.6548 (mtt180) cc_final: 0.6017 (mtp180) REVERT: S 936 ARG cc_start: 0.7675 (ttt180) cc_final: 0.7452 (mtt180) REVERT: S 938 ARG cc_start: 0.7501 (tmm-80) cc_final: 0.7127 (tmm-80) REVERT: S 966 ASP cc_start: 0.6792 (t0) cc_final: 0.6408 (m-30) REVERT: S 992 GLU cc_start: 0.7136 (tp30) cc_final: 0.6778 (tp30) REVERT: S 1003 LYS cc_start: 0.7541 (tttp) cc_final: 0.7101 (ttpp) REVERT: S 1050 ASP cc_start: 0.8455 (m-30) cc_final: 0.8008 (m-30) REVERT: S 1062 ARG cc_start: 0.7851 (ptt90) cc_final: 0.7626 (ptm-80) REVERT: S 1067 MET cc_start: 0.7585 (mtp) cc_final: 0.7300 (mtm) REVERT: S 1077 ARG cc_start: 0.6750 (tpt-90) cc_final: 0.6243 (tpm170) REVERT: S 1078 GLU cc_start: 0.6560 (tm-30) cc_final: 0.6300 (tm-30) REVERT: S 1105 MET cc_start: 0.8514 (ttp) cc_final: 0.8282 (ttp) REVERT: S 1136 GLN cc_start: 0.7908 (tm-30) cc_final: 0.7639 (tm-30) REVERT: S 1140 ASP cc_start: 0.8013 (t70) cc_final: 0.7697 (t0) REVERT: S 1235 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7165 (tm-30) REVERT: S 1347 MET cc_start: 0.8591 (mmm) cc_final: 0.8220 (mmt) REVERT: S 1351 GLN cc_start: 0.8552 (mm110) cc_final: 0.7963 (tp40) REVERT: T 191 MET cc_start: 0.8181 (tpt) cc_final: 0.7402 (tpp) REVERT: T 195 GLN cc_start: 0.7144 (mt0) cc_final: 0.6706 (mt0) REVERT: T 202 PHE cc_start: 0.7060 (m-80) cc_final: 0.6746 (m-80) REVERT: T 218 MET cc_start: 0.8415 (ttm) cc_final: 0.8093 (ttp) REVERT: T 251 MET cc_start: 0.8524 (ttm) cc_final: 0.7958 (ttm) REVERT: T 291 LEU cc_start: 0.7990 (mt) cc_final: 0.7459 (pp) REVERT: T 382 GLU cc_start: 0.8433 (pt0) cc_final: 0.8231 (pt0) REVERT: T 415 ASN cc_start: 0.6942 (t0) cc_final: 0.6519 (t0) REVERT: T 432 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7778 (mm110) REVERT: T 454 ASN cc_start: 0.8140 (t0) cc_final: 0.7935 (t0) REVERT: T 495 ASN cc_start: 0.7177 (p0) cc_final: 0.6612 (t0) REVERT: T 500 LEU cc_start: 0.7738 (tp) cc_final: 0.7538 (tp) REVERT: T 535 TYR cc_start: 0.7802 (t80) cc_final: 0.7492 (t80) REVERT: T 541 GLU cc_start: 0.7222 (tp30) cc_final: 0.6690 (tp30) REVERT: T 542 LEU cc_start: 0.8225 (mt) cc_final: 0.7806 (mp) REVERT: T 547 ASP cc_start: 0.7669 (t0) cc_final: 0.7406 (t0) REVERT: T 557 ARG cc_start: 0.6796 (tpt-90) cc_final: 0.5926 (tpp-160) REVERT: T 567 MET cc_start: 0.8596 (mtm) cc_final: 0.7960 (mtm) REVERT: T 568 VAL cc_start: 0.9013 (m) cc_final: 0.8792 (p) REVERT: T 619 PHE cc_start: 0.7736 (m-10) cc_final: 0.7110 (m-80) REVERT: T 635 MET cc_start: 0.8068 (mtp) cc_final: 0.7836 (ttm) REVERT: T 672 ASN cc_start: 0.6878 (t0) cc_final: 0.5684 (p0) REVERT: T 678 GLU cc_start: 0.8379 (tt0) cc_final: 0.7947 (tt0) REVERT: T 689 GLU cc_start: 0.7699 (tp30) cc_final: 0.7295 (tt0) REVERT: T 698 MET cc_start: 0.8215 (tmm) cc_final: 0.7938 (tmm) REVERT: T 709 GLU cc_start: 0.6999 (pm20) cc_final: 0.6715 (pm20) REVERT: T 722 ASN cc_start: 0.7990 (m110) cc_final: 0.7303 (t0) REVERT: T 765 ARG cc_start: 0.8387 (ttt-90) cc_final: 0.7407 (mtp85) REVERT: T 772 MET cc_start: 0.6255 (mmm) cc_final: 0.6000 (mmm) REVERT: T 788 HIS cc_start: 0.7048 (p-80) cc_final: 0.6758 (t-170) REVERT: T 815 VAL cc_start: 0.8682 (p) cc_final: 0.8362 (p) REVERT: T 832 PHE cc_start: 0.8192 (m-80) cc_final: 0.7910 (m-10) REVERT: T 899 ARG cc_start: 0.6665 (tpt170) cc_final: 0.6338 (tpt170) REVERT: T 920 GLU cc_start: 0.7346 (mt-10) cc_final: 0.7038 (mt-10) REVERT: T 935 GLU cc_start: 0.8115 (tp30) cc_final: 0.7870 (tp30) REVERT: T 972 MET cc_start: 0.7399 (mmp) cc_final: 0.5633 (ttp) REVERT: T 995 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7781 (mt-10) REVERT: T 1004 TYR cc_start: 0.8368 (t80) cc_final: 0.7997 (t80) REVERT: T 1021 MET cc_start: 0.8192 (mtp) cc_final: 0.7865 (mtp) REVERT: T 1050 ASP cc_start: 0.8041 (m-30) cc_final: 0.7471 (p0) REVERT: T 1056 ASN cc_start: 0.9026 (m110) cc_final: 0.8446 (m110) REVERT: T 1105 MET cc_start: 0.8122 (ttp) cc_final: 0.7833 (ttp) REVERT: T 1122 GLN cc_start: 0.9066 (pt0) cc_final: 0.8712 (pt0) REVERT: T 1229 ARG cc_start: 0.7734 (mtm180) cc_final: 0.7363 (ptp90) REVERT: T 1252 ASP cc_start: 0.8182 (t0) cc_final: 0.7815 (t0) REVERT: T 1297 ARG cc_start: 0.8063 (ptp90) cc_final: 0.7822 (mtm-85) REVERT: T 1320 PHE cc_start: 0.7032 (OUTLIER) cc_final: 0.5606 (p90) REVERT: T 1340 ARG cc_start: 0.8060 (mtp180) cc_final: 0.7218 (ppt170) REVERT: T 1345 GLU cc_start: 0.7296 (tm-30) cc_final: 0.6962 (tm-30) REVERT: T 1365 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8158 (tm-30) REVERT: W 20 ASP cc_start: 0.6347 (m-30) cc_final: 0.6055 (m-30) REVERT: W 31 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7504 (mm-30) REVERT: W 81 GLU cc_start: 0.8478 (tp30) cc_final: 0.8096 (tt0) REVERT: W 132 GLU cc_start: 0.7644 (tt0) cc_final: 0.6757 (tm-30) REVERT: W 150 GLU cc_start: 0.7908 (tt0) cc_final: 0.7505 (tp30) REVERT: W 153 GLU cc_start: 0.8669 (tp30) cc_final: 0.7979 (tp30) REVERT: W 191 MET cc_start: 0.8124 (tpt) cc_final: 0.7539 (tpp) REVERT: W 221 ARG cc_start: 0.8319 (ttm110) cc_final: 0.7716 (ttt-90) REVERT: W 303 MET cc_start: 0.6782 (mmt) cc_final: 0.6318 (ttm) REVERT: W 361 ASP cc_start: 0.6996 (p0) cc_final: 0.6465 (t70) REVERT: W 413 MET cc_start: 0.8919 (mmm) cc_final: 0.8683 (mmp) REVERT: W 437 GLU cc_start: 0.8095 (pm20) cc_final: 0.7765 (pm20) REVERT: W 498 ASN cc_start: 0.8200 (t0) cc_final: 0.7551 (t0) REVERT: W 502 ILE cc_start: 0.7559 (mt) cc_final: 0.7350 (mt) REVERT: W 522 CYS cc_start: 0.6406 (p) cc_final: 0.5998 (p) REVERT: W 527 GLU cc_start: 0.7635 (mp0) cc_final: 0.6967 (mm-30) REVERT: W 599 ASP cc_start: 0.7614 (m-30) cc_final: 0.7186 (p0) REVERT: W 640 VAL cc_start: 0.8417 (m) cc_final: 0.8119 (m) REVERT: W 693 LEU cc_start: 0.8530 (mp) cc_final: 0.8038 (mp) REVERT: W 699 ARG cc_start: 0.8422 (mtm180) cc_final: 0.8214 (mtm110) REVERT: W 714 TYR cc_start: 0.8192 (m-80) cc_final: 0.7949 (m-10) REVERT: W 745 GLN cc_start: 0.7802 (tt0) cc_final: 0.7590 (mt0) REVERT: W 769 MET cc_start: 0.7195 (mmm) cc_final: 0.6496 (ttt) REVERT: W 772 MET cc_start: 0.7936 (mpp) cc_final: 0.7183 (mpp) REVERT: W 806 ASP cc_start: 0.7919 (m-30) cc_final: 0.7640 (t0) REVERT: W 918 ARG cc_start: 0.7562 (mtt-85) cc_final: 0.7319 (mtt-85) REVERT: W 973 ARG cc_start: 0.7210 (ptt-90) cc_final: 0.6815 (ptt90) REVERT: W 999 SER cc_start: 0.8636 (p) cc_final: 0.8323 (p) REVERT: W 1024 LYS cc_start: 0.6965 (mttt) cc_final: 0.6670 (mtpt) REVERT: W 1067 MET cc_start: 0.7473 (ptp) cc_final: 0.7187 (ptp) REVERT: W 1117 MET cc_start: 0.8535 (ptp) cc_final: 0.8257 (ptm) REVERT: W 1198 LYS cc_start: 0.2502 (mttt) cc_final: 0.1539 (mmtt) REVERT: W 1268 TYR cc_start: 0.8244 (t80) cc_final: 0.7886 (t80) REVERT: W 1282 ARG cc_start: 0.4463 (ttp80) cc_final: 0.3159 (mtt-85) REVERT: W 1335 LEU cc_start: 0.9177 (tp) cc_final: 0.8833 (tt) REVERT: x 79 ASN cc_start: 0.8625 (OUTLIER) cc_final: 0.8417 (p0) REVERT: x 83 LYS cc_start: 0.8568 (mtpt) cc_final: 0.8275 (mtmm) REVERT: x 84 ASP cc_start: 0.7527 (p0) cc_final: 0.7132 (p0) REVERT: x 117 ILE cc_start: 0.9084 (mt) cc_final: 0.8839 (tt) REVERT: x 153 GLU cc_start: 0.5107 (mm-30) cc_final: 0.4770 (mm-30) REVERT: x 191 MET cc_start: 0.8380 (tpt) cc_final: 0.7722 (tpt) REVERT: x 218 MET cc_start: 0.8289 (mtp) cc_final: 0.8076 (mtm) REVERT: x 250 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8170 (mt-10) REVERT: x 258 GLU cc_start: 0.7870 (pm20) cc_final: 0.7519 (pm20) REVERT: x 267 TYR cc_start: 0.8691 (m-80) cc_final: 0.8238 (m-10) REVERT: x 301 GLN cc_start: 0.8412 (pt0) cc_final: 0.7933 (pm20) REVERT: x 303 MET cc_start: 0.8066 (mmm) cc_final: 0.7835 (mmm) REVERT: x 386 LYS cc_start: 0.8744 (ttpt) cc_final: 0.8374 (tptt) REVERT: x 413 MET cc_start: 0.8768 (mmm) cc_final: 0.8229 (mmp) REVERT: x 489 LEU cc_start: 0.7928 (mt) cc_final: 0.7721 (mt) REVERT: x 496 HIS cc_start: 0.7099 (m-70) cc_final: 0.6702 (m90) REVERT: x 497 MET cc_start: 0.7925 (tpp) cc_final: 0.7709 (tpp) REVERT: x 518 ILE cc_start: 0.9150 (mt) cc_final: 0.8896 (mm) REVERT: x 528 ASP cc_start: 0.8513 (p0) cc_final: 0.7637 (t0) REVERT: x 549 TYR cc_start: 0.8214 (p90) cc_final: 0.7825 (p90) REVERT: x 561 ARG cc_start: 0.7297 (mtm180) cc_final: 0.7010 (mtp85) REVERT: x 635 MET cc_start: 0.8834 (mtp) cc_final: 0.8617 (mtp) REVERT: x 643 CYS cc_start: 0.8333 (m) cc_final: 0.8099 (m) REVERT: x 658 ASN cc_start: 0.8752 (p0) cc_final: 0.7401 (p0) REVERT: x 659 SER cc_start: 0.8921 (p) cc_final: 0.8463 (m) REVERT: x 662 MET cc_start: 0.8539 (tpp) cc_final: 0.8218 (tpp) REVERT: x 677 LYS cc_start: 0.7906 (tptt) cc_final: 0.7317 (mmmt) REVERT: x 755 ASP cc_start: 0.6322 (m-30) cc_final: 0.6000 (m-30) REVERT: x 779 LEU cc_start: 0.7510 (tp) cc_final: 0.7246 (tp) REVERT: x 782 TYR cc_start: 0.7113 (t80) cc_final: 0.6704 (t80) REVERT: x 831 ASP cc_start: 0.7574 (t70) cc_final: 0.6501 (m-30) REVERT: x 869 LEU cc_start: 0.8968 (mm) cc_final: 0.8759 (mp) REVERT: x 916 ASP cc_start: 0.7565 (m-30) cc_final: 0.7323 (m-30) REVERT: x 920 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7516 (mt-10) REVERT: x 942 GLN cc_start: 0.7871 (pt0) cc_final: 0.7503 (pm20) REVERT: x 988 GLN cc_start: 0.7896 (pt0) cc_final: 0.7404 (pm20) REVERT: x 1001 MET cc_start: 0.7818 (mmt) cc_final: 0.7517 (mmm) REVERT: x 1024 LYS cc_start: 0.8288 (mttt) cc_final: 0.8023 (mttp) REVERT: x 1050 ASP cc_start: 0.8135 (m-30) cc_final: 0.7935 (m-30) REVERT: x 1076 ARG cc_start: 0.8246 (mtp180) cc_final: 0.7850 (mmm160) REVERT: x 1080 ARG cc_start: 0.7229 (mtm-85) cc_final: 0.6842 (tpm170) REVERT: x 1096 ASP cc_start: 0.7240 (t0) cc_final: 0.7039 (t0) REVERT: x 1117 MET cc_start: 0.8588 (mpp) cc_final: 0.8353 (mpp) REVERT: x 1235 GLU cc_start: 0.8004 (tp30) cc_final: 0.7501 (tp30) REVERT: x 1240 VAL cc_start: 0.8908 (t) cc_final: 0.8655 (p) REVERT: x 1257 SER cc_start: 0.8164 (t) cc_final: 0.7369 (m) REVERT: x 1305 SER cc_start: 0.8493 (t) cc_final: 0.8168 (m) REVERT: x 1308 GLU cc_start: 0.7517 (pm20) cc_final: 0.7131 (pm20) REVERT: x 1330 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7454 (mm-30) REVERT: x 1347 MET cc_start: 0.8590 (mmt) cc_final: 0.8373 (mmm) REVERT: x 1369 VAL cc_start: 0.9002 (OUTLIER) cc_final: 0.8735 (p) REVERT: y 3 ARG cc_start: 0.8065 (ptp-110) cc_final: 0.7493 (mtm110) REVERT: y 10 LEU cc_start: 0.6668 (mp) cc_final: 0.6224 (pt) REVERT: e 168 LEU cc_start: 0.8143 (mm) cc_final: 0.7825 (mp) REVERT: e 193 GLU cc_start: 0.7416 (tt0) cc_final: 0.7057 (tt0) REVERT: e 204 THR cc_start: 0.9009 (m) cc_final: 0.8457 (p) REVERT: e 232 ASP cc_start: 0.7725 (t0) cc_final: 0.7354 (t0) REVERT: e 290 MET cc_start: 0.7311 (ptp) cc_final: 0.7086 (mmm) REVERT: e 292 ILE cc_start: 0.7721 (tt) cc_final: 0.7189 (mt) REVERT: e 305 TYR cc_start: 0.6896 (t80) cc_final: 0.6403 (t80) REVERT: e 359 ASP cc_start: 0.7238 (p0) cc_final: 0.6616 (p0) REVERT: f 21 MET cc_start: 0.8576 (tpp) cc_final: 0.8217 (tpp) REVERT: f 56 ASP cc_start: 0.7850 (t0) cc_final: 0.7509 (t70) REVERT: f 62 ASN cc_start: 0.7703 (m-40) cc_final: 0.6709 (t0) REVERT: f 74 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7686 (tm-30) REVERT: f 144 GLU cc_start: 0.7433 (tp30) cc_final: 0.7218 (tp30) REVERT: f 154 ASN cc_start: 0.7644 (t0) cc_final: 0.7393 (t0) REVERT: f 186 TYR cc_start: 0.6434 (m-80) cc_final: 0.6211 (m-80) REVERT: f 223 LEU cc_start: 0.7057 (tt) cc_final: 0.6845 (tt) REVERT: f 249 ARG cc_start: 0.6332 (ptp-170) cc_final: 0.5904 (mtm-85) REVERT: f 250 ILE cc_start: 0.6510 (mt) cc_final: 0.5902 (mt) REVERT: g 20 LYS cc_start: 0.9105 (mtpt) cc_final: 0.8696 (mtmm) REVERT: g 40 VAL cc_start: 0.7823 (t) cc_final: 0.7458 (m) REVERT: g 74 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7315 (tm-30) REVERT: g 91 TYR cc_start: 0.7377 (m-80) cc_final: 0.6031 (m-80) REVERT: g 161 MET cc_start: 0.7764 (mtt) cc_final: 0.7127 (ttp) REVERT: g 169 MET cc_start: 0.8071 (tpt) cc_final: 0.7391 (tmm) REVERT: g 197 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6834 (tt) REVERT: g 203 ASP cc_start: 0.8126 (p0) cc_final: 0.7614 (p0) REVERT: g 230 HIS cc_start: 0.6515 (m-70) cc_final: 0.6267 (m90) REVERT: g 274 LEU cc_start: 0.9013 (tp) cc_final: 0.8813 (tp) REVERT: g 278 PHE cc_start: 0.8541 (m-10) cc_final: 0.8180 (m-80) REVERT: l 44 ASP cc_start: 0.6642 (t70) cc_final: 0.5447 (m-30) REVERT: l 96 ARG cc_start: 0.7799 (mtt-85) cc_final: 0.5761 (pmt-80) REVERT: l 131 MET cc_start: 0.8270 (mtm) cc_final: 0.8065 (mtp) REVERT: l 132 GLU cc_start: 0.8211 (tp30) cc_final: 0.7941 (tp30) REVERT: l 191 MET cc_start: 0.7363 (tpt) cc_final: 0.7114 (tpp) REVERT: l 218 MET cc_start: 0.7369 (ttm) cc_final: 0.7146 (mtp) REVERT: l 236 MET cc_start: 0.7585 (ptp) cc_final: 0.7282 (ptm) REVERT: l 296 GLU cc_start: 0.7889 (tp30) cc_final: 0.7649 (tp30) REVERT: l 300 ASN cc_start: 0.8258 (p0) cc_final: 0.7591 (t0) REVERT: l 303 MET cc_start: 0.7558 (mmt) cc_final: 0.7250 (mmm) REVERT: l 332 GLU cc_start: 0.8337 (tm-30) cc_final: 0.8027 (tp30) REVERT: l 382 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7264 (tp30) REVERT: l 399 ARG cc_start: 0.8010 (mtt-85) cc_final: 0.7432 (mtp85) REVERT: l 401 MET cc_start: 0.8132 (mmm) cc_final: 0.7598 (mmt) REVERT: l 443 LYS cc_start: 0.8518 (pttt) cc_final: 0.8312 (ptmt) REVERT: l 459 LEU cc_start: 0.8036 (mm) cc_final: 0.7802 (mm) REVERT: l 497 MET cc_start: 0.7361 (tpp) cc_final: 0.6628 (mmm) REVERT: l 498 ASN cc_start: 0.7805 (t0) cc_final: 0.7167 (t0) REVERT: l 531 HIS cc_start: 0.8029 (t-90) cc_final: 0.7736 (t-90) REVERT: l 550 ILE cc_start: 0.7801 (tt) cc_final: 0.7597 (mt) REVERT: l 567 MET cc_start: 0.8711 (mtm) cc_final: 0.8445 (mtm) REVERT: l 608 ASP cc_start: 0.7886 (t0) cc_final: 0.7634 (t0) REVERT: l 623 GLU cc_start: 0.6864 (mm-30) cc_final: 0.6653 (tp30) REVERT: l 649 GLU cc_start: 0.7499 (mp0) cc_final: 0.7294 (tp30) REVERT: l 664 LYS cc_start: 0.7894 (tptt) cc_final: 0.7511 (tttt) REVERT: l 668 ARG cc_start: 0.7563 (mmp-170) cc_final: 0.7360 (mmp-170) REVERT: l 678 GLU cc_start: 0.7430 (pm20) cc_final: 0.7039 (mp0) REVERT: l 697 LEU cc_start: 0.8663 (mm) cc_final: 0.8390 (mt) REVERT: l 751 GLU cc_start: 0.7463 (mp0) cc_final: 0.6874 (tp30) REVERT: l 776 PHE cc_start: 0.6604 (m-10) cc_final: 0.6250 (m-80) REVERT: l 796 LEU cc_start: 0.7416 (mm) cc_final: 0.7171 (mm) REVERT: l 812 PHE cc_start: 0.8486 (t80) cc_final: 0.7749 (t80) REVERT: l 814 TYR cc_start: 0.7192 (m-80) cc_final: 0.6928 (m-80) REVERT: l 964 HIS cc_start: 0.5657 (t-90) cc_final: 0.5395 (t70) REVERT: l 1018 MET cc_start: 0.7072 (tpp) cc_final: 0.6657 (tpp) REVERT: l 1025 MET cc_start: 0.7295 (mmm) cc_final: 0.7079 (mmp) REVERT: l 1030 TYR cc_start: 0.8328 (m-10) cc_final: 0.7454 (m-80) REVERT: l 1033 GLN cc_start: 0.7867 (mt0) cc_final: 0.7306 (mp10) REVERT: l 1051 GLU cc_start: 0.8114 (tt0) cc_final: 0.7799 (tt0) REVERT: l 1096 ASP cc_start: 0.8173 (t70) cc_final: 0.7565 (t0) REVERT: l 1123 ASP cc_start: 0.7907 (t0) cc_final: 0.7489 (t70) REVERT: l 1127 VAL cc_start: 0.8883 (p) cc_final: 0.8648 (m) REVERT: l 1217 GLN cc_start: 0.7468 (mm-40) cc_final: 0.7241 (tp40) REVERT: l 1237 ARG cc_start: 0.8263 (ttp-110) cc_final: 0.7138 (ttp-170) REVERT: l 1253 ILE cc_start: 0.8667 (pt) cc_final: 0.8311 (pt) REVERT: l 1323 GLN cc_start: 0.6854 (tp40) cc_final: 0.5439 (tp-100) REVERT: l 1347 MET cc_start: 0.6457 (mmt) cc_final: 0.6114 (mmp) REVERT: 5 4 GLN cc_start: 0.7508 (tp40) cc_final: 0.6447 (tt0) REVERT: 5 19 LEU cc_start: 0.8667 (tp) cc_final: 0.8240 (tp) REVERT: 5 34 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7288 (mp0) REVERT: 5 45 GLU cc_start: 0.7500 (tm-30) cc_final: 0.7134 (tm-30) REVERT: 5 101 ASN cc_start: 0.6832 (t0) cc_final: 0.6574 (t0) REVERT: 5 115 GLN cc_start: 0.8592 (mm-40) cc_final: 0.8056 (mt0) REVERT: 5 132 PHE cc_start: 0.7075 (t80) cc_final: 0.6756 (t80) REVERT: 5 136 ASN cc_start: 0.7259 (m-40) cc_final: 0.6824 (m-40) REVERT: 5 174 ARG cc_start: 0.7430 (ttt-90) cc_final: 0.6533 (mmm160) REVERT: 5 202 LYS cc_start: 0.8410 (tttt) cc_final: 0.8209 (ttpt) REVERT: 5 204 THR cc_start: 0.7241 (m) cc_final: 0.6680 (p) REVERT: 5 290 MET cc_start: 0.7416 (mpp) cc_final: 0.6977 (mpp) REVERT: 5 304 ARG cc_start: 0.7508 (mmm160) cc_final: 0.7213 (tpp80) REVERT: 5 310 PRO cc_start: 0.5934 (Cg_endo) cc_final: 0.5659 (Cg_exo) REVERT: 5 333 TRP cc_start: 0.7179 (p-90) cc_final: 0.6879 (p-90) REVERT: 5 341 ARG cc_start: 0.7836 (mmp80) cc_final: 0.7194 (ptt90) REVERT: 6 2 ASP cc_start: 0.6356 (t0) cc_final: 0.5909 (t0) REVERT: 6 3 LEU cc_start: 0.6241 (mm) cc_final: 0.6029 (mm) REVERT: 6 108 SER cc_start: 0.4494 (t) cc_final: 0.3357 (t) REVERT: 6 136 MET cc_start: 0.4866 (tpt) cc_final: 0.4556 (tpt) REVERT: 6 146 VAL cc_start: 0.7739 (t) cc_final: 0.7463 (t) REVERT: 6 147 LEU cc_start: 0.7830 (mt) cc_final: 0.7568 (tp) REVERT: 6 164 PRO cc_start: 0.5890 (Cg_endo) cc_final: 0.5634 (Cg_exo) REVERT: 6 218 ARG cc_start: 0.6608 (mmp80) cc_final: 0.5761 (mmm-85) REVERT: 6 229 ARG cc_start: 0.7410 (mmm160) cc_final: 0.6754 (ttm-80) REVERT: 7 20 LYS cc_start: 0.7543 (ptpp) cc_final: 0.7067 (tppt) REVERT: 7 136 MET cc_start: 0.7260 (tpt) cc_final: 0.6589 (tpp) REVERT: 7 144 GLU cc_start: 0.7795 (pp20) cc_final: 0.6949 (pp20) REVERT: 7 175 HIS cc_start: 0.4978 (m170) cc_final: 0.4341 (m170) REVERT: 7 176 LEU cc_start: 0.5969 (mp) cc_final: 0.5727 (tt) REVERT: 7 184 HIS cc_start: 0.5725 (m-70) cc_final: 0.5265 (m-70) REVERT: 7 207 LEU cc_start: 0.8123 (mt) cc_final: 0.7818 (mt) REVERT: 7 221 MET cc_start: 0.6765 (ptm) cc_final: 0.5651 (mmm) REVERT: 7 230 HIS cc_start: 0.3375 (t70) cc_final: 0.3163 (t70) REVERT: 7 239 PHE cc_start: 0.6927 (m-80) cc_final: 0.5962 (t80) REVERT: 7 263 ARG cc_start: 0.7610 (mtp85) cc_final: 0.7243 (mtt-85) REVERT: 7 267 MET cc_start: 0.6875 (tmm) cc_final: 0.6616 (tmm) outliers start: 56 outliers final: 20 residues processed: 2147 average time/residue: 0.7371 time to fit residues: 2609.3023 Evaluate side-chains 1482 residues out of total 7954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1456 time to evaluate : 6.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.3874 > 50: distance: 76 - 90: 3.088 distance: 79 - 95: 10.185 distance: 83 - 100: 15.545 distance: 87 - 107: 9.154 distance: 92 - 95: 7.796 distance: 95 - 96: 22.553 distance: 96 - 97: 13.842 distance: 96 - 99: 14.860 distance: 97 - 98: 21.172 distance: 97 - 100: 27.883 distance: 100 - 101: 15.654 distance: 101 - 102: 17.339 distance: 101 - 104: 12.529 distance: 102 - 103: 22.991 distance: 102 - 107: 8.161 distance: 104 - 105: 14.275 distance: 104 - 106: 9.006 distance: 108 - 111: 7.735 distance: 109 - 110: 7.385 distance: 109 - 115: 7.875 distance: 111 - 112: 5.242 distance: 112 - 113: 12.292 distance: 113 - 114: 9.626 distance: 115 - 116: 6.580 distance: 116 - 117: 4.997 distance: 116 - 119: 5.630 distance: 117 - 118: 5.292 distance: 117 - 125: 4.127 distance: 118 - 149: 11.027 distance: 119 - 120: 9.816 distance: 120 - 121: 14.687 distance: 120 - 122: 18.777 distance: 121 - 123: 16.870 distance: 122 - 124: 12.849 distance: 123 - 124: 18.910 distance: 125 - 126: 5.113 distance: 127 - 128: 8.407 distance: 127 - 134: 5.861 distance: 129 - 130: 11.753 distance: 130 - 131: 9.730 distance: 131 - 132: 5.879 distance: 131 - 133: 12.856 distance: 134 - 135: 6.913 distance: 135 - 136: 7.829 distance: 135 - 138: 6.834 distance: 136 - 137: 8.120 distance: 136 - 142: 8.351 distance: 137 - 161: 14.902 distance: 138 - 139: 8.042 distance: 139 - 140: 11.349 distance: 139 - 141: 6.781 distance: 142 - 143: 7.658 distance: 143 - 144: 4.356 distance: 143 - 146: 11.378 distance: 144 - 145: 8.256 distance: 144 - 149: 8.151 distance: 145 - 172: 13.198 distance: 146 - 147: 8.431 distance: 146 - 148: 13.725 distance: 149 - 150: 7.358 distance: 150 - 153: 15.803 distance: 151 - 152: 3.601 distance: 151 - 154: 5.765 distance: 152 - 179: 8.358 distance: 155 - 156: 3.975 distance: 155 - 158: 8.202 distance: 156 - 157: 4.302 distance: 156 - 161: 5.843 distance: 157 - 185: 6.887 distance: 158 - 159: 4.954 distance: 158 - 160: 5.920 distance: 162 - 165: 10.036 distance: 163 - 164: 4.286 distance: 164 - 196: 5.894 distance: 165 - 166: 7.754 distance: 166 - 167: 8.699 distance: 167 - 169: 5.208 distance: 168 - 170: 4.862 distance: 169 - 171: 3.954 distance: 170 - 171: 5.021