Starting phenix.real_space_refine on Sat Feb 17 03:21:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q6g_4465/02_2024/6q6g_4465.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q6g_4465/02_2024/6q6g_4465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q6g_4465/02_2024/6q6g_4465.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q6g_4465/02_2024/6q6g_4465.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q6g_4465/02_2024/6q6g_4465.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q6g_4465/02_2024/6q6g_4465.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 72 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 415 5.16 5 C 43557 2.51 5 N 11654 2.21 5 O 12507 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 111": "OE1" <-> "OE2" Residue "R ASP 173": "OD1" <-> "OD2" Residue "R GLU 223": "OE1" <-> "OE2" Residue "R TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 270": "NH1" <-> "NH2" Residue "R ARG 296": "NH1" <-> "NH2" Residue "R GLU 311": "OE1" <-> "OE2" Residue "R ARG 383": "NH1" <-> "NH2" Residue "R TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 445": "NH1" <-> "NH2" Residue "R ARG 468": "NH1" <-> "NH2" Residue "R GLU 474": "OE1" <-> "OE2" Residue "S GLU 28": "OE1" <-> "OE2" Residue "S ASP 29": "OD1" <-> "OD2" Residue "S PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 12": "OD1" <-> "OD2" Residue "L TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 34": "OE1" <-> "OE2" Residue "A ASP 26": "OD1" <-> "OD2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 218": "OD1" <-> "OD2" Residue "A ASP 252": "OD1" <-> "OD2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A GLU 598": "OE1" <-> "OE2" Residue "A TYR 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 734": "OE1" <-> "OE2" Residue "A ASP 796": "OD1" <-> "OD2" Residue "A TYR 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 943": "OD1" <-> "OD2" Residue "A GLU 964": "OE1" <-> "OE2" Residue "A ASP 969": "OD1" <-> "OD2" Residue "A GLU 972": "OE1" <-> "OE2" Residue "A GLU 1022": "OE1" <-> "OE2" Residue "A ARG 1048": "NH1" <-> "NH2" Residue "A GLU 1064": "OE1" <-> "OE2" Residue "A GLU 1067": "OE1" <-> "OE2" Residue "A ARG 1110": "NH1" <-> "NH2" Residue "A ASP 1221": "OD1" <-> "OD2" Residue "A GLU 1271": "OE1" <-> "OE2" Residue "A GLU 1276": "OE1" <-> "OE2" Residue "A GLU 1323": "OE1" <-> "OE2" Residue "A ASP 1356": "OD1" <-> "OD2" Residue "A ASP 1361": "OD1" <-> "OD2" Residue "A TYR 1375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1381": "NH1" <-> "NH2" Residue "A ASP 1427": "OD1" <-> "OD2" Residue "A TYR 1463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1540": "NH1" <-> "NH2" Residue "A PHE 1566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1694": "OD1" <-> "OD2" Residue "A ARG 1726": "NH1" <-> "NH2" Residue "A GLU 1729": "OE1" <-> "OE2" Residue "A GLU 1752": "OE1" <-> "OE2" Residue "A GLU 1766": "OE1" <-> "OE2" Residue "A TYR 1790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1879": "OE1" <-> "OE2" Residue "N GLU 171": "OE1" <-> "OE2" Residue "N GLU 192": "OE1" <-> "OE2" Residue "N ASP 204": "OD1" <-> "OD2" Residue "N TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 259": "OE1" <-> "OE2" Residue "N GLU 271": "OE1" <-> "OE2" Residue "N GLU 280": "OE1" <-> "OE2" Residue "N GLU 282": "OE1" <-> "OE2" Residue "N ARG 283": "NH1" <-> "NH2" Residue "N ARG 287": "NH1" <-> "NH2" Residue "N PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 323": "NH1" <-> "NH2" Residue "N ARG 325": "NH1" <-> "NH2" Residue "N GLU 342": "OE1" <-> "OE2" Residue "N ASP 350": "OD1" <-> "OD2" Residue "N GLU 359": "OE1" <-> "OE2" Residue "N ARG 367": "NH1" <-> "NH2" Residue "N GLU 383": "OE1" <-> "OE2" Residue "N ARG 385": "NH1" <-> "NH2" Residue "N ASP 395": "OD1" <-> "OD2" Residue "N GLU 418": "OE1" <-> "OE2" Residue "N ASP 433": "OD1" <-> "OD2" Residue "N GLU 478": "OE1" <-> "OE2" Residue "N ASP 486": "OD1" <-> "OD2" Residue "N ASP 500": "OD1" <-> "OD2" Residue "N ASP 513": "OD1" <-> "OD2" Residue "N TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 525": "OD1" <-> "OD2" Residue "N PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 536": "OE1" <-> "OE2" Residue "N PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 569": "NH1" <-> "NH2" Residue "N GLU 576": "OE1" <-> "OE2" Residue "N ASP 578": "OD1" <-> "OD2" Residue "N GLU 584": "OE1" <-> "OE2" Residue "N PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 613": "OE1" <-> "OE2" Residue "N ASP 614": "OD1" <-> "OD2" Residue "N GLU 627": "OE1" <-> "OE2" Residue "N ASP 647": "OD1" <-> "OD2" Residue "N GLU 649": "OE1" <-> "OE2" Residue "N PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 672": "OD1" <-> "OD2" Residue "N GLU 679": "OE1" <-> "OE2" Residue "N GLU 680": "OE1" <-> "OE2" Residue "N GLU 708": "OE1" <-> "OE2" Residue "N PHE 713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 717": "OE1" <-> "OE2" Residue "N GLU 718": "OE1" <-> "OE2" Residue "N ASP 723": "OD1" <-> "OD2" Residue "I ASP 33": "OD1" <-> "OD2" Residue "I PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 94": "OD1" <-> "OD2" Residue "I GLU 158": "OE1" <-> "OE2" Residue "I TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 274": "OE1" <-> "OE2" Residue "I GLU 277": "OE1" <-> "OE2" Residue "I ASP 382": "OD1" <-> "OD2" Residue "I ARG 419": "NH1" <-> "NH2" Residue "I ASP 444": "OD1" <-> "OD2" Residue "I PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 483": "OD1" <-> "OD2" Residue "I ASP 534": "OD1" <-> "OD2" Residue "I TYR 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 629": "OE1" <-> "OE2" Residue "I GLU 647": "OE1" <-> "OE2" Residue "I ASP 655": "OD1" <-> "OD2" Residue "I GLU 715": "OE1" <-> "OE2" Residue "I ASP 747": "OD1" <-> "OD2" Residue "O PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 113": "OD1" <-> "OD2" Residue "O ASP 114": "OD1" <-> "OD2" Residue "O GLU 239": "OE1" <-> "OE2" Residue "O PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 249": "OD1" <-> "OD2" Residue "O GLU 362": "OE1" <-> "OE2" Residue "O ASP 400": "OD1" <-> "OD2" Residue "O ASP 404": "OD1" <-> "OD2" Residue "O ASP 406": "OD1" <-> "OD2" Residue "O GLU 589": "OE1" <-> "OE2" Residue "O GLU 613": "OE1" <-> "OE2" Residue "O TYR 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 622": "OE1" <-> "OE2" Residue "O ASP 659": "OD1" <-> "OD2" Residue "O ASP 705": "OD1" <-> "OD2" Residue "K ARG 34": "NH1" <-> "NH2" Residue "K TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 144": "OD1" <-> "OD2" Residue "K ARG 146": "NH1" <-> "NH2" Residue "K TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 401": "OD1" <-> "OD2" Residue "K PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 427": "OD1" <-> "OD2" Residue "K GLU 430": "OE1" <-> "OE2" Residue "K TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 510": "NH1" <-> "NH2" Residue "K PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 43": "OD1" <-> "OD2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 23": "NH1" <-> "NH2" Residue "M ASP 8": "OD1" <-> "OD2" Residue "M ASP 28": "OD1" <-> "OD2" Residue "M GLU 38": "OE1" <-> "OE2" Residue "M GLU 54": "OE1" <-> "OE2" Residue "H GLU 88": "OE1" <-> "OE2" Residue "J ASP 104": "OD1" <-> "OD2" Residue "J PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 129": "OD1" <-> "OD2" Residue "J GLU 136": "OE1" <-> "OE2" Residue "J PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 163": "OD1" <-> "OD2" Residue "J GLU 514": "OE1" <-> "OE2" Residue "J ASP 558": "OD1" <-> "OD2" Residue "J PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 663": "OD1" <-> "OD2" Residue "J GLU 727": "OE1" <-> "OE2" Residue "J ASP 765": "OD1" <-> "OD2" Residue "P PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 163": "OD1" <-> "OD2" Residue "P GLU 460": "OE1" <-> "OE2" Residue "P GLU 468": "OE1" <-> "OE2" Residue "P ASP 549": "OD1" <-> "OD2" Residue "P ASP 561": "OD1" <-> "OD2" Residue "P PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 615": "OE1" <-> "OE2" Residue "Q ASP 15": "OD1" <-> "OD2" Residue "Q ARG 34": "NH1" <-> "NH2" Residue "Q ASP 39": "OD1" <-> "OD2" Residue "Q ARG 78": "NH1" <-> "NH2" Residue "Q ASP 91": "OD1" <-> "OD2" Residue "Q ASP 141": "OD1" <-> "OD2" Residue "Q TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 232": "OD1" <-> "OD2" Residue "Q ARG 240": "NH1" <-> "NH2" Residue "Q ASP 246": "OD1" <-> "OD2" Residue "Q GLU 317": "OE1" <-> "OE2" Residue "Q ASP 442": "OD1" <-> "OD2" Residue "Q ARG 469": "NH1" <-> "NH2" Residue "Q PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 511": "OD1" <-> "OD2" Residue "Y GLU 92": "OE1" <-> "OE2" Residue "Y ASP 301": "OD1" <-> "OD2" Residue "Y ASP 323": "OD1" <-> "OD2" Residue "Y ARG 354": "NH1" <-> "NH2" Residue "Y GLU 484": "OE1" <-> "OE2" Residue "Y GLU 524": "OE1" <-> "OE2" Residue "Y TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 28": "OD1" <-> "OD2" Residue "U ARG 44": "NH1" <-> "NH2" Residue "U ASP 80": "OD1" <-> "OD2" Residue "U PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 95": "OD1" <-> "OD2" Residue "U ARG 101": "NH1" <-> "NH2" Residue "U GLU 153": "OE1" <-> "OE2" Residue "U ARG 165": "NH1" <-> "NH2" Residue "U GLU 217": "OE1" <-> "OE2" Residue "U GLU 231": "OE1" <-> "OE2" Residue "U GLU 240": "OE1" <-> "OE2" Residue "U GLU 246": "OE1" <-> "OE2" Residue "U ASP 256": "OD1" <-> "OD2" Residue "U ARG 296": "NH1" <-> "NH2" Residue "U ARG 330": "NH1" <-> "NH2" Residue "U ARG 363": "NH1" <-> "NH2" Residue "U ARG 397": "NH1" <-> "NH2" Residue "U TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 441": "OE1" <-> "OE2" Residue "U GLU 466": "OE1" <-> "OE2" Residue "U ASP 527": "OD1" <-> "OD2" Residue "V GLU 45": "OE1" <-> "OE2" Residue "V ASP 85": "OD1" <-> "OD2" Residue "V ARG 101": "NH1" <-> "NH2" Residue "V ARG 165": "NH1" <-> "NH2" Residue "V GLU 166": "OE1" <-> "OE2" Residue "V ASP 168": "OD1" <-> "OD2" Residue "V GLU 194": "OE1" <-> "OE2" Residue "V GLU 217": "OE1" <-> "OE2" Residue "V GLU 231": "OE1" <-> "OE2" Residue "V GLU 246": "OE1" <-> "OE2" Residue "V PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 296": "NH1" <-> "NH2" Residue "V ASP 301": "OD1" <-> "OD2" Residue "V GLU 325": "OE1" <-> "OE2" Residue "V ARG 330": "NH1" <-> "NH2" Residue "V ARG 397": "NH1" <-> "NH2" Residue "V GLU 544": "OE1" <-> "OE2" Residue "Z ASP 160": "OD1" <-> "OD2" Residue "Z GLU 194": "OE1" <-> "OE2" Residue "Z GLU 295": "OE1" <-> "OE2" Residue "Z ASP 309": "OD1" <-> "OD2" Residue "Z TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 354": "NH1" <-> "NH2" Residue "Z GLU 391": "OE1" <-> "OE2" Residue "Z ASP 466": "OD1" <-> "OD2" Residue "Z GLU 484": "OE1" <-> "OE2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 68133 Number of models: 1 Model: "" Number of chains: 21 Chain: "R" Number of atoms: 2957 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 382, 2943 Classifications: {'peptide': 382} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 365} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Conformer: "B" Number of residues, atoms: 382, 2943 Classifications: {'peptide': 382} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 365} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 bond proxies already assigned to first conformer: 3002 Chain: "S" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 216 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "L" Number of atoms: 1446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1446 Classifications: {'peptide': 179} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 166} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 470 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 56, 462 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 5, 'TRANS': 50} Conformer: "B" Number of residues, atoms: 56, 462 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 5, 'TRANS': 50} bond proxies already assigned to first conformer: 465 Chain: "A" Number of atoms: 12152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1553, 12152 Classifications: {'peptide': 1553} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 87, 'TRANS': 1464} Chain breaks: 17 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 78 Chain: "N" Number of atoms: 5260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5260 Classifications: {'peptide': 656} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 624} Chain breaks: 6 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 70 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 79 Chain: "I" Number of atoms: 5752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5752 Classifications: {'peptide': 729} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 705} Chain breaks: 3 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 79 Chain: "O" Number of atoms: 5532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5532 Classifications: {'peptide': 703} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 19, 'TRANS': 683} Chain breaks: 3 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "K" Number of atoms: 4187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 4187 Classifications: {'peptide': 518} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 501} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 657 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 79} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'GLU%COO:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 226 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 25} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "W" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 225 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 24} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 499 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 56} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 459 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 54} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "J" Number of atoms: 3964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3964 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 480} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "P" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3883 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 15, 'TRANS': 468} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "Q" Number of atoms: 4059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 4059 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 14, 'TRANS': 489} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "Y" Number of atoms: 3911 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 499, 3903 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 483} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Conformer: "B" Number of residues, atoms: 499, 3903 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 483} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 bond proxies already assigned to first conformer: 3954 Chain: "U" Number of atoms: 4160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4160 Classifications: {'peptide': 515} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 12, 'TRANS': 502} Chain breaks: 2 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "V" Number of atoms: 4311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4311 Classifications: {'peptide': 530} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 13, 'TRANS': 516} Chain breaks: 1 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "Z" Number of atoms: 3807 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 486, 3799 Classifications: {'peptide': 486} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 470} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Conformer: "B" Number of residues, atoms: 486, 3799 Classifications: {'peptide': 486} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 470} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 bond proxies already assigned to first conformer: 3850 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ACYS R 388 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS R 388 " occ=0.50 residue: pdb=" N AMET R 451 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET R 451 " occ=0.50 Time building chain proxies: 35.17, per 1000 atoms: 0.52 Number of scatterers: 68133 At special positions: 0 Unit cell: (231.387, 196.836, 228.246, 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 415 16.00 O 12507 8.00 N 11654 7.00 C 43557 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: 21.95 Conformation dependent library (CDL) restraints added in 11.8 seconds 16902 Ramachandran restraints generated. 8451 Oldfield, 0 Emsley, 8451 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16396 Finding SS restraints... Secondary structure from input PDB file: 415 helices and 31 sheets defined 65.2% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.65 Creating SS restraints... Processing helix chain 'R' and resid 84 through 97 Processing helix chain 'R' and resid 106 through 121 Processing helix chain 'R' and resid 124 through 128 removed outlier: 3.629A pdb=" N ALA R 128 " --> pdb=" O VAL R 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 12 through 19 removed outlier: 3.857A pdb=" N LEU L 16 " --> pdb=" O ASP L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 46 Processing helix chain 'L' and resid 101 through 105 removed outlier: 3.633A pdb=" N ASN L 104 " --> pdb=" O ASN L 101 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU L 105 " --> pdb=" O PHE L 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 101 through 105' Processing helix chain 'L' and resid 146 through 148 No H-bonds generated for 'chain 'L' and resid 146 through 148' Processing helix chain 'L' and resid 175 through 180 Processing helix chain 'D' and resid 25 through 46 removed outlier: 4.012A pdb=" N GLU D 29 " --> pdb=" O VAL D 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 29 removed outlier: 3.835A pdb=" N ASP A 26 " --> pdb=" O PRO A 22 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 629 removed outlier: 3.708A pdb=" N PHE A 627 " --> pdb=" O GLN A 623 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 629 " --> pdb=" O ILE A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 646 removed outlier: 3.640A pdb=" N GLN A 636 " --> pdb=" O GLU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 665 removed outlier: 3.528A pdb=" N CYS A 663 " --> pdb=" O LEU A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 669 removed outlier: 3.518A pdb=" N GLY A 669 " --> pdb=" O ASN A 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 666 through 669' Processing helix chain 'A' and resid 704 through 712 removed outlier: 3.735A pdb=" N GLU A 708 " --> pdb=" O ASP A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 721 Processing helix chain 'A' and resid 754 through 757 removed outlier: 4.426A pdb=" N THR A 757 " --> pdb=" O LEU A 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 754 through 757' Processing helix chain 'A' and resid 758 through 774 removed outlier: 3.637A pdb=" N LYS A 774 " --> pdb=" O TYR A 770 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 780 Processing helix chain 'A' and resid 782 through 797 removed outlier: 4.027A pdb=" N GLU A 788 " --> pdb=" O CYS A 784 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A 789 " --> pdb=" O SER A 785 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN A 792 " --> pdb=" O GLU A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 808 removed outlier: 4.049A pdb=" N VAL A 803 " --> pdb=" O LEU A 799 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP A 804 " --> pdb=" O GLY A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 852 Processing helix chain 'A' and resid 867 through 881 Processing helix chain 'A' and resid 925 through 938 removed outlier: 3.577A pdb=" N ARG A 929 " --> pdb=" O SER A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 947 Processing helix chain 'A' and resid 948 through 965 Proline residue: A 954 - end of helix Processing helix chain 'A' and resid 971 through 979 removed outlier: 3.675A pdb=" N CYS A 975 " --> pdb=" O PRO A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1028 Processing helix chain 'A' and resid 1032 through 1041 removed outlier: 3.578A pdb=" N ASP A1036 " --> pdb=" O LEU A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1078 removed outlier: 3.920A pdb=" N ARG A1076 " --> pdb=" O GLN A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1088 removed outlier: 4.525A pdb=" N GLY A1083 " --> pdb=" O ALA A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1145 Processing helix chain 'A' and resid 1154 through 1161 removed outlier: 3.574A pdb=" N ASN A1161 " --> pdb=" O TRP A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1181 Processing helix chain 'A' and resid 1184 through 1188 Processing helix chain 'A' and resid 1189 through 1198 Processing helix chain 'A' and resid 1201 through 1217 removed outlier: 3.511A pdb=" N SER A1205 " --> pdb=" O HIS A1201 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER A1213 " --> pdb=" O LEU A1209 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS A1216 " --> pdb=" O VAL A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1230 removed outlier: 3.629A pdb=" N ILE A1230 " --> pdb=" O ARG A1226 " (cutoff:3.500A) Processing helix chain 'A' and resid 1246 through 1261 Processing helix chain 'A' and resid 1266 through 1278 removed outlier: 3.562A pdb=" N ALA A1275 " --> pdb=" O GLU A1271 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY A1278 " --> pdb=" O LEU A1274 " (cutoff:3.500A) Processing helix chain 'A' and resid 1290 through 1307 removed outlier: 3.664A pdb=" N CYS A1306 " --> pdb=" O LEU A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1331 removed outlier: 3.549A pdb=" N GLY A1331 " --> pdb=" O GLN A1327 " (cutoff:3.500A) Processing helix chain 'A' and resid 1359 through 1375 Proline residue: A1365 - end of helix removed outlier: 3.559A pdb=" N TYR A1375 " --> pdb=" O LEU A1371 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1385 Processing helix chain 'A' and resid 1392 through 1397 removed outlier: 3.830A pdb=" N ASP A1397 " --> pdb=" O MET A1393 " (cutoff:3.500A) Processing helix chain 'A' and resid 1400 through 1415 removed outlier: 3.709A pdb=" N LEU A1406 " --> pdb=" O GLU A1402 " (cutoff:3.500A) Processing helix chain 'A' and resid 1422 through 1428 Processing helix chain 'A' and resid 1453 through 1476 removed outlier: 4.289A pdb=" N LEU A1457 " --> pdb=" O ASN A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1481 through 1500 removed outlier: 3.806A pdb=" N CYS A1487 " --> pdb=" O SER A1483 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A1488 " --> pdb=" O ALA A1484 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER A1500 " --> pdb=" O MET A1496 " (cutoff:3.500A) Processing helix chain 'A' and resid 1503 through 1508 Processing helix chain 'A' and resid 1508 through 1527 Processing helix chain 'A' and resid 1532 through 1544 removed outlier: 3.548A pdb=" N MET A1544 " --> pdb=" O ARG A1540 " (cutoff:3.500A) Processing helix chain 'A' and resid 1551 through 1566 removed outlier: 3.569A pdb=" N PHE A1566 " --> pdb=" O LEU A1562 " (cutoff:3.500A) Processing helix chain 'A' and resid 1567 through 1570 Processing helix chain 'A' and resid 1577 through 1588 removed outlier: 4.068A pdb=" N ALA A1582 " --> pdb=" O ASN A1578 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS A1586 " --> pdb=" O ALA A1582 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1612 removed outlier: 4.358A pdb=" N TYR A1610 " --> pdb=" O ARG A1607 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A1611 " --> pdb=" O HIS A1608 " (cutoff:3.500A) Processing helix chain 'A' and resid 1683 through 1693 removed outlier: 3.697A pdb=" N LYS A1693 " --> pdb=" O SER A1689 " (cutoff:3.500A) Processing helix chain 'A' and resid 1726 through 1732 Processing helix chain 'A' and resid 1736 through 1741 removed outlier: 4.355A pdb=" N SER A1739 " --> pdb=" O GLU A1736 " (cutoff:3.500A) Processing helix chain 'A' and resid 1744 through 1754 Processing helix chain 'A' and resid 1764 through 1781 removed outlier: 4.113A pdb=" N LEU A1768 " --> pdb=" O LYS A1764 " (cutoff:3.500A) Processing helix chain 'A' and resid 1786 through 1802 removed outlier: 3.757A pdb=" N ARG A1802 " --> pdb=" O ARG A1798 " (cutoff:3.500A) Processing helix chain 'A' and resid 1808 through 1821 removed outlier: 3.636A pdb=" N PHE A1821 " --> pdb=" O VAL A1817 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1829 removed outlier: 3.579A pdb=" N ARG A1829 " --> pdb=" O HIS A1826 " (cutoff:3.500A) Processing helix chain 'A' and resid 1844 through 1863 Processing helix chain 'A' and resid 1864 through 1874 Processing helix chain 'A' and resid 1881 through 1893 removed outlier: 3.684A pdb=" N ALA A1886 " --> pdb=" O LEU A1882 " (cutoff:3.500A) Processing helix chain 'A' and resid 1911 through 1921 removed outlier: 3.739A pdb=" N GLN A1920 " --> pdb=" O PHE A1916 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A1921 " --> pdb=" O LYS A1917 " (cutoff:3.500A) Processing helix chain 'A' and resid 1924 through 1931 removed outlier: 3.722A pdb=" N LEU A1928 " --> pdb=" O PRO A1924 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A1929 " --> pdb=" O VAL A1925 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ARG A1930 " --> pdb=" O ARG A1926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1932 through 1936 Processing helix chain 'N' and resid 17 through 30 Processing helix chain 'N' and resid 53 through 65 removed outlier: 4.206A pdb=" N ALA N 57 " --> pdb=" O GLU N 53 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA N 58 " --> pdb=" O GLU N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 69 through 86 removed outlier: 4.266A pdb=" N GLU N 73 " --> pdb=" O SER N 69 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 101 removed outlier: 4.861A pdb=" N ALA N 94 " --> pdb=" O GLU N 90 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE N 95 " --> pdb=" O PHE N 91 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER N 96 " --> pdb=" O TRP N 92 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER N 101 " --> pdb=" O GLN N 97 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 138 removed outlier: 3.828A pdb=" N CYS N 107 " --> pdb=" O ASP N 103 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU N 108 " --> pdb=" O GLU N 104 " (cutoff:3.500A) Proline residue: N 124 - end of helix Processing helix chain 'N' and resid 148 through 162 removed outlier: 3.578A pdb=" N LEU N 161 " --> pdb=" O LEU N 157 " (cutoff:3.500A) Processing helix chain 'N' and resid 166 through 190 Processing helix chain 'N' and resid 191 through 193 No H-bonds generated for 'chain 'N' and resid 191 through 193' Processing helix chain 'N' and resid 205 through 215 removed outlier: 3.945A pdb=" N ARG N 210 " --> pdb=" O ARG N 206 " (cutoff:3.500A) Processing helix chain 'N' and resid 234 through 250 removed outlier: 3.941A pdb=" N GLU N 238 " --> pdb=" O ARG N 234 " (cutoff:3.500A) Processing helix chain 'N' and resid 252 through 257 Processing helix chain 'N' and resid 257 through 278 removed outlier: 4.071A pdb=" N THR N 262 " --> pdb=" O ALA N 258 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N THR N 263 " --> pdb=" O GLU N 259 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG N 270 " --> pdb=" O HIS N 266 " (cutoff:3.500A) Processing helix chain 'N' and resid 285 through 304 removed outlier: 3.714A pdb=" N PHE N 289 " --> pdb=" O PHE N 285 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLU N 294 " --> pdb=" O HIS N 290 " (cutoff:3.500A) Processing helix chain 'N' and resid 315 through 343 removed outlier: 3.915A pdb=" N SER N 338 " --> pdb=" O ARG N 334 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU N 343 " --> pdb=" O LEU N 339 " (cutoff:3.500A) Processing helix chain 'N' and resid 343 through 350 removed outlier: 3.749A pdb=" N ASP N 350 " --> pdb=" O SER N 346 " (cutoff:3.500A) Processing helix chain 'N' and resid 355 through 366 removed outlier: 3.513A pdb=" N GLU N 359 " --> pdb=" O ARG N 355 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU N 366 " --> pdb=" O LYS N 362 " (cutoff:3.500A) Processing helix chain 'N' and resid 370 through 386 removed outlier: 3.933A pdb=" N THR N 384 " --> pdb=" O ALA N 380 " (cutoff:3.500A) Processing helix chain 'N' and resid 392 through 411 removed outlier: 3.733A pdb=" N ARG N 408 " --> pdb=" O ILE N 404 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL N 409 " --> pdb=" O LYS N 405 " (cutoff:3.500A) Processing helix chain 'N' and resid 415 through 421 removed outlier: 3.665A pdb=" N VAL N 419 " --> pdb=" O VAL N 415 " (cutoff:3.500A) Processing helix chain 'N' and resid 421 through 430 Processing helix chain 'N' and resid 433 through 441 removed outlier: 3.685A pdb=" N GLN N 437 " --> pdb=" O ASP N 433 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE N 438 " --> pdb=" O THR N 434 " (cutoff:3.500A) Processing helix chain 'N' and resid 450 through 456 removed outlier: 3.843A pdb=" N VAL N 454 " --> pdb=" O GLY N 450 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU N 455 " --> pdb=" O ASP N 451 " (cutoff:3.500A) Processing helix chain 'N' and resid 500 through 506 Processing helix chain 'N' and resid 507 through 509 No H-bonds generated for 'chain 'N' and resid 507 through 509' Processing helix chain 'N' and resid 512 through 528 removed outlier: 3.835A pdb=" N ILE N 516 " --> pdb=" O LYS N 512 " (cutoff:3.500A) Processing helix chain 'N' and resid 536 through 550 removed outlier: 4.015A pdb=" N ARG N 540 " --> pdb=" O GLU N 536 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU N 544 " --> pdb=" O ARG N 540 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU N 545 " --> pdb=" O ASN N 541 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS N 546 " --> pdb=" O VAL N 542 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU N 547 " --> pdb=" O GLU N 543 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG N 548 " --> pdb=" O LEU N 544 " (cutoff:3.500A) Processing helix chain 'N' and resid 551 through 556 removed outlier: 3.807A pdb=" N HIS N 555 " --> pdb=" O ALA N 552 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE N 556 " --> pdb=" O PRO N 553 " (cutoff:3.500A) Processing helix chain 'N' and resid 557 through 566 removed outlier: 3.666A pdb=" N ASP N 563 " --> pdb=" O VAL N 559 " (cutoff:3.500A) Processing helix chain 'N' and resid 568 through 574 removed outlier: 3.710A pdb=" N ALA N 572 " --> pdb=" O ARG N 568 " (cutoff:3.500A) Processing helix chain 'N' and resid 614 through 630 removed outlier: 4.447A pdb=" N ALA N 618 " --> pdb=" O ASP N 614 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR N 622 " --> pdb=" O ALA N 618 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N CYS N 623 " --> pdb=" O LEU N 619 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN N 628 " --> pdb=" O LYS N 624 " (cutoff:3.500A) Processing helix chain 'N' and resid 660 through 669 removed outlier: 3.597A pdb=" N VAL N 665 " --> pdb=" O PRO N 661 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE N 666 " --> pdb=" O VAL N 662 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU N 667 " --> pdb=" O GLN N 663 " (cutoff:3.500A) Processing helix chain 'N' and resid 677 through 685 removed outlier: 4.333A pdb=" N LYS N 683 " --> pdb=" O GLU N 679 " (cutoff:3.500A) Processing helix chain 'N' and resid 688 through 693 removed outlier: 3.799A pdb=" N LEU N 692 " --> pdb=" O PRO N 688 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ARG N 693 " --> pdb=" O VAL N 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 688 through 693' Processing helix chain 'N' and resid 698 through 703 removed outlier: 3.730A pdb=" N GLN N 702 " --> pdb=" O VAL N 698 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 123 Processing helix chain 'I' and resid 161 through 165 removed outlier: 3.633A pdb=" N ILE I 164 " --> pdb=" O SER I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 244 Processing helix chain 'I' and resid 244 through 275 removed outlier: 3.776A pdb=" N HIS I 257 " --> pdb=" O ARG I 253 " (cutoff:3.500A) Processing helix chain 'I' and resid 281 through 289 Processing helix chain 'I' and resid 289 through 294 Processing helix chain 'I' and resid 299 through 310 Processing helix chain 'I' and resid 314 through 324 Processing helix chain 'I' and resid 328 through 349 removed outlier: 4.034A pdb=" N LYS I 332 " --> pdb=" O LYS I 328 " (cutoff:3.500A) Processing helix chain 'I' and resid 351 through 372 removed outlier: 3.601A pdb=" N GLU I 365 " --> pdb=" O TYR I 361 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TRP I 372 " --> pdb=" O GLY I 368 " (cutoff:3.500A) Processing helix chain 'I' and resid 382 through 427 removed outlier: 3.685A pdb=" N ILE I 386 " --> pdb=" O ASP I 382 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA I 416 " --> pdb=" O LYS I 412 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG I 427 " --> pdb=" O VAL I 423 " (cutoff:3.500A) Processing helix chain 'I' and resid 441 through 456 removed outlier: 3.544A pdb=" N PHE I 456 " --> pdb=" O LEU I 452 " (cutoff:3.500A) Processing helix chain 'I' and resid 475 through 480 removed outlier: 3.931A pdb=" N LEU I 479 " --> pdb=" O VAL I 475 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 503 Processing helix chain 'I' and resid 506 through 510 Processing helix chain 'I' and resid 521 through 547 removed outlier: 3.608A pdb=" N VAL I 525 " --> pdb=" O SER I 521 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE I 532 " --> pdb=" O ARG I 528 " (cutoff:3.500A) Proline residue: I 540 - end of helix Processing helix chain 'I' and resid 560 through 564 Processing helix chain 'I' and resid 676 through 681 removed outlier: 3.977A pdb=" N ALA I 681 " --> pdb=" O SER I 677 " (cutoff:3.500A) Processing helix chain 'O' and resid 31 through 45 Processing helix chain 'O' and resid 53 through 70 removed outlier: 3.603A pdb=" N LEU O 63 " --> pdb=" O ARG O 59 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU O 65 " --> pdb=" O ASN O 61 " (cutoff:3.500A) Proline residue: O 66 - end of helix removed outlier: 3.531A pdb=" N GLN O 69 " --> pdb=" O LEU O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 86 removed outlier: 3.608A pdb=" N GLU O 84 " --> pdb=" O LYS O 80 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER O 85 " --> pdb=" O LEU O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 86 through 103 removed outlier: 3.707A pdb=" N ALA O 90 " --> pdb=" O CYS O 86 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN O 91 " --> pdb=" O PRO O 87 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG O 96 " --> pdb=" O SER O 92 " (cutoff:3.500A) Processing helix chain 'O' and resid 104 through 116 removed outlier: 3.770A pdb=" N MET O 108 " --> pdb=" O GLU O 104 " (cutoff:3.500A) Processing helix chain 'O' and resid 117 through 120 Processing helix chain 'O' and resid 130 through 145 Processing helix chain 'O' and resid 147 through 167 Processing helix chain 'O' and resid 208 through 226 Processing helix chain 'O' and resid 232 through 247 removed outlier: 3.883A pdb=" N PHE O 246 " --> pdb=" O ASN O 242 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN O 247 " --> pdb=" O LEU O 243 " (cutoff:3.500A) Processing helix chain 'O' and resid 251 through 263 removed outlier: 3.673A pdb=" N TYR O 255 " --> pdb=" O ALA O 251 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG O 263 " --> pdb=" O LEU O 259 " (cutoff:3.500A) Processing helix chain 'O' and resid 267 through 281 removed outlier: 3.721A pdb=" N LEU O 275 " --> pdb=" O THR O 271 " (cutoff:3.500A) Processing helix chain 'O' and resid 298 through 314 removed outlier: 3.738A pdb=" N TYR O 302 " --> pdb=" O ARG O 298 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA O 304 " --> pdb=" O LEU O 300 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU O 305 " --> pdb=" O ARG O 301 " (cutoff:3.500A) Processing helix chain 'O' and resid 316 through 334 removed outlier: 3.629A pdb=" N GLU O 326 " --> pdb=" O LEU O 322 " (cutoff:3.500A) Processing helix chain 'O' and resid 337 through 351 removed outlier: 3.604A pdb=" N VAL O 349 " --> pdb=" O SER O 345 " (cutoff:3.500A) Processing helix chain 'O' and resid 356 through 370 removed outlier: 3.698A pdb=" N LEU O 360 " --> pdb=" O ASP O 356 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS O 370 " --> pdb=" O LYS O 366 " (cutoff:3.500A) Processing helix chain 'O' and resid 373 through 390 removed outlier: 3.574A pdb=" N ALA O 377 " --> pdb=" O LEU O 373 " (cutoff:3.500A) Processing helix chain 'O' and resid 394 through 412 removed outlier: 3.898A pdb=" N ASP O 404 " --> pdb=" O ASP O 400 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER O 405 " --> pdb=" O ALA O 401 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU O 408 " --> pdb=" O ASP O 404 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRP O 410 " --> pdb=" O ASP O 406 " (cutoff:3.500A) Processing helix chain 'O' and resid 415 through 432 removed outlier: 3.640A pdb=" N ARG O 430 " --> pdb=" O THR O 426 " (cutoff:3.500A) Processing helix chain 'O' and resid 434 through 448 removed outlier: 3.523A pdb=" N ALA O 438 " --> pdb=" O ARG O 434 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET O 448 " --> pdb=" O MET O 444 " (cutoff:3.500A) Processing helix chain 'O' and resid 463 through 480 removed outlier: 3.636A pdb=" N ALA O 467 " --> pdb=" O THR O 463 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN O 480 " --> pdb=" O LEU O 476 " (cutoff:3.500A) Processing helix chain 'O' and resid 482 through 497 Processing helix chain 'O' and resid 503 through 521 removed outlier: 4.082A pdb=" N TRP O 507 " --> pdb=" O HIS O 503 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS O 510 " --> pdb=" O LEU O 506 " (cutoff:3.500A) Processing helix chain 'O' and resid 524 through 539 removed outlier: 4.322A pdb=" N THR O 533 " --> pdb=" O ASP O 529 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY O 534 " --> pdb=" O SER O 530 " (cutoff:3.500A) Processing helix chain 'O' and resid 539 through 553 Processing helix chain 'O' and resid 556 through 575 Processing helix chain 'O' and resid 576 through 592 Processing helix chain 'O' and resid 596 through 599 removed outlier: 3.558A pdb=" N ILE O 599 " --> pdb=" O SER O 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 596 through 599' Processing helix chain 'O' and resid 600 through 613 removed outlier: 3.586A pdb=" N ALA O 609 " --> pdb=" O LEU O 605 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU O 613 " --> pdb=" O ALA O 609 " (cutoff:3.500A) Processing helix chain 'O' and resid 616 through 634 Processing helix chain 'O' and resid 636 through 645 Processing helix chain 'O' and resid 648 through 654 Processing helix chain 'O' and resid 656 through 675 removed outlier: 3.628A pdb=" N MET O 664 " --> pdb=" O LYS O 660 " (cutoff:3.500A) Processing helix chain 'O' and resid 676 through 678 No H-bonds generated for 'chain 'O' and resid 676 through 678' Processing helix chain 'O' and resid 679 through 705 removed outlier: 4.010A pdb=" N ALA O 689 " --> pdb=" O GLU O 685 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ALA O 690 " --> pdb=" O ALA O 686 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE O 691 " --> pdb=" O LEU O 687 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU O 692 " --> pdb=" O GLU O 688 " (cutoff:3.500A) Processing helix chain 'O' and resid 706 through 725 Processing helix chain 'O' and resid 726 through 742 removed outlier: 4.685A pdb=" N ARG O 732 " --> pdb=" O GLN O 728 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N CYS O 733 " --> pdb=" O GLU O 729 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLN O 742 " --> pdb=" O ARG O 738 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 16 Processing helix chain 'K' and resid 18 through 33 removed outlier: 3.537A pdb=" N TRP K 25 " --> pdb=" O SER K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 50 Processing helix chain 'K' and resid 52 through 62 removed outlier: 3.649A pdb=" N LEU K 60 " --> pdb=" O ALA K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 83 Processing helix chain 'K' and resid 85 through 93 removed outlier: 3.577A pdb=" N LEU K 93 " --> pdb=" O ALA K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 143 Processing helix chain 'K' and resid 145 through 160 Processing helix chain 'K' and resid 163 through 171 Processing helix chain 'K' and resid 177 through 188 removed outlier: 3.840A pdb=" N LEU K 185 " --> pdb=" O GLU K 181 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU K 186 " --> pdb=" O LYS K 182 " (cutoff:3.500A) Processing helix chain 'K' and resid 194 through 210 Processing helix chain 'K' and resid 225 through 230 removed outlier: 3.783A pdb=" N GLU K 229 " --> pdb=" O GLY K 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 232 through 244 Processing helix chain 'K' and resid 246 through 261 removed outlier: 3.709A pdb=" N VAL K 256 " --> pdb=" O LYS K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 266 through 278 removed outlier: 4.601A pdb=" N VAL K 270 " --> pdb=" O SER K 266 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU K 277 " --> pdb=" O GLY K 273 " (cutoff:3.500A) Processing helix chain 'K' and resid 280 through 295 Processing helix chain 'K' and resid 298 through 313 removed outlier: 4.151A pdb=" N TRP K 302 " --> pdb=" O ASN K 298 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY K 313 " --> pdb=" O TYR K 309 " (cutoff:3.500A) Processing helix chain 'K' and resid 315 through 330 removed outlier: 3.775A pdb=" N ARG K 321 " --> pdb=" O GLU K 317 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER K 324 " --> pdb=" O ARG K 320 " (cutoff:3.500A) Processing helix chain 'K' and resid 333 through 346 removed outlier: 4.175A pdb=" N TRP K 337 " --> pdb=" O TYR K 333 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE K 338 " --> pdb=" O GLY K 334 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE K 344 " --> pdb=" O TYR K 340 " (cutoff:3.500A) Processing helix chain 'K' and resid 349 through 364 removed outlier: 3.928A pdb=" N LEU K 363 " --> pdb=" O THR K 359 " (cutoff:3.500A) Processing helix chain 'K' and resid 368 through 380 Processing helix chain 'K' and resid 383 through 398 removed outlier: 4.125A pdb=" N PHE K 390 " --> pdb=" O LEU K 386 " (cutoff:3.500A) Processing helix chain 'K' and resid 401 through 416 removed outlier: 3.566A pdb=" N MET K 405 " --> pdb=" O ASP K 401 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN K 415 " --> pdb=" O VAL K 411 " (cutoff:3.500A) Processing helix chain 'K' and resid 417 through 435 removed outlier: 3.722A pdb=" N GLU K 422 " --> pdb=" O TRP K 418 " (cutoff:3.500A) Processing helix chain 'K' and resid 440 through 443 removed outlier: 3.613A pdb=" N LYS K 443 " --> pdb=" O THR K 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 440 through 443' Processing helix chain 'K' and resid 444 through 458 Processing helix chain 'K' and resid 460 through 475 removed outlier: 3.580A pdb=" N VAL K 473 " --> pdb=" O ARG K 469 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU K 474 " --> pdb=" O GLN K 470 " (cutoff:3.500A) Processing helix chain 'K' and resid 478 through 492 Processing helix chain 'K' and resid 494 through 509 Processing helix chain 'K' and resid 512 through 528 removed outlier: 3.646A pdb=" N GLU K 524 " --> pdb=" O GLY K 520 " (cutoff:3.500A) Processing helix chain 'K' and resid 555 through 560 Processing helix chain 'C' and resid 57 through 66 removed outlier: 4.186A pdb=" N LYS C 62 " --> pdb=" O HIS C 58 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TRP C 63 " --> pdb=" O CYS C 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 14 No H-bonds generated for 'chain 'G' and resid 12 through 14' Processing helix chain 'G' and resid 15 through 27 removed outlier: 3.840A pdb=" N PHE G 19 " --> pdb=" O ASP G 15 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE G 22 " --> pdb=" O GLU G 18 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 14 No H-bonds generated for 'chain 'W' and resid 12 through 14' Processing helix chain 'W' and resid 15 through 25 removed outlier: 4.148A pdb=" N ILE W 22 " --> pdb=" O GLU W 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 15 Processing helix chain 'M' and resid 16 through 21 Processing helix chain 'H' and resid 52 through 91 removed outlier: 3.547A pdb=" N GLN H 75 " --> pdb=" O LYS H 71 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL H 86 " --> pdb=" O LEU H 82 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLU H 87 " --> pdb=" O ALA H 83 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU H 88 " --> pdb=" O GLY H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 96 Processing helix chain 'H' and resid 98 through 103 Processing helix chain 'J' and resid 6 through 18 Processing helix chain 'J' and resid 20 through 35 Processing helix chain 'J' and resid 37 through 51 Processing helix chain 'J' and resid 53 through 63 removed outlier: 3.783A pdb=" N ALA J 57 " --> pdb=" O LYS J 53 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 82 Processing helix chain 'J' and resid 84 through 94 Processing helix chain 'J' and resid 102 through 111 Processing helix chain 'J' and resid 113 through 128 Processing helix chain 'J' and resid 130 through 145 Processing helix chain 'J' and resid 148 through 158 removed outlier: 4.309A pdb=" N PHE J 152 " --> pdb=" O LEU J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 163 through 168 Processing helix chain 'J' and resid 452 through 478 removed outlier: 4.011A pdb=" N ALA J 458 " --> pdb=" O LEU J 454 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU J 462 " --> pdb=" O ALA J 458 " (cutoff:3.500A) Processing helix chain 'J' and resid 480 through 489 Processing helix chain 'J' and resid 492 through 497 Processing helix chain 'J' and resid 498 through 512 Processing helix chain 'J' and resid 514 through 529 Processing helix chain 'J' and resid 535 through 546 removed outlier: 3.847A pdb=" N TYR J 539 " --> pdb=" O GLY J 535 " (cutoff:3.500A) Processing helix chain 'J' and resid 548 through 563 Processing helix chain 'J' and resid 566 through 580 removed outlier: 3.805A pdb=" N TRP J 570 " --> pdb=" O SER J 566 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN J 580 " --> pdb=" O CYS J 576 " (cutoff:3.500A) Processing helix chain 'J' and resid 582 through 597 Processing helix chain 'J' and resid 600 through 614 removed outlier: 3.807A pdb=" N TYR J 604 " --> pdb=" O TYR J 600 " (cutoff:3.500A) Processing helix chain 'J' and resid 616 through 631 Processing helix chain 'J' and resid 634 through 648 removed outlier: 3.633A pdb=" N TRP J 638 " --> pdb=" O HIS J 634 " (cutoff:3.500A) Processing helix chain 'J' and resid 650 through 665 Processing helix chain 'J' and resid 668 through 682 Processing helix chain 'J' and resid 684 through 699 Processing helix chain 'J' and resid 702 through 716 removed outlier: 3.573A pdb=" N LYS J 706 " --> pdb=" O ASN J 702 " (cutoff:3.500A) Processing helix chain 'J' and resid 718 through 731 removed outlier: 3.678A pdb=" N GLU J 728 " --> pdb=" O GLN J 724 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN J 731 " --> pdb=" O GLU J 727 " (cutoff:3.500A) Processing helix chain 'J' and resid 736 through 750 removed outlier: 4.049A pdb=" N TYR J 740 " --> pdb=" O GLU J 736 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS J 749 " --> pdb=" O LYS J 745 " (cutoff:3.500A) Processing helix chain 'J' and resid 752 through 767 removed outlier: 3.592A pdb=" N TRP J 762 " --> pdb=" O MET J 758 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP J 767 " --> pdb=" O ALA J 763 " (cutoff:3.500A) Processing helix chain 'J' and resid 771 through 780 removed outlier: 4.292A pdb=" N ILE J 775 " --> pdb=" O ALA J 771 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS J 776 " --> pdb=" O ASN J 772 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 17 Processing helix chain 'P' and resid 20 through 35 removed outlier: 3.586A pdb=" N LEU P 27 " --> pdb=" O ASP P 23 " (cutoff:3.500A) Processing helix chain 'P' and resid 37 through 51 Processing helix chain 'P' and resid 53 through 61 removed outlier: 3.589A pdb=" N ALA P 57 " --> pdb=" O LYS P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 82 Processing helix chain 'P' and resid 84 through 93 Processing helix chain 'P' and resid 102 through 111 Processing helix chain 'P' and resid 113 through 128 Processing helix chain 'P' and resid 130 through 145 Processing helix chain 'P' and resid 149 through 159 Processing helix chain 'P' and resid 163 through 168 removed outlier: 3.622A pdb=" N PHE P 168 " --> pdb=" O PRO P 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 453 through 478 removed outlier: 3.966A pdb=" N ALA P 457 " --> pdb=" O ASN P 453 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N GLY P 461 " --> pdb=" O ALA P 457 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LEU P 462 " --> pdb=" O ALA P 458 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY P 472 " --> pdb=" O GLU P 468 " (cutoff:3.500A) Processing helix chain 'P' and resid 480 through 489 Processing helix chain 'P' and resid 492 through 497 Processing helix chain 'P' and resid 498 through 512 Processing helix chain 'P' and resid 514 through 529 Processing helix chain 'P' and resid 535 through 547 removed outlier: 3.688A pdb=" N TYR P 539 " --> pdb=" O GLY P 535 " (cutoff:3.500A) Processing helix chain 'P' and resid 548 through 561 Processing helix chain 'P' and resid 566 through 580 removed outlier: 4.058A pdb=" N TRP P 570 " --> pdb=" O SER P 566 " (cutoff:3.500A) Processing helix chain 'P' and resid 582 through 597 Processing helix chain 'P' and resid 600 through 614 removed outlier: 3.928A pdb=" N TYR P 604 " --> pdb=" O TYR P 600 " (cutoff:3.500A) Processing helix chain 'P' and resid 616 through 631 removed outlier: 3.876A pdb=" N ALA P 622 " --> pdb=" O ASP P 618 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS P 623 " --> pdb=" O LYS P 619 " (cutoff:3.500A) Processing helix chain 'P' and resid 634 through 648 removed outlier: 3.744A pdb=" N TRP P 638 " --> pdb=" O HIS P 634 " (cutoff:3.500A) Processing helix chain 'P' and resid 650 through 663 Processing helix chain 'P' and resid 668 through 682 Processing helix chain 'P' and resid 684 through 699 removed outlier: 3.622A pdb=" N ASP P 690 " --> pdb=" O GLU P 686 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE P 698 " --> pdb=" O LYS P 694 " (cutoff:3.500A) Processing helix chain 'P' and resid 702 through 716 removed outlier: 4.160A pdb=" N LYS P 706 " --> pdb=" O ASN P 702 " (cutoff:3.500A) Processing helix chain 'P' and resid 718 through 731 Processing helix chain 'P' and resid 736 through 750 removed outlier: 4.331A pdb=" N TYR P 740 " --> pdb=" O GLU P 736 " (cutoff:3.500A) Processing helix chain 'P' and resid 752 through 766 removed outlier: 3.735A pdb=" N ASN P 759 " --> pdb=" O LEU P 755 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP P 762 " --> pdb=" O MET P 758 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 16 Processing helix chain 'Q' and resid 18 through 33 removed outlier: 3.521A pdb=" N TRP Q 25 " --> pdb=" O SER Q 21 " (cutoff:3.500A) Processing helix chain 'Q' and resid 36 through 50 Processing helix chain 'Q' and resid 52 through 62 Processing helix chain 'Q' and resid 64 through 69 removed outlier: 3.842A pdb=" N LEU Q 68 " --> pdb=" O LYS Q 64 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 83 Processing helix chain 'Q' and resid 85 through 94 Processing helix chain 'Q' and resid 126 through 143 removed outlier: 3.547A pdb=" N SER Q 130 " --> pdb=" O SER Q 126 " (cutoff:3.500A) Processing helix chain 'Q' and resid 145 through 160 removed outlier: 4.028A pdb=" N TYR Q 151 " --> pdb=" O THR Q 147 " (cutoff:3.500A) Processing helix chain 'Q' and resid 163 through 173 removed outlier: 3.852A pdb=" N PHE Q 167 " --> pdb=" O CYS Q 163 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS Q 173 " --> pdb=" O LEU Q 169 " (cutoff:3.500A) Processing helix chain 'Q' and resid 177 through 188 removed outlier: 3.629A pdb=" N LYS Q 182 " --> pdb=" O ALA Q 178 " (cutoff:3.500A) Processing helix chain 'Q' and resid 194 through 207 removed outlier: 3.590A pdb=" N GLN Q 198 " --> pdb=" O CYS Q 194 " (cutoff:3.500A) Processing helix chain 'Q' and resid 230 through 244 Processing helix chain 'Q' and resid 246 through 255 Processing helix chain 'Q' and resid 266 through 278 removed outlier: 4.527A pdb=" N VAL Q 270 " --> pdb=" O SER Q 266 " (cutoff:3.500A) Processing helix chain 'Q' and resid 280 through 295 removed outlier: 3.641A pdb=" N LYS Q 290 " --> pdb=" O TYR Q 286 " (cutoff:3.500A) Processing helix chain 'Q' and resid 298 through 313 removed outlier: 3.835A pdb=" N TRP Q 302 " --> pdb=" O ASN Q 298 " (cutoff:3.500A) Processing helix chain 'Q' and resid 315 through 330 removed outlier: 3.638A pdb=" N ARG Q 321 " --> pdb=" O GLU Q 317 " (cutoff:3.500A) Processing helix chain 'Q' and resid 333 through 346 removed outlier: 4.180A pdb=" N TRP Q 337 " --> pdb=" O TYR Q 333 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE Q 338 " --> pdb=" O GLY Q 334 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE Q 344 " --> pdb=" O TYR Q 340 " (cutoff:3.500A) Processing helix chain 'Q' and resid 349 through 364 Processing helix chain 'Q' and resid 368 through 381 Processing helix chain 'Q' and resid 383 through 398 Processing helix chain 'Q' and resid 401 through 416 removed outlier: 3.722A pdb=" N GLU Q 407 " --> pdb=" O PHE Q 403 " (cutoff:3.500A) Processing helix chain 'Q' and resid 417 through 433 Processing helix chain 'Q' and resid 444 through 458 removed outlier: 3.676A pdb=" N CYS Q 455 " --> pdb=" O LEU Q 451 " (cutoff:3.500A) Processing helix chain 'Q' and resid 460 through 475 removed outlier: 3.503A pdb=" N ASP Q 466 " --> pdb=" O ALA Q 462 " (cutoff:3.500A) Processing helix chain 'Q' and resid 478 through 493 Processing helix chain 'Q' and resid 494 through 509 Processing helix chain 'Q' and resid 513 through 528 removed outlier: 3.757A pdb=" N THR Q 517 " --> pdb=" O THR Q 513 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE Q 527 " --> pdb=" O ILE Q 523 " (cutoff:3.500A) Processing helix chain 'Y' and resid 37 through 47 Processing helix chain 'Y' and resid 49 through 67 removed outlier: 3.786A pdb=" N LEU Y 55 " --> pdb=" O SER Y 51 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR Y 62 " --> pdb=" O SER Y 58 " (cutoff:3.500A) Processing helix chain 'Y' and resid 72 through 90 Processing helix chain 'Y' and resid 92 through 109 removed outlier: 3.723A pdb=" N MET Y 102 " --> pdb=" O SER Y 98 " (cutoff:3.500A) Processing helix chain 'Y' and resid 134 through 149 removed outlier: 3.572A pdb=" N VAL Y 138 " --> pdb=" O SER Y 134 " (cutoff:3.500A) Processing helix chain 'Y' and resid 151 through 162 removed outlier: 3.675A pdb=" N ILE Y 162 " --> pdb=" O ILE Y 158 " (cutoff:3.500A) Processing helix chain 'Y' and resid 163 through 167 removed outlier: 3.875A pdb=" N ARG Y 167 " --> pdb=" O SER Y 164 " (cutoff:3.500A) Processing helix chain 'Y' and resid 168 through 183 removed outlier: 3.609A pdb=" N ASN Y 172 " --> pdb=" O THR Y 168 " (cutoff:3.500A) Processing helix chain 'Y' and resid 184 through 199 removed outlier: 3.568A pdb=" N THR Y 190 " --> pdb=" O ARG Y 186 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER Y 191 " --> pdb=" O PRO Y 187 " (cutoff:3.500A) Processing helix chain 'Y' and resid 202 through 211 Processing helix chain 'Y' and resid 215 through 223 removed outlier: 3.537A pdb=" N VAL Y 219 " --> pdb=" O LYS Y 215 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR Y 223 " --> pdb=" O VAL Y 219 " (cutoff:3.500A) Processing helix chain 'Y' and resid 223 through 230 Processing helix chain 'Y' and resid 234 through 247 removed outlier: 4.356A pdb=" N VAL Y 238 " --> pdb=" O ASP Y 234 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE Y 245 " --> pdb=" O LYS Y 241 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL Y 246 " --> pdb=" O ALA Y 242 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N HIS Y 247 " --> pdb=" O TYR Y 243 " (cutoff:3.500A) Processing helix chain 'Y' and resid 250 through 265 Processing helix chain 'Y' and resid 270 through 285 Processing helix chain 'Y' and resid 288 through 301 Processing helix chain 'Y' and resid 307 through 318 Processing helix chain 'Y' and resid 320 through 333 Processing helix chain 'Y' and resid 339 through 352 Processing helix chain 'Y' and resid 354 through 369 removed outlier: 3.512A pdb=" N TYR Y 360 " --> pdb=" O SER Y 356 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA Y 365 " --> pdb=" O LEU Y 361 " (cutoff:3.500A) Processing helix chain 'Y' and resid 372 through 387 removed outlier: 3.580A pdb=" N LEU Y 376 " --> pdb=" O SER Y 372 " (cutoff:3.500A) Processing helix chain 'Y' and resid 388 through 403 removed outlier: 3.796A pdb=" N ILE Y 394 " --> pdb=" O GLN Y 390 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS Y 395 " --> pdb=" O GLU Y 391 " (cutoff:3.500A) Processing helix chain 'Y' and resid 406 through 420 removed outlier: 3.983A pdb=" N TYR Y 410 " --> pdb=" O ARG Y 406 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU Y 413 " --> pdb=" O CYS Y 409 " (cutoff:3.500A) Processing helix chain 'Y' and resid 422 through 438 Processing helix chain 'Y' and resid 440 through 451 removed outlier: 3.796A pdb=" N VAL Y 450 " --> pdb=" O LEU Y 446 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N CYS Y 451 " --> pdb=" O LEU Y 447 " (cutoff:3.500A) Processing helix chain 'Y' and resid 454 through 456 No H-bonds generated for 'chain 'Y' and resid 454 through 456' Processing helix chain 'Y' and resid 457 through 470 removed outlier: 3.559A pdb=" N THR Y 463 " --> pdb=" O GLU Y 459 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU Y 465 " --> pdb=" O ALA Y 461 " (cutoff:3.500A) Processing helix chain 'Y' and resid 475 through 489 Processing helix chain 'Y' and resid 492 through 504 Processing helix chain 'Y' and resid 508 through 520 Processing helix chain 'Y' and resid 524 through 539 Processing helix chain 'Y' and resid 542 through 555 removed outlier: 3.647A pdb=" N MET Y 552 " --> pdb=" O GLY Y 548 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS Y 554 " --> pdb=" O GLN Y 550 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU Y 555 " --> pdb=" O LYS Y 551 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 46 Processing helix chain 'U' and resid 48 through 62 Processing helix chain 'U' and resid 77 through 82 Processing helix chain 'U' and resid 83 through 96 removed outlier: 3.684A pdb=" N VAL U 96 " --> pdb=" O ALA U 92 " (cutoff:3.500A) Processing helix chain 'U' and resid 98 through 106 Processing helix chain 'U' and resid 111 through 134 removed outlier: 3.611A pdb=" N THR U 134 " --> pdb=" O LYS U 130 " (cutoff:3.500A) Processing helix chain 'U' and resid 148 through 164 removed outlier: 3.622A pdb=" N LEU U 154 " --> pdb=" O ALA U 150 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA U 164 " --> pdb=" O LYS U 160 " (cutoff:3.500A) Processing helix chain 'U' and resid 169 through 182 Processing helix chain 'U' and resid 184 through 199 removed outlier: 4.144A pdb=" N ASP U 190 " --> pdb=" O LYS U 186 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL U 191 " --> pdb=" O GLU U 187 " (cutoff:3.500A) Processing helix chain 'U' and resid 202 through 211 removed outlier: 4.146A pdb=" N TRP U 206 " --> pdb=" O HIS U 202 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN U 211 " --> pdb=" O LEU U 207 " (cutoff:3.500A) Processing helix chain 'U' and resid 215 through 222 Processing helix chain 'U' and resid 228 through 241 removed outlier: 3.823A pdb=" N PHE U 232 " --> pdb=" O TRP U 228 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR U 239 " --> pdb=" O ALA U 235 " (cutoff:3.500A) Processing helix chain 'U' and resid 243 through 258 removed outlier: 3.663A pdb=" N ALA U 247 " --> pdb=" O LEU U 243 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY U 258 " --> pdb=" O LEU U 254 " (cutoff:3.500A) Processing helix chain 'U' and resid 262 through 277 removed outlier: 3.520A pdb=" N VAL U 266 " --> pdb=" O SER U 262 " (cutoff:3.500A) Processing helix chain 'U' and resid 278 through 293 removed outlier: 3.820A pdb=" N SER U 284 " --> pdb=" O ASP U 280 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE U 285 " --> pdb=" O LYS U 281 " (cutoff:3.500A) Processing helix chain 'U' and resid 299 through 309 Processing helix chain 'U' and resid 312 through 327 removed outlier: 3.615A pdb=" N TYR U 318 " --> pdb=" O SER U 314 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE U 326 " --> pdb=" O ASN U 322 " (cutoff:3.500A) Processing helix chain 'U' and resid 330 through 344 Processing helix chain 'U' and resid 346 through 361 Processing helix chain 'U' and resid 364 through 378 removed outlier: 4.325A pdb=" N TRP U 368 " --> pdb=" O TYR U 364 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR U 369 " --> pdb=" O LEU U 365 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU U 370 " --> pdb=" O GLY U 366 " (cutoff:3.500A) Processing helix chain 'U' and resid 380 through 395 Processing helix chain 'U' and resid 398 through 412 removed outlier: 3.529A pdb=" N TRP U 402 " --> pdb=" O ASP U 398 " (cutoff:3.500A) Processing helix chain 'U' and resid 414 through 429 removed outlier: 3.883A pdb=" N LEU U 428 " --> pdb=" O ARG U 424 " (cutoff:3.500A) Processing helix chain 'U' and resid 433 through 446 Processing helix chain 'U' and resid 448 through 462 Processing helix chain 'U' and resid 468 through 480 removed outlier: 3.719A pdb=" N GLU U 478 " --> pdb=" O ALA U 474 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN U 479 " --> pdb=" O LYS U 475 " (cutoff:3.500A) Processing helix chain 'U' and resid 483 through 500 removed outlier: 3.581A pdb=" N ALA U 487 " --> pdb=" O SER U 483 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS U 492 " --> pdb=" O GLN U 488 " (cutoff:3.500A) Processing helix chain 'U' and resid 512 through 517 removed outlier: 4.281A pdb=" N LEU U 516 " --> pdb=" O ALA U 512 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA U 517 " --> pdb=" O PHE U 513 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 512 through 517' Processing helix chain 'U' and resid 518 through 523 removed outlier: 3.791A pdb=" N LYS U 522 " --> pdb=" O GLN U 518 " (cutoff:3.500A) Processing helix chain 'U' and resid 526 through 533 Processing helix chain 'U' and resid 542 through 554 Processing helix chain 'V' and resid 28 through 46 removed outlier: 3.534A pdb=" N ILE V 32 " --> pdb=" O ASP V 28 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 62 removed outlier: 3.590A pdb=" N SER V 61 " --> pdb=" O GLU V 57 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU V 62 " --> pdb=" O LEU V 58 " (cutoff:3.500A) Processing helix chain 'V' and resid 77 through 83 removed outlier: 3.815A pdb=" N ASP V 83 " --> pdb=" O GLU V 79 " (cutoff:3.500A) Processing helix chain 'V' and resid 83 through 96 removed outlier: 3.656A pdb=" N VAL V 96 " --> pdb=" O ALA V 92 " (cutoff:3.500A) Processing helix chain 'V' and resid 98 through 105 removed outlier: 3.867A pdb=" N ALA V 102 " --> pdb=" O GLU V 98 " (cutoff:3.500A) Processing helix chain 'V' and resid 112 through 136 removed outlier: 3.570A pdb=" N GLY V 126 " --> pdb=" O ARG V 122 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL V 135 " --> pdb=" O ASP V 131 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASP V 136 " --> pdb=" O ASP V 132 " (cutoff:3.500A) Processing helix chain 'V' and resid 150 through 164 Processing helix chain 'V' and resid 168 through 181 Processing helix chain 'V' and resid 184 through 199 removed outlier: 3.693A pdb=" N ASP V 190 " --> pdb=" O LYS V 186 " (cutoff:3.500A) Processing helix chain 'V' and resid 202 through 213 removed outlier: 4.268A pdb=" N TRP V 206 " --> pdb=" O HIS V 202 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN V 211 " --> pdb=" O LEU V 207 " (cutoff:3.500A) Processing helix chain 'V' and resid 216 through 222 removed outlier: 3.754A pdb=" N LYS V 220 " --> pdb=" O LYS V 216 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU V 222 " --> pdb=" O MET V 218 " (cutoff:3.500A) Processing helix chain 'V' and resid 228 through 241 removed outlier: 3.745A pdb=" N PHE V 232 " --> pdb=" O TRP V 228 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA V 235 " --> pdb=" O GLU V 231 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR V 239 " --> pdb=" O ALA V 235 " (cutoff:3.500A) Processing helix chain 'V' and resid 243 through 257 Processing helix chain 'V' and resid 262 through 276 Processing helix chain 'V' and resid 278 through 293 Processing helix chain 'V' and resid 299 through 310 removed outlier: 3.813A pdb=" N ARG V 310 " --> pdb=" O LEU V 306 " (cutoff:3.500A) Processing helix chain 'V' and resid 312 through 325 removed outlier: 3.535A pdb=" N CYS V 324 " --> pdb=" O ALA V 320 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU V 325 " --> pdb=" O HIS V 321 " (cutoff:3.500A) Processing helix chain 'V' and resid 330 through 344 Processing helix chain 'V' and resid 346 through 361 Processing helix chain 'V' and resid 365 through 378 removed outlier: 4.345A pdb=" N THR V 369 " --> pdb=" O LEU V 365 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU V 370 " --> pdb=" O GLY V 366 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU V 374 " --> pdb=" O LEU V 370 " (cutoff:3.500A) Processing helix chain 'V' and resid 380 through 395 removed outlier: 3.760A pdb=" N VAL V 394 " --> pdb=" O HIS V 390 " (cutoff:3.500A) Processing helix chain 'V' and resid 398 through 412 removed outlier: 3.697A pdb=" N TYR V 409 " --> pdb=" O LEU V 405 " (cutoff:3.500A) Processing helix chain 'V' and resid 414 through 417 Processing helix chain 'V' and resid 418 through 429 Processing helix chain 'V' and resid 432 through 445 removed outlier: 3.916A pdb=" N LEU V 436 " --> pdb=" O ASP V 432 " (cutoff:3.500A) Processing helix chain 'V' and resid 448 through 463 Processing helix chain 'V' and resid 468 through 480 removed outlier: 3.625A pdb=" N LYS V 472 " --> pdb=" O MET V 468 " (cutoff:3.500A) Processing helix chain 'V' and resid 482 through 500 removed outlier: 3.997A pdb=" N GLN V 488 " --> pdb=" O GLU V 484 " (cutoff:3.500A) Processing helix chain 'V' and resid 508 through 523 removed outlier: 3.603A pdb=" N GLN V 518 " --> pdb=" O ARG V 514 " (cutoff:3.500A) Processing helix chain 'V' and resid 532 through 537 Processing helix chain 'V' and resid 542 through 556 removed outlier: 3.816A pdb=" N LYS V 547 " --> pdb=" O ARG V 543 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA V 548 " --> pdb=" O GLU V 544 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU V 550 " --> pdb=" O GLY V 546 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG V 551 " --> pdb=" O LYS V 547 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU V 556 " --> pdb=" O GLN V 552 " (cutoff:3.500A) Processing helix chain 'Z' and resid 37 through 47 Processing helix chain 'Z' and resid 50 through 67 Processing helix chain 'Z' and resid 72 through 90 Processing helix chain 'Z' and resid 92 through 111 removed outlier: 3.619A pdb=" N SER Z 111 " --> pdb=" O LYS Z 107 " (cutoff:3.500A) Processing helix chain 'Z' and resid 134 through 149 removed outlier: 3.500A pdb=" N VAL Z 138 " --> pdb=" O SER Z 134 " (cutoff:3.500A) Processing helix chain 'Z' and resid 151 through 161 removed outlier: 3.595A pdb=" N LEU Z 159 " --> pdb=" O ALA Z 155 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY Z 161 " --> pdb=" O ALA Z 157 " (cutoff:3.500A) Processing helix chain 'Z' and resid 168 through 183 Processing helix chain 'Z' and resid 185 through 199 removed outlier: 3.617A pdb=" N SER Z 191 " --> pdb=" O PRO Z 187 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU Z 194 " --> pdb=" O THR Z 190 " (cutoff:3.500A) Processing helix chain 'Z' and resid 202 through 212 Processing helix chain 'Z' and resid 215 through 223 Processing helix chain 'Z' and resid 223 through 230 removed outlier: 3.585A pdb=" N GLN Z 228 " --> pdb=" O MET Z 224 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR Z 229 " --> pdb=" O ASN Z 225 " (cutoff:3.500A) Processing helix chain 'Z' and resid 233 through 249 removed outlier: 4.246A pdb=" N SER Z 237 " --> pdb=" O LEU Z 233 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL Z 238 " --> pdb=" O ASP Z 234 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY Z 249 " --> pdb=" O PHE Z 245 " (cutoff:3.500A) Processing helix chain 'Z' and resid 250 through 264 removed outlier: 3.833A pdb=" N CYS Z 259 " --> pdb=" O ILE Z 255 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER Z 260 " --> pdb=" O SER Z 256 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU Z 261 " --> pdb=" O THR Z 257 " (cutoff:3.500A) Processing helix chain 'Z' and resid 270 through 284 Processing helix chain 'Z' and resid 286 through 301 removed outlier: 3.557A pdb=" N VAL Z 291 " --> pdb=" O ASN Z 287 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU Z 292 " --> pdb=" O LYS Z 288 " (cutoff:3.500A) Processing helix chain 'Z' and resid 307 through 318 Processing helix chain 'Z' and resid 320 through 335 removed outlier: 3.754A pdb=" N ARG Z 330 " --> pdb=" O ASN Z 326 " (cutoff:3.500A) Processing helix chain 'Z' and resid 338 through 352 removed outlier: 4.231A pdb=" N TRP Z 342 " --> pdb=" O HIS Z 338 " (cutoff:3.500A) Processing helix chain 'Z' and resid 354 through 369 removed outlier: 3.650A pdb=" N TYR Z 360 " --> pdb=" O SER Z 356 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA Z 365 " --> pdb=" O LEU Z 361 " (cutoff:3.500A) Processing helix chain 'Z' and resid 372 through 386 removed outlier: 3.551A pdb=" N LEU Z 376 " --> pdb=" O SER Z 372 " (cutoff:3.500A) Processing helix chain 'Z' and resid 391 through 403 removed outlier: 3.803A pdb=" N HIS Z 395 " --> pdb=" O GLU Z 391 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG Z 401 " --> pdb=" O ARG Z 397 " (cutoff:3.500A) Processing helix chain 'Z' and resid 406 through 420 removed outlier: 3.853A pdb=" N TYR Z 410 " --> pdb=" O ARG Z 406 " (cutoff:3.500A) Processing helix chain 'Z' and resid 423 through 437 Processing helix chain 'Z' and resid 440 through 451 Processing helix chain 'Z' and resid 454 through 458 Processing helix chain 'Z' and resid 459 through 472 removed outlier: 4.065A pdb=" N THR Z 463 " --> pdb=" O GLU Z 459 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU Z 464 " --> pdb=" O LYS Z 460 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU Z 465 " --> pdb=" O ALA Z 461 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP Z 466 " --> pdb=" O LYS Z 462 " (cutoff:3.500A) Processing helix chain 'Z' and resid 475 through 489 Processing helix chain 'Z' and resid 492 through 504 removed outlier: 3.522A pdb=" N ALA Z 497 " --> pdb=" O GLU Z 493 " (cutoff:3.500A) Processing helix chain 'Z' and resid 508 through 514 Processing helix chain 'Z' and resid 518 through 523 removed outlier: 3.635A pdb=" N VAL Z 522 " --> pdb=" O PHE Z 518 " (cutoff:3.500A) Processing helix chain 'Z' and resid 527 through 538 Processing sheet with id=AA1, first strand: chain 'R' and resid 174 through 176 removed outlier: 3.565A pdb=" N ARG R 174 " --> pdb=" O LEU R 469 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR R 466 " --> pdb=" O ALA R 462 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N THR R 457 " --> pdb=" O AMET R 451 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N AMET R 451 " --> pdb=" O THR R 457 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA R 459 " --> pdb=" O LEU R 449 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU R 449 " --> pdb=" O ALA R 459 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA R 461 " --> pdb=" O LEU R 447 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 190 through 192 removed outlier: 7.045A pdb=" N VAL R 206 " --> pdb=" O LEU R 219 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU R 219 " --> pdb=" O VAL R 206 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 229 through 234 removed outlier: 6.368A pdb=" N VAL R 250 " --> pdb=" O ASN R 263 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASN R 263 " --> pdb=" O VAL R 250 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU R 252 " --> pdb=" O LEU R 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'R' and resid 271 through 276 removed outlier: 3.998A pdb=" N SER R 273 " --> pdb=" O GLY R 284 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N HIS R 289 " --> pdb=" O SER R 285 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA R 303 " --> pdb=" O HIS R 292 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASP R 294 " --> pdb=" O HIS R 301 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N HIS R 301 " --> pdb=" O ASP R 294 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 312 through 314 Processing sheet with id=AA6, first strand: chain 'R' and resid 360 through 363 removed outlier: 4.185A pdb=" N ALA R 360 " --> pdb=" O GLY R 374 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE R 382 " --> pdb=" O ALA R 395 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA R 395 " --> pdb=" O ILE R 382 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE R 384 " --> pdb=" O LEU R 393 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 402 through 408 removed outlier: 4.494A pdb=" N SER R 404 " --> pdb=" O GLY R 417 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY R 417 " --> pdb=" O SER R 404 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU R 425 " --> pdb=" O GLU R 438 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU R 438 " --> pdb=" O LEU R 425 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE R 427 " --> pdb=" O VAL R 436 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 22 through 24 Processing sheet with id=AA9, first strand: chain 'L' and resid 106 through 112 removed outlier: 5.441A pdb=" N GLU L 107 " --> pdb=" O VAL L 98 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL L 98 " --> pdb=" O GLU L 107 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA L 143 " --> pdb=" O SER L 92 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE L 94 " --> pdb=" O VAL L 141 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL L 141 " --> pdb=" O ILE L 94 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL L 96 " --> pdb=" O ILE L 139 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE L 139 " --> pdb=" O VAL L 96 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL L 98 " --> pdb=" O ILE L 137 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE L 137 " --> pdb=" O VAL L 98 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N MET L 136 " --> pdb=" O ARG L 70 " (cutoff:3.500A) removed outlier: 10.685A pdb=" N ARG L 70 " --> pdb=" O MET L 136 " (cutoff:3.500A) removed outlier: 11.582A pdb=" N GLN L 138 " --> pdb=" O PHE L 68 " (cutoff:3.500A) removed outlier: 12.098A pdb=" N PHE L 68 " --> pdb=" O GLN L 138 " (cutoff:3.500A) removed outlier: 11.143A pdb=" N ALA L 140 " --> pdb=" O ILE L 66 " (cutoff:3.500A) removed outlier: 12.251A pdb=" N ILE L 66 " --> pdb=" O ALA L 140 " (cutoff:3.500A) removed outlier: 11.227A pdb=" N LEU L 142 " --> pdb=" O VAL L 64 " (cutoff:3.500A) removed outlier: 12.456A pdb=" N VAL L 64 " --> pdb=" O LEU L 142 " (cutoff:3.500A) removed outlier: 9.881A pdb=" N ASN L 144 " --> pdb=" O HIS L 62 " (cutoff:3.500A) removed outlier: 11.442A pdb=" N HIS L 62 " --> pdb=" O ASN L 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 54 through 55 Processing sheet with id=AB2, first strand: chain 'A' and resid 12 through 13 removed outlier: 5.959A pdb=" N ILE A 12 " --> pdb=" O PHE A 510 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY A 507 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LEU A 497 " --> pdb=" O VAL A 509 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 18 through 19 removed outlier: 5.968A pdb=" N ARG A 594 " --> pdb=" O ASP A 589 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASP A 589 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N THR A 596 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILE A 587 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLU A 598 " --> pdb=" O HIS A 585 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 76 through 78 Processing sheet with id=AB5, first strand: chain 'A' and resid 125 through 132 Processing sheet with id=AB6, first strand: chain 'A' and resid 177 through 182 Processing sheet with id=AB7, first strand: chain 'A' and resid 237 through 238 removed outlier: 6.540A pdb=" N VAL A 224 " --> pdb=" O ILE A 409 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N HIS A 411 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LYS A 226 " --> pdb=" O HIS A 411 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N TRP A 413 " --> pdb=" O LYS A 226 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL A 268 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N THR A 414 " --> pdb=" O HIS A 266 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N HIS A 266 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE A 255 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LEU A 249 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N MET A 257 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 430 through 434 removed outlier: 3.943A pdb=" N LYS A 440 " --> pdb=" O PHE A 457 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU A 452 " --> pdb=" O ASN A 473 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ASN A 473 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N CYS A 454 " --> pdb=" O VAL A 471 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL A 471 " --> pdb=" O CYS A 454 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LYS A 456 " --> pdb=" O GLY A 469 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 860 through 862 removed outlier: 6.243A pdb=" N TYR A 860 " --> pdb=" O THR A 897 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1108 through 1111 Processing sheet with id=AC2, first strand: chain 'A' and resid 1572 through 1574 Processing sheet with id=AC3, first strand: chain 'A' and resid 1655 through 1656 removed outlier: 4.239A pdb=" N THR A1655 " --> pdb=" O LEU A1619 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1647 through 1652 removed outlier: 6.952A pdb=" N LEU A1633 " --> pdb=" O VAL A1668 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL A1668 " --> pdb=" O LEU A1633 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLU A1635 " --> pdb=" O ILE A1666 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE A1666 " --> pdb=" O GLU A1635 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR A1637 " --> pdb=" O LYS A1664 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A1676 " --> pdb=" O VAL A1668 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 593 through 594 Processing sheet with id=AC6, first strand: chain 'N' and resid 647 through 648 Processing sheet with id=AC7, first strand: chain 'I' and resid 12 through 15 removed outlier: 5.725A pdb=" N VAL I 13 " --> pdb=" O GLU I 745 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLU I 745 " --> pdb=" O VAL I 13 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 23 through 28 removed outlier: 3.733A pdb=" N LEU I 46 " --> pdb=" O TRP I 56 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N TRP I 56 " --> pdb=" O LEU I 46 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 68 through 73 removed outlier: 4.085A pdb=" N CYS I 70 " --> pdb=" O ALA I 83 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 114 through 117 removed outlier: 5.983A pdb=" N ILE I 185 " --> pdb=" O ARG I 197 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG I 197 " --> pdb=" O ILE I 185 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU I 187 " --> pdb=" O ILE I 195 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 204 through 210 removed outlier: 6.765A pdb=" N VAL I 220 " --> pdb=" O LEU I 206 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LEU I 208 " --> pdb=" O SER I 218 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N SER I 218 " --> pdb=" O LEU I 208 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU I 210 " --> pdb=" O SER I 216 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N SER I 216 " --> pdb=" O LEU I 210 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N SER I 229 " --> pdb=" O ARG I 558 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG I 558 " --> pdb=" O SER I 229 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL I 231 " --> pdb=" O LEU I 556 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 574 through 578 removed outlier: 11.760A pdb=" N TYR I 596 " --> pdb=" O PHE I 620 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N PHE I 620 " --> pdb=" O TYR I 596 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N MET I 598 " --> pdb=" O ILE I 618 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N PHE I 707 " --> pdb=" O GLY I 621 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE I 623 " --> pdb=" O PHE I 707 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 638 through 643 removed outlier: 5.084A pdb=" N CYS I 638 " --> pdb=" O LYS I 654 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LYS I 654 " --> pdb=" O CYS I 638 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP I 640 " --> pdb=" O VAL I 652 " (cutoff:3.500A) 3865 hydrogen bonds defined for protein. 11383 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: 30.76 Time building geometry restraints manager: 23.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 11193 1.30 - 1.43: 18308 1.43 - 1.56: 39477 1.56 - 1.69: 0 1.69 - 1.82: 631 Bond restraints: 69609 Sorted by residual: bond pdb=" C THR A1097 " pdb=" N GLU A1098 " ideal model delta sigma weight residual 1.331 1.262 0.069 1.59e-02 3.96e+03 1.87e+01 bond pdb=" C HIS A1591 " pdb=" N PHE A1592 " ideal model delta sigma weight residual 1.339 1.169 0.171 5.57e-02 3.22e+02 9.41e+00 bond pdb=" CA THR K 171 " pdb=" CB THR K 171 " ideal model delta sigma weight residual 1.525 1.484 0.041 1.47e-02 4.63e+03 7.82e+00 bond pdb=" C VAL C 39 " pdb=" N PRO C 40 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.66e+00 bond pdb=" CA ASP Q 246 " pdb=" CB ASP Q 246 " ideal model delta sigma weight residual 1.526 1.486 0.040 1.76e-02 3.23e+03 5.14e+00 ... (remaining 69604 not shown) Histogram of bond angle deviations from ideal: 97.33 - 106.23: 1652 106.23 - 115.12: 42463 115.12 - 124.02: 48431 124.02 - 132.91: 1596 132.91 - 141.81: 138 Bond angle restraints: 94280 Sorted by residual: angle pdb=" N PRO R 101 " pdb=" CA PRO R 101 " pdb=" CB PRO R 101 " ideal model delta sigma weight residual 103.25 110.82 -7.57 1.05e+00 9.07e-01 5.20e+01 angle pdb=" C VAL R 335 " pdb=" N TRP R 336 " pdb=" CA TRP R 336 " ideal model delta sigma weight residual 122.15 141.81 -19.66 3.47e+00 8.31e-02 3.21e+01 angle pdb=" CA LEU A 728 " pdb=" CB LEU A 728 " pdb=" CG LEU A 728 " ideal model delta sigma weight residual 116.30 134.35 -18.05 3.50e+00 8.16e-02 2.66e+01 angle pdb=" C LYS A1545 " pdb=" N THR A1546 " pdb=" CA THR A1546 " ideal model delta sigma weight residual 121.54 130.34 -8.80 1.91e+00 2.74e-01 2.12e+01 angle pdb=" C VAL N 481 " pdb=" CA VAL N 481 " pdb=" CB VAL N 481 " ideal model delta sigma weight residual 109.33 113.82 -4.49 9.80e-01 1.04e+00 2.10e+01 ... (remaining 94275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 36965 17.97 - 35.93: 4058 35.93 - 53.90: 717 53.90 - 71.87: 165 71.87 - 89.83: 52 Dihedral angle restraints: 41957 sinusoidal: 16658 harmonic: 25299 Sorted by residual: dihedral pdb=" CA LEU R 202 " pdb=" C LEU R 202 " pdb=" N ASP R 203 " pdb=" CA ASP R 203 " ideal model delta harmonic sigma weight residual -180.00 -135.56 -44.44 0 5.00e+00 4.00e-02 7.90e+01 dihedral pdb=" CA GLU O 123 " pdb=" C GLU O 123 " pdb=" N PRO O 124 " pdb=" CA PRO O 124 " ideal model delta harmonic sigma weight residual -180.00 -137.11 -42.89 0 5.00e+00 4.00e-02 7.36e+01 dihedral pdb=" CA ASP A1385 " pdb=" C ASP A1385 " pdb=" N TRP A1386 " pdb=" CA TRP A1386 " ideal model delta harmonic sigma weight residual 180.00 152.12 27.88 0 5.00e+00 4.00e-02 3.11e+01 ... (remaining 41954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 9266 0.077 - 0.154: 1194 0.154 - 0.231: 86 0.231 - 0.308: 5 0.308 - 0.385: 1 Chirality restraints: 10552 Sorted by residual: chirality pdb=" CB ILE U 297 " pdb=" CA ILE U 297 " pdb=" CG1 ILE U 297 " pdb=" CG2 ILE U 297 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CB VAL N 715 " pdb=" CA VAL N 715 " pdb=" CG1 VAL N 715 " pdb=" CG2 VAL N 715 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA ASN A 593 " pdb=" N ASN A 593 " pdb=" C ASN A 593 " pdb=" CB ASN A 593 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 10549 not shown) Planarity restraints: 11989 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1386 " -0.030 2.00e-02 2.50e+03 2.24e-02 1.25e+01 pdb=" CG TRP A1386 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP A1386 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A1386 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A1386 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A1386 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A1386 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1386 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1386 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A1386 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO Z 73 " 0.052 5.00e-02 4.00e+02 7.81e-02 9.76e+00 pdb=" N PRO Z 74 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO Z 74 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO Z 74 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU O 123 " 0.050 5.00e-02 4.00e+02 7.62e-02 9.30e+00 pdb=" N PRO O 124 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO O 124 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO O 124 " 0.043 5.00e-02 4.00e+02 ... (remaining 11986 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 10997 2.75 - 3.29: 66231 3.29 - 3.83: 121169 3.83 - 4.36: 139691 4.36 - 4.90: 235740 Nonbonded interactions: 573828 Sorted by model distance: nonbonded pdb=" OH TYR K 487 " pdb=" O ASP W 15 " model vdw 2.219 2.440 nonbonded pdb=" OH TYR I 625 " pdb=" O TRP I 711 " model vdw 2.235 2.440 nonbonded pdb=" O ASP L 86 " pdb=" OG1 THR L 90 " model vdw 2.245 2.440 nonbonded pdb=" OD1 ASP Z 85 " pdb=" OH TYR Z 100 " model vdw 2.260 2.440 nonbonded pdb=" O LEU N 428 " pdb=" OG1 THR N 434 " model vdw 2.272 2.440 ... (remaining 573823 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 'G' and resid 1 through 26) selection = (chain 'W' and (resid 1 through 23 or (resid 24 through 25 and (name N or name C \ A or name C or name O or name CB )) or resid 26)) } ncs_group { reference = (chain 'J' and (resid 5 through 170 or (resid 452 and (name N or name CA or name \ C or name O or name CB )) or resid 453 through 766 or (resid 767 through 768 an \ d (name N or name CA or name C or name O or name CB )))) selection = (chain 'P' and (resid 5 through 170 or resid 452 through 768)) } ncs_group { reference = (chain 'K' and ((resid 2 and (name N or name CA or name C or name O or name CB ) \ ) or resid 3 through 528 or (resid 548 and (name N or name CA or name C or name \ O or name CB )) or (resid 560 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain 'Q' and (resid 2 through 94 or resid 127 through 436 or (resid 437 throug \ h 438 and (name N or name CA or name C or name O or name CB )) or resid 439 thro \ ugh 530)) } ncs_group { reference = (chain 'U' and (resid 26 through 108 or (resid 109 and (name N or name CA or nam \ e C or name O or name CB )) or resid 110 through 507 or (resid 508 through 509 a \ nd (name N or name CA or name C or name O or name CB )) or resid 510 through 513 \ or (resid 514 and (name N or name CA or name C or name O or name CB )) or resid \ 515 through 554)) selection = (chain 'V' and (resid 26 through 135 or (resid 147 and (name N or name CA or nam \ e C or name O or name CB )) or resid 148 through 280 or (resid 281 through 282 a \ nd (name N or name CA or name C or name O or name CB )) or resid 283 through 496 \ or (resid 497 and (name N or name CA or name C or name O or name CB or name CG1 \ or name CG2)) or resid 498 through 508 or (resid 509 and (name N or name CA or \ name C or name O or name CB )) or resid 510 through 536 or (resid 537 through 54 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 546 or (resi \ d 547 through 554 and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'Y' and (resid 36 through 499 or resid 501 through 540)) selection = (chain 'Z' and (resid 36 through 110 or resid 132 through 263 or (resid 264 and \ (name N or name CA or name C or name O or name CB )) or resid 265 through 499 or \ resid 501 through 540)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.330 Construct map_model_manager: 0.080 Extract box with map and model: 15.660 Check model and map are aligned: 0.800 Set scattering table: 0.540 Process input model: 160.450 Find NCS groups from input model: 2.990 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 187.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.171 69609 Z= 0.432 Angle : 0.850 19.655 94280 Z= 0.469 Chirality : 0.052 0.385 10552 Planarity : 0.006 0.078 11989 Dihedral : 15.493 89.832 25561 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.16 % Favored : 95.81 % Rotamer: Outliers : 0.23 % Allowed : 7.58 % Favored : 92.19 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.31 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.07), residues: 8451 helix: -2.31 (0.05), residues: 5269 sheet: -1.26 (0.20), residues: 577 loop : -2.62 (0.10), residues: 2605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP A1386 HIS 0.015 0.001 HIS O 645 PHE 0.029 0.002 PHE Y 518 TYR 0.020 0.002 TYR Y 192 ARG 0.007 0.001 ARG R 296 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16902 Ramachandran restraints generated. 8451 Oldfield, 0 Emsley, 8451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16902 Ramachandran restraints generated. 8451 Oldfield, 0 Emsley, 8451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 7506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 521 time to evaluate : 6.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 124 ASP cc_start: 0.8768 (t0) cc_final: 0.8348 (t0) REVERT: R 467 LEU cc_start: 0.9767 (pp) cc_final: 0.9563 (tt) REVERT: S 47 ARG cc_start: 0.7606 (ttt180) cc_final: 0.7401 (tmt170) REVERT: L 12 ASP cc_start: 0.9110 (t70) cc_final: 0.8545 (t0) REVERT: L 14 LYS cc_start: 0.9635 (mptt) cc_final: 0.9435 (mmtm) REVERT: L 75 LYS cc_start: 0.9614 (tttt) cc_final: 0.9373 (ttmm) REVERT: L 84 LYS cc_start: 0.9412 (tmtt) cc_final: 0.9187 (tppt) REVERT: L 136 MET cc_start: 0.9165 (ttt) cc_final: 0.8758 (ttm) REVERT: L 153 MET cc_start: 0.8657 (tpt) cc_final: 0.8424 (tpp) REVERT: D 26 GLU cc_start: 0.8570 (mp0) cc_final: 0.8233 (mp0) REVERT: D 29 GLU cc_start: 0.8810 (pt0) cc_final: 0.8415 (tm-30) REVERT: D 31 GLN cc_start: 0.9169 (tm-30) cc_final: 0.8629 (tm-30) REVERT: D 33 GLN cc_start: 0.9129 (mt0) cc_final: 0.7681 (mt0) REVERT: D 34 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8721 (pp20) REVERT: D 36 GLN cc_start: 0.9267 (tm-30) cc_final: 0.8965 (tm-30) REVERT: A 668 MET cc_start: 0.9348 (mtp) cc_final: 0.8898 (mtp) REVERT: A 1024 MET cc_start: 0.9286 (mtt) cc_final: 0.9067 (mtp) REVERT: A 1086 MET cc_start: 0.8911 (mtt) cc_final: 0.8630 (mtt) REVERT: A 1316 MET cc_start: 0.8750 (mtm) cc_final: 0.8089 (mpp) REVERT: A 1550 MET cc_start: 0.8518 (tpp) cc_final: 0.8245 (tpp) REVERT: A 1793 MET cc_start: 0.9378 (mtm) cc_final: 0.9082 (mtm) REVERT: N 156 MET cc_start: 0.9458 (tmm) cc_final: 0.8997 (tmm) REVERT: N 350 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7621 (p0) REVERT: N 445 ASP cc_start: 0.7514 (m-30) cc_final: 0.7120 (p0) REVERT: N 560 MET cc_start: 0.0940 (mtt) cc_final: 0.0439 (mtt) REVERT: I 116 MET cc_start: 0.8627 (ppp) cc_final: 0.8329 (ppp) REVERT: I 322 MET cc_start: 0.8726 (mmm) cc_final: 0.8319 (mmm) REVERT: I 425 MET cc_start: 0.8723 (mtp) cc_final: 0.8516 (mtp) REVERT: I 534 ASP cc_start: 0.9146 (t0) cc_final: 0.8794 (p0) REVERT: O 242 ASN cc_start: 0.8907 (m110) cc_final: 0.8695 (t0) REVERT: O 400 ASP cc_start: 0.8832 (m-30) cc_final: 0.8583 (m-30) REVERT: O 414 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8870 (pp) REVERT: O 646 MET cc_start: 0.8075 (mmm) cc_final: 0.7355 (ttt) REVERT: O 664 MET cc_start: 0.9457 (mmt) cc_final: 0.8896 (mmm) REVERT: G 16 ILE cc_start: 0.9604 (mt) cc_final: 0.8810 (mp) REVERT: W 23 ARG cc_start: 0.8564 (ttm-80) cc_final: 0.8285 (tpp80) REVERT: M 51 LYS cc_start: 0.9599 (tttp) cc_final: 0.9253 (ttmm) REVERT: M 53 GLN cc_start: 0.9009 (pt0) cc_final: 0.8657 (pp30) REVERT: M 54 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8453 (mm-30) REVERT: H 85 LEU cc_start: 0.9590 (mp) cc_final: 0.9188 (mt) REVERT: H 97 LYS cc_start: 0.8963 (ttmt) cc_final: 0.8718 (mtpp) REVERT: J 85 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8729 (pp) REVERT: P 643 MET cc_start: 0.8832 (tpt) cc_final: 0.8508 (tpp) REVERT: P 656 MET cc_start: 0.8878 (tmm) cc_final: 0.8276 (tmm) REVERT: Q 442 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.8383 (t0) REVERT: Y 63 MET cc_start: 0.8913 (mmm) cc_final: 0.8540 (mmm) REVERT: Y 91 LYS cc_start: 0.9593 (mttt) cc_final: 0.9077 (ptmm) REVERT: Y 144 GLU cc_start: 0.9258 (mt-10) cc_final: 0.9003 (mt-10) REVERT: Y 386 MET cc_start: 0.8376 (mtm) cc_final: 0.8060 (ptm) REVERT: Y 427 MET cc_start: 0.9150 (tpt) cc_final: 0.8924 (tpp) REVERT: Y 429 MET cc_start: 0.9425 (mmt) cc_final: 0.9201 (mmm) REVERT: U 119 MET cc_start: 0.9103 (tpp) cc_final: 0.8699 (mpp) REVERT: Z 308 MET cc_start: 0.9176 (mmt) cc_final: 0.8972 (mmt) REVERT: Z 427 MET cc_start: 0.8345 (tpt) cc_final: 0.8087 (tpp) outliers start: 15 outliers final: 4 residues processed: 534 average time/residue: 0.6846 time to fit residues: 612.3598 Evaluate side-chains 408 residues out of total 7506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 400 time to evaluate : 6.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 52 VAL Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain N residue 350 ASP Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain K residue 233 VAL Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain Q residue 442 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 847 random chunks: chunk 715 optimal weight: 0.9990 chunk 641 optimal weight: 0.9990 chunk 356 optimal weight: 9.9990 chunk 219 optimal weight: 0.0170 chunk 433 optimal weight: 2.9990 chunk 342 optimal weight: 4.9990 chunk 663 optimal weight: 0.9990 chunk 256 optimal weight: 10.0000 chunk 403 optimal weight: 3.9990 chunk 494 optimal weight: 8.9990 chunk 769 optimal weight: 4.9990 overall best weight: 1.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 188 ASN R 218 GLN R 221 GLN R 289 HIS R 355 GLN R 367 GLN ** R 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 ASN L 62 HIS L 128 HIS L 146 GLN L 155 GLN D 19 ASN A 38 GLN ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 HIS ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 HIS A 426 GLN ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN A 717 GLN ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 832 HIS ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1161 ASN A1170 ASN A1192 ASN A1247 HIS A1250 GLN A1262 GLN A1266 HIS A1327 GLN A1380 ASN A1486 ASN A1511 ASN ** A1559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1591 HIS A1595 HIS ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1813 GLN N 81 ASN N 186 GLN N 306 GLN N 370 GLN N 373 GLN N 388 HIS N 671 GLN ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 47 HIS I 257 HIS I 301 GLN I 323 ASN I 442 GLN I 577 ASN I 578 ASN I 668 GLN ** I 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 684 GLN ** I 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 91 ASN O 110 GLN O 160 GLN ** O 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 382 GLN O 424 GLN O 449 ASN O 472 HIS O 552 GLN O 565 GLN ** O 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 699 ASN O 722 HIS O 742 GLN O 747 HIS K 45 GLN K 54 HIS ** K 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 264 HIS K 316 ASN K 550 HIS H 75 GLN J 14 GLN J 103 HIS J 497 ASN J 580 GLN J 583 HIS J 595 GLN J 657 HIS J 674 HIS J 708 HIS P 455 GLN P 497 ASN P 634 HIS ** P 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 680 HIS Q 18 GLN ** Q 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 58 HIS Q 80 HIS Q 342 HIS Q 503 HIS Y 66 ASN Y 67 ASN Y 78 GLN Y 172 ASN Y 251 ASN Y 270 ASN Y 338 HIS ** Y 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 506 GLN U 197 HIS U 252 GLN U 299 ASN U 305 ASN ** U 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 373 HIS V 202 HIS V 287 ASN V 305 ASN V 347 HIS V 373 HIS V 488 GLN ** V 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 40 HIS Z 50 HIS Z 151 GLN Z 172 ASN Z 184 GLN Z 338 HIS ** Z 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 385 ASN ** Z 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 523 ASN Total number of N/Q/H flips: 113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 69609 Z= 0.163 Angle : 0.538 12.176 94280 Z= 0.278 Chirality : 0.039 0.227 10552 Planarity : 0.004 0.072 11989 Dihedral : 4.959 49.717 9325 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.08 % Allowed : 10.79 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.31 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.09), residues: 8451 helix: -0.31 (0.07), residues: 5361 sheet: -0.82 (0.21), residues: 571 loop : -2.12 (0.11), residues: 2519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A1386 HIS 0.007 0.001 HIS P 64 PHE 0.015 0.001 PHE A1821 TYR 0.016 0.001 TYR Q 378 ARG 0.008 0.000 ARG R 262 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16902 Ramachandran restraints generated. 8451 Oldfield, 0 Emsley, 8451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16902 Ramachandran restraints generated. 8451 Oldfield, 0 Emsley, 8451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 7506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 452 time to evaluate : 6.391 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: R 124 ASP cc_start: 0.8706 (t0) cc_final: 0.7112 (t0) REVERT: R 127 GLU cc_start: 0.8281 (mp0) cc_final: 0.7789 (mp0) REVERT: R 420 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.7696 (m-10) REVERT: R 467 LEU cc_start: 0.9793 (pp) cc_final: 0.9580 (tt) REVERT: L 12 ASP cc_start: 0.9169 (t70) cc_final: 0.8651 (t0) REVERT: L 14 LYS cc_start: 0.9692 (mptt) cc_final: 0.9489 (mmtm) REVERT: L 75 LYS cc_start: 0.9603 (tttt) cc_final: 0.9393 (ttmm) REVERT: L 84 LYS cc_start: 0.9432 (tmtt) cc_final: 0.9174 (tppt) REVERT: L 136 MET cc_start: 0.9273 (ttt) cc_final: 0.8836 (ptm) REVERT: D 26 GLU cc_start: 0.8560 (mp0) cc_final: 0.8204 (mp0) REVERT: D 29 GLU cc_start: 0.8791 (pt0) cc_final: 0.8459 (tm-30) REVERT: D 31 GLN cc_start: 0.9193 (tm-30) cc_final: 0.8548 (tm-30) REVERT: D 33 GLN cc_start: 0.9204 (mt0) cc_final: 0.7561 (mt0) REVERT: D 34 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8702 (pp20) REVERT: D 36 GLN cc_start: 0.9324 (tm-30) cc_final: 0.8861 (tm-30) REVERT: D 42 GLN cc_start: 0.8951 (mt0) cc_final: 0.8553 (mm-40) REVERT: D 46 GLU cc_start: 0.8553 (pm20) cc_final: 0.7752 (pm20) REVERT: A 11 MET cc_start: 0.8466 (mmm) cc_final: 0.7658 (mmm) REVERT: A 604 MET cc_start: 0.8819 (mtp) cc_final: 0.8616 (mtp) REVERT: A 668 MET cc_start: 0.9310 (mtp) cc_final: 0.8915 (mtp) REVERT: A 1316 MET cc_start: 0.8772 (mtm) cc_final: 0.8201 (mpp) REVERT: A 1326 TYR cc_start: 0.8949 (t80) cc_final: 0.8735 (t80) REVERT: A 1550 MET cc_start: 0.8340 (tpp) cc_final: 0.7951 (tpp) REVERT: A 1783 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.8141 (t) REVERT: N 156 MET cc_start: 0.9432 (tmm) cc_final: 0.8976 (tmm) REVERT: N 350 ASP cc_start: 0.8164 (OUTLIER) cc_final: 0.7540 (p0) REVERT: N 385 ARG cc_start: 0.8713 (mtt-85) cc_final: 0.8427 (mmm-85) REVERT: N 414 MET cc_start: 0.8555 (mtt) cc_final: 0.8249 (ttp) REVERT: N 560 MET cc_start: 0.0614 (mtt) cc_final: 0.0174 (mtt) REVERT: I 116 MET cc_start: 0.8665 (ppp) cc_final: 0.8378 (ppp) REVERT: I 322 MET cc_start: 0.8999 (mmm) cc_final: 0.8475 (mmm) REVERT: I 534 ASP cc_start: 0.9155 (t0) cc_final: 0.8811 (p0) REVERT: O 646 MET cc_start: 0.8043 (mmm) cc_final: 0.7371 (ttt) REVERT: O 664 MET cc_start: 0.9449 (mmt) cc_final: 0.8903 (mmm) REVERT: K 88 GLN cc_start: 0.9153 (mt0) cc_final: 0.8918 (mt0) REVERT: W 14 ASP cc_start: 0.8217 (p0) cc_final: 0.8003 (p0) REVERT: W 20 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8746 (mm-30) REVERT: W 21 ASN cc_start: 0.8924 (m-40) cc_final: 0.8325 (m-40) REVERT: M 35 GLU cc_start: 0.9338 (mp0) cc_final: 0.9086 (mp0) REVERT: M 51 LYS cc_start: 0.9607 (tttp) cc_final: 0.9228 (ttmm) REVERT: M 53 GLN cc_start: 0.9024 (pt0) cc_final: 0.8536 (pt0) REVERT: H 69 GLN cc_start: 0.8901 (tp-100) cc_final: 0.8645 (tp40) REVERT: H 85 LEU cc_start: 0.9459 (mp) cc_final: 0.9052 (mt) REVERT: H 88 GLU cc_start: 0.8576 (mp0) cc_final: 0.8324 (mp0) REVERT: H 97 LYS cc_start: 0.8910 (ttmt) cc_final: 0.8665 (mtpp) REVERT: P 463 MET cc_start: 0.9416 (tpp) cc_final: 0.8895 (tpp) REVERT: P 516 MET cc_start: 0.8082 (mmt) cc_final: 0.7536 (mmt) REVERT: P 519 GLU cc_start: 0.8818 (tm-30) cc_final: 0.8377 (pp20) REVERT: P 643 MET cc_start: 0.8773 (tpt) cc_final: 0.8530 (tpp) REVERT: P 656 MET cc_start: 0.9110 (tmm) cc_final: 0.8317 (tmm) REVERT: Q 20 GLN cc_start: 0.9096 (mm110) cc_final: 0.8798 (mp10) REVERT: Y 63 MET cc_start: 0.8791 (mmm) cc_final: 0.8437 (mmm) REVERT: Y 91 LYS cc_start: 0.9642 (mttt) cc_final: 0.9016 (ptmm) REVERT: Y 386 MET cc_start: 0.8311 (mtm) cc_final: 0.7936 (ptp) REVERT: Y 427 MET cc_start: 0.9193 (tpt) cc_final: 0.8946 (tpp) REVERT: Y 429 MET cc_start: 0.9450 (mmt) cc_final: 0.9215 (mmm) REVERT: V 398 ASP cc_start: 0.8851 (t0) cc_final: 0.8612 (t0) REVERT: Z 239 TRP cc_start: 0.9317 (t60) cc_final: 0.8990 (t60) REVERT: Z 523 ASN cc_start: 0.5992 (OUTLIER) cc_final: 0.5663 (m110) outliers start: 77 outliers final: 40 residues processed: 505 average time/residue: 0.6535 time to fit residues: 569.0855 Evaluate side-chains 447 residues out of total 7506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 403 time to evaluate : 6.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 167 TYR Chi-restraints excluded: chain R residue 240 TYR Chi-restraints excluded: chain R residue 322 ARG Chi-restraints excluded: chain R residue 420 PHE Chi-restraints excluded: chain S residue 52 VAL Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 101 ASN Chi-restraints excluded: chain L residue 177 ASP Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1677 LEU Chi-restraints excluded: chain A residue 1760 ASN Chi-restraints excluded: chain A residue 1783 THR Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain A residue 1915 LEU Chi-restraints excluded: chain N residue 350 ASP Chi-restraints excluded: chain O residue 603 MET Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 749 VAL Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 439 VAL Chi-restraints excluded: chain K residue 442 ASP Chi-restraints excluded: chain K residue 549 VAL Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 595 GLN Chi-restraints excluded: chain P residue 617 LEU Chi-restraints excluded: chain Q residue 152 SER Chi-restraints excluded: chain Q residue 451 LEU Chi-restraints excluded: chain Y residue 272 ASP Chi-restraints excluded: chain U residue 414 MET Chi-restraints excluded: chain V residue 333 THR Chi-restraints excluded: chain V residue 450 VAL Chi-restraints excluded: chain V residue 542 THR Chi-restraints excluded: chain Z residue 371 ASN Chi-restraints excluded: chain Z residue 523 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 847 random chunks: chunk 427 optimal weight: 7.9990 chunk 238 optimal weight: 5.9990 chunk 640 optimal weight: 5.9990 chunk 523 optimal weight: 5.9990 chunk 212 optimal weight: 0.0770 chunk 770 optimal weight: 0.6980 chunk 832 optimal weight: 0.5980 chunk 686 optimal weight: 6.9990 chunk 764 optimal weight: 9.9990 chunk 262 optimal weight: 6.9990 chunk 618 optimal weight: 6.9990 overall best weight: 2.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 188 ASN ** R 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 HIS ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1309 HIS ** A1559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 506 HIS I 609 GLN ** I 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 GLN ** O 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 671 GLN O 693 ASN ** K 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 271 HIS K 497 ASN K 550 HIS J 595 GLN P 530 ASN P 583 HIS P 657 HIS Q 20 GLN ** Q 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 50 HIS ** U 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 477 HIS ** V 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 247 HIS ** Z 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 69609 Z= 0.249 Angle : 0.550 10.912 94280 Z= 0.282 Chirality : 0.039 0.174 10552 Planarity : 0.004 0.072 11989 Dihedral : 4.611 37.545 9320 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.74 % Favored : 96.24 % Rotamer: Outliers : 1.27 % Allowed : 12.85 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.31 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.09), residues: 8451 helix: 0.62 (0.07), residues: 5386 sheet: -0.59 (0.21), residues: 582 loop : -1.83 (0.12), residues: 2483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A1386 HIS 0.006 0.001 HIS U 321 PHE 0.022 0.001 PHE Q 164 TYR 0.015 0.001 TYR Y 140 ARG 0.007 0.000 ARG Z 253 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16902 Ramachandran restraints generated. 8451 Oldfield, 0 Emsley, 8451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16902 Ramachandran restraints generated. 8451 Oldfield, 0 Emsley, 8451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 7506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 412 time to evaluate : 6.332 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: R 124 ASP cc_start: 0.8689 (t0) cc_final: 0.8266 (t0) REVERT: R 222 MET cc_start: 0.5960 (mmm) cc_final: 0.5623 (mmm) REVERT: R 420 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7655 (m-80) REVERT: R 467 LEU cc_start: 0.9805 (pp) cc_final: 0.9576 (tt) REVERT: L 12 ASP cc_start: 0.9117 (t70) cc_final: 0.8552 (t0) REVERT: L 14 LYS cc_start: 0.9684 (mptt) cc_final: 0.9399 (mmtm) REVERT: L 75 LYS cc_start: 0.9611 (tttt) cc_final: 0.9398 (ttmm) REVERT: L 84 LYS cc_start: 0.9455 (tmtt) cc_final: 0.9172 (tmtt) REVERT: L 112 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7836 (tm-30) REVERT: L 114 VAL cc_start: 0.9479 (OUTLIER) cc_final: 0.9275 (m) REVERT: L 136 MET cc_start: 0.9266 (ttt) cc_final: 0.8740 (ptm) REVERT: D 26 GLU cc_start: 0.8561 (mp0) cc_final: 0.8202 (mp0) REVERT: D 29 GLU cc_start: 0.8782 (pt0) cc_final: 0.8379 (tm-30) REVERT: D 31 GLN cc_start: 0.9205 (tm-30) cc_final: 0.8562 (tm-30) REVERT: D 33 GLN cc_start: 0.9160 (mt0) cc_final: 0.7527 (mt0) REVERT: D 34 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8729 (pp20) REVERT: D 36 GLN cc_start: 0.9298 (tm-30) cc_final: 0.8861 (tm-30) REVERT: D 42 GLN cc_start: 0.8969 (mt0) cc_final: 0.8761 (mt0) REVERT: A 11 MET cc_start: 0.8416 (mmm) cc_final: 0.7320 (mmm) REVERT: A 604 MET cc_start: 0.8873 (mtp) cc_final: 0.8622 (mtp) REVERT: A 668 MET cc_start: 0.9306 (mtp) cc_final: 0.8832 (mtp) REVERT: A 1316 MET cc_start: 0.8900 (mtm) cc_final: 0.8271 (mpp) REVERT: A 1550 MET cc_start: 0.8303 (tpp) cc_final: 0.7890 (tpp) REVERT: A 1915 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9180 (mt) REVERT: N 156 MET cc_start: 0.9437 (tmm) cc_final: 0.8984 (tmm) REVERT: N 350 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7556 (p0) REVERT: N 414 MET cc_start: 0.8635 (mtt) cc_final: 0.8313 (ttp) REVERT: N 560 MET cc_start: 0.0648 (mtt) cc_final: 0.0214 (mtt) REVERT: I 116 MET cc_start: 0.8712 (ppp) cc_final: 0.8398 (ppp) REVERT: I 322 MET cc_start: 0.8945 (mmm) cc_final: 0.8500 (mmm) REVERT: I 534 ASP cc_start: 0.9151 (t0) cc_final: 0.8819 (p0) REVERT: O 414 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8558 (pp) REVERT: O 646 MET cc_start: 0.8100 (mmm) cc_final: 0.7404 (ttt) REVERT: O 664 MET cc_start: 0.9465 (mmt) cc_final: 0.9236 (mmm) REVERT: K 88 GLN cc_start: 0.9158 (mt0) cc_final: 0.8921 (mt0) REVERT: K 249 MET cc_start: 0.8775 (tpp) cc_final: 0.8519 (tpp) REVERT: W 21 ASN cc_start: 0.8730 (m-40) cc_final: 0.8295 (m-40) REVERT: M 53 GLN cc_start: 0.9008 (pt0) cc_final: 0.8500 (pt0) REVERT: H 69 GLN cc_start: 0.8926 (tp-100) cc_final: 0.8694 (tp40) REVERT: H 85 LEU cc_start: 0.9529 (mp) cc_final: 0.8963 (tp) REVERT: H 97 LYS cc_start: 0.8912 (ttmt) cc_final: 0.8678 (mtpp) REVERT: P 463 MET cc_start: 0.9445 (tpp) cc_final: 0.8942 (tpp) REVERT: P 643 MET cc_start: 0.8820 (tpt) cc_final: 0.8523 (tpp) REVERT: P 656 MET cc_start: 0.9159 (tmm) cc_final: 0.8377 (tmm) REVERT: P 733 VAL cc_start: 0.9333 (OUTLIER) cc_final: 0.9071 (m) REVERT: Y 63 MET cc_start: 0.8788 (mmm) cc_final: 0.8449 (mmm) REVERT: Y 91 LYS cc_start: 0.9682 (mttt) cc_final: 0.9045 (ptmm) REVERT: Y 142 MET cc_start: 0.9430 (mmm) cc_final: 0.8660 (mmm) REVERT: Y 386 MET cc_start: 0.8381 (mtm) cc_final: 0.7987 (ptp) REVERT: Y 427 MET cc_start: 0.9180 (tpt) cc_final: 0.8932 (tpp) REVERT: Y 429 MET cc_start: 0.9465 (mmt) cc_final: 0.9231 (mmm) REVERT: V 398 ASP cc_start: 0.8908 (t0) cc_final: 0.8700 (t0) REVERT: V 444 GLU cc_start: 0.9133 (tt0) cc_final: 0.8713 (tm-30) REVERT: Z 239 TRP cc_start: 0.9327 (t60) cc_final: 0.9017 (t60) outliers start: 91 outliers final: 57 residues processed: 479 average time/residue: 0.6473 time to fit residues: 543.9241 Evaluate side-chains 459 residues out of total 7506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 396 time to evaluate : 6.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 167 TYR Chi-restraints excluded: chain R residue 240 TYR Chi-restraints excluded: chain R residue 420 PHE Chi-restraints excluded: chain S residue 52 VAL Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 101 ASN Chi-restraints excluded: chain L residue 114 VAL Chi-restraints excluded: chain L residue 177 ASP Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1496 MET Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1677 LEU Chi-restraints excluded: chain A residue 1760 ASN Chi-restraints excluded: chain A residue 1848 VAL Chi-restraints excluded: chain A residue 1865 ASP Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain A residue 1915 LEU Chi-restraints excluded: chain N residue 142 MET Chi-restraints excluded: chain N residue 350 ASP Chi-restraints excluded: chain N residue 687 MET Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 419 ASP Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 749 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 351 ASP Chi-restraints excluded: chain K residue 439 VAL Chi-restraints excluded: chain K residue 442 ASP Chi-restraints excluded: chain K residue 549 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 540 SER Chi-restraints excluded: chain J residue 595 GLN Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 584 ASP Chi-restraints excluded: chain P residue 733 VAL Chi-restraints excluded: chain Q residue 152 SER Chi-restraints excluded: chain Q residue 219 VAL Chi-restraints excluded: chain Q residue 451 LEU Chi-restraints excluded: chain Y residue 272 ASP Chi-restraints excluded: chain V residue 36 LEU Chi-restraints excluded: chain V residue 333 THR Chi-restraints excluded: chain V residue 358 LEU Chi-restraints excluded: chain V residue 450 VAL Chi-restraints excluded: chain V residue 542 THR Chi-restraints excluded: chain Z residue 371 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 847 random chunks: chunk 761 optimal weight: 4.9990 chunk 579 optimal weight: 0.6980 chunk 399 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 367 optimal weight: 7.9990 chunk 517 optimal weight: 2.9990 chunk 773 optimal weight: 0.8980 chunk 818 optimal weight: 3.9990 chunk 404 optimal weight: 2.9990 chunk 732 optimal weight: 6.9990 chunk 220 optimal weight: 0.0170 overall best weight: 1.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 99 ASN ** R 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 418 HIS ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1558 HIS ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 114 HIS ** I 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 595 GLN P 716 ASN ** Q 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 268 GLN ** Z 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 395 HIS ** Z 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 69609 Z= 0.156 Angle : 0.506 10.237 94280 Z= 0.257 Chirality : 0.038 0.252 10552 Planarity : 0.003 0.068 11989 Dihedral : 4.398 36.190 9320 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.60 % Allowed : 13.71 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.31 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.09), residues: 8451 helix: 1.05 (0.07), residues: 5384 sheet: -0.36 (0.21), residues: 579 loop : -1.64 (0.12), residues: 2488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A1386 HIS 0.007 0.001 HIS U 321 PHE 0.016 0.001 PHE A 444 TYR 0.015 0.001 TYR Y 140 ARG 0.005 0.000 ARG R 262 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16902 Ramachandran restraints generated. 8451 Oldfield, 0 Emsley, 8451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16902 Ramachandran restraints generated. 8451 Oldfield, 0 Emsley, 8451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 7506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 421 time to evaluate : 6.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 124 ASP cc_start: 0.8685 (t0) cc_final: 0.8290 (t0) REVERT: R 198 LEU cc_start: 0.9664 (tt) cc_final: 0.9458 (pp) REVERT: R 420 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7794 (m-10) REVERT: L 12 ASP cc_start: 0.9045 (t70) cc_final: 0.8504 (t0) REVERT: L 14 LYS cc_start: 0.9659 (mptt) cc_final: 0.9415 (mmtm) REVERT: L 84 LYS cc_start: 0.9440 (tmtt) cc_final: 0.9150 (tmtt) REVERT: L 136 MET cc_start: 0.9253 (ttt) cc_final: 0.8775 (ptm) REVERT: D 26 GLU cc_start: 0.8535 (mp0) cc_final: 0.8202 (mp0) REVERT: D 29 GLU cc_start: 0.8769 (pt0) cc_final: 0.8430 (tm-30) REVERT: D 31 GLN cc_start: 0.9209 (tm-30) cc_final: 0.8545 (tm-30) REVERT: D 33 GLN cc_start: 0.9124 (mt0) cc_final: 0.7613 (mt0) REVERT: D 34 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8737 (pp20) REVERT: D 36 GLN cc_start: 0.9272 (tm-30) cc_final: 0.8990 (tm-30) REVERT: A 11 MET cc_start: 0.8421 (mmm) cc_final: 0.7104 (mmm) REVERT: A 604 MET cc_start: 0.8812 (mtp) cc_final: 0.8574 (mtp) REVERT: A 1316 MET cc_start: 0.8863 (mtm) cc_final: 0.8289 (mpp) REVERT: A 1550 MET cc_start: 0.8179 (tpp) cc_final: 0.7792 (tpp) REVERT: A 1915 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9191 (mt) REVERT: N 156 MET cc_start: 0.9430 (tmm) cc_final: 0.8981 (tmm) REVERT: N 350 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7420 (p0) REVERT: N 414 MET cc_start: 0.8686 (mtt) cc_final: 0.8384 (ttp) REVERT: N 445 ASP cc_start: 0.7969 (m-30) cc_final: 0.7455 (p0) REVERT: N 554 MET cc_start: 0.1150 (tpt) cc_final: 0.0830 (tpt) REVERT: N 560 MET cc_start: 0.0538 (mtt) cc_final: 0.0146 (mtt) REVERT: I 116 MET cc_start: 0.8693 (ppp) cc_final: 0.8382 (ppp) REVERT: I 305 MET cc_start: 0.9048 (mtp) cc_final: 0.8420 (ptm) REVERT: I 322 MET cc_start: 0.8889 (mmm) cc_final: 0.8635 (mmm) REVERT: I 411 MET cc_start: 0.8755 (tmm) cc_final: 0.8420 (tmm) REVERT: K 88 GLN cc_start: 0.9156 (mt0) cc_final: 0.8929 (mt0) REVERT: K 249 MET cc_start: 0.8774 (tpp) cc_final: 0.8567 (tpp) REVERT: G 14 ASP cc_start: 0.8672 (p0) cc_final: 0.8090 (p0) REVERT: M 53 GLN cc_start: 0.8960 (pt0) cc_final: 0.8392 (pt0) REVERT: H 69 GLN cc_start: 0.8905 (tp-100) cc_final: 0.8599 (tp40) REVERT: H 90 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8113 (mt-10) REVERT: H 97 LYS cc_start: 0.8877 (ttmt) cc_final: 0.8648 (mtpp) REVERT: J 463 MET cc_start: 0.8944 (tpp) cc_final: 0.8569 (tpp) REVERT: P 463 MET cc_start: 0.9418 (tpp) cc_final: 0.8912 (tpp) REVERT: P 616 GLU cc_start: 0.8387 (mp0) cc_final: 0.8108 (mp0) REVERT: P 643 MET cc_start: 0.8770 (tpt) cc_final: 0.8495 (tpp) REVERT: P 656 MET cc_start: 0.9122 (tmm) cc_final: 0.8304 (tmm) REVERT: Y 63 MET cc_start: 0.8774 (mmm) cc_final: 0.8444 (mmm) REVERT: Y 91 LYS cc_start: 0.9694 (mttt) cc_final: 0.9012 (ptmm) REVERT: Y 142 MET cc_start: 0.9403 (mmm) cc_final: 0.8804 (mmm) REVERT: Y 386 MET cc_start: 0.8324 (mtm) cc_final: 0.7947 (ptp) REVERT: Y 427 MET cc_start: 0.9155 (tpt) cc_final: 0.8911 (tpp) REVERT: Y 429 MET cc_start: 0.9470 (mmt) cc_final: 0.9225 (mmm) REVERT: V 444 GLU cc_start: 0.9142 (tt0) cc_final: 0.8693 (tm-30) REVERT: Z 239 TRP cc_start: 0.9315 (t60) cc_final: 0.9003 (t60) outliers start: 115 outliers final: 70 residues processed: 514 average time/residue: 0.6176 time to fit residues: 558.7445 Evaluate side-chains 474 residues out of total 7506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 401 time to evaluate : 6.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 167 TYR Chi-restraints excluded: chain R residue 240 TYR Chi-restraints excluded: chain R residue 264 MET Chi-restraints excluded: chain R residue 358 VAL Chi-restraints excluded: chain R residue 420 PHE Chi-restraints excluded: chain S residue 52 VAL Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 101 ASN Chi-restraints excluded: chain L residue 114 VAL Chi-restraints excluded: chain L residue 177 ASP Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1496 MET Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1677 LEU Chi-restraints excluded: chain A residue 1760 ASN Chi-restraints excluded: chain A residue 1865 ASP Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain A residue 1915 LEU Chi-restraints excluded: chain N residue 142 MET Chi-restraints excluded: chain N residue 265 LEU Chi-restraints excluded: chain N residue 350 ASP Chi-restraints excluded: chain N residue 687 MET Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 674 VAL Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain O residue 256 LEU Chi-restraints excluded: chain O residue 284 THR Chi-restraints excluded: chain O residue 436 THR Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 749 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 351 ASP Chi-restraints excluded: chain K residue 363 LEU Chi-restraints excluded: chain K residue 549 VAL Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 540 SER Chi-restraints excluded: chain J residue 595 GLN Chi-restraints excluded: chain J residue 739 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 584 ASP Chi-restraints excluded: chain P residue 739 VAL Chi-restraints excluded: chain Q residue 152 SER Chi-restraints excluded: chain Q residue 219 VAL Chi-restraints excluded: chain Y residue 272 ASP Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain V residue 36 LEU Chi-restraints excluded: chain V residue 333 THR Chi-restraints excluded: chain V residue 450 VAL Chi-restraints excluded: chain V residue 542 THR Chi-restraints excluded: chain Z residue 371 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 847 random chunks: chunk 681 optimal weight: 0.8980 chunk 464 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 609 optimal weight: 0.7980 chunk 337 optimal weight: 8.9990 chunk 698 optimal weight: 4.9990 chunk 565 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 418 optimal weight: 9.9990 chunk 734 optimal weight: 0.0570 chunk 206 optimal weight: 0.9990 overall best weight: 0.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 67 GLN ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 174 HIS J 595 GLN ** Q 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 69609 Z= 0.132 Angle : 0.502 12.428 94280 Z= 0.252 Chirality : 0.038 0.190 10552 Planarity : 0.003 0.064 11989 Dihedral : 4.256 35.546 9320 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.46 % Allowed : 14.64 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.09), residues: 8451 helix: 1.28 (0.07), residues: 5385 sheet: -0.25 (0.21), residues: 586 loop : -1.52 (0.12), residues: 2480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1386 HIS 0.007 0.000 HIS U 321 PHE 0.010 0.001 PHE P 577 TYR 0.013 0.001 TYR Y 140 ARG 0.007 0.000 ARG G 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16902 Ramachandran restraints generated. 8451 Oldfield, 0 Emsley, 8451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16902 Ramachandran restraints generated. 8451 Oldfield, 0 Emsley, 8451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 7506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 427 time to evaluate : 6.227 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: R 124 ASP cc_start: 0.8657 (t0) cc_final: 0.8260 (t0) REVERT: R 198 LEU cc_start: 0.9652 (tt) cc_final: 0.9406 (pp) REVERT: R 420 PHE cc_start: 0.7983 (OUTLIER) cc_final: 0.7742 (m-10) REVERT: L 12 ASP cc_start: 0.8999 (t70) cc_final: 0.8417 (t0) REVERT: L 14 LYS cc_start: 0.9671 (mptt) cc_final: 0.9423 (mmtm) REVERT: L 84 LYS cc_start: 0.9425 (tmtt) cc_final: 0.9144 (tmtt) REVERT: L 112 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7808 (tm-30) REVERT: L 114 VAL cc_start: 0.9480 (OUTLIER) cc_final: 0.9257 (m) REVERT: L 136 MET cc_start: 0.9224 (ttt) cc_final: 0.8792 (ptm) REVERT: D 26 GLU cc_start: 0.8525 (mp0) cc_final: 0.8176 (mp0) REVERT: D 29 GLU cc_start: 0.8818 (pt0) cc_final: 0.8443 (tm-30) REVERT: D 31 GLN cc_start: 0.9192 (tm-30) cc_final: 0.8525 (tm-30) REVERT: D 33 GLN cc_start: 0.9184 (mt0) cc_final: 0.7677 (mt0) REVERT: D 34 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8736 (pp20) REVERT: D 36 GLN cc_start: 0.9289 (tm-30) cc_final: 0.8963 (tm-30) REVERT: A 11 MET cc_start: 0.8478 (mmm) cc_final: 0.7265 (mmm) REVERT: A 161 MET cc_start: 0.8480 (mpp) cc_final: 0.8264 (mpp) REVERT: A 604 MET cc_start: 0.8811 (mtp) cc_final: 0.8575 (mtp) REVERT: A 668 MET cc_start: 0.9259 (mtp) cc_final: 0.8986 (mtm) REVERT: A 970 TRP cc_start: 0.5881 (OUTLIER) cc_final: 0.4882 (p90) REVERT: A 1316 MET cc_start: 0.8842 (mtm) cc_final: 0.8268 (mpp) REVERT: A 1550 MET cc_start: 0.8193 (tpp) cc_final: 0.7850 (tpp) REVERT: N 156 MET cc_start: 0.9436 (tmm) cc_final: 0.8997 (tmm) REVERT: N 350 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7572 (p0) REVERT: N 414 MET cc_start: 0.8671 (mtt) cc_final: 0.8379 (ttp) REVERT: N 445 ASP cc_start: 0.8028 (m-30) cc_final: 0.7517 (p0) REVERT: N 633 ARG cc_start: 0.2638 (OUTLIER) cc_final: 0.1938 (ttp-170) REVERT: I 116 MET cc_start: 0.8681 (ppp) cc_final: 0.8393 (ppp) REVERT: I 305 MET cc_start: 0.9025 (mtp) cc_final: 0.8407 (ptm) REVERT: I 322 MET cc_start: 0.8926 (mmm) cc_final: 0.8654 (mmm) REVERT: I 411 MET cc_start: 0.8826 (tmm) cc_final: 0.8498 (tmm) REVERT: I 425 MET cc_start: 0.8746 (mtp) cc_final: 0.8499 (mtp) REVERT: K 88 GLN cc_start: 0.9155 (mt0) cc_final: 0.8928 (mt0) REVERT: K 249 MET cc_start: 0.8773 (tpp) cc_final: 0.8489 (tpp) REVERT: K 364 MET cc_start: 0.8708 (mtt) cc_final: 0.8456 (mtp) REVERT: M 53 GLN cc_start: 0.8881 (pt0) cc_final: 0.8370 (pt0) REVERT: H 97 LYS cc_start: 0.8862 (ttmt) cc_final: 0.8636 (mtpp) REVERT: P 463 MET cc_start: 0.9431 (tpp) cc_final: 0.8931 (tpp) REVERT: P 643 MET cc_start: 0.8757 (tpt) cc_final: 0.8490 (tpp) REVERT: P 656 MET cc_start: 0.9122 (tmm) cc_final: 0.8317 (tmm) REVERT: Y 91 LYS cc_start: 0.9702 (mttt) cc_final: 0.9169 (ptmm) REVERT: Y 142 MET cc_start: 0.9400 (mmm) cc_final: 0.9024 (mmt) REVERT: Y 386 MET cc_start: 0.8257 (mtm) cc_final: 0.7949 (ptp) REVERT: Y 427 MET cc_start: 0.9150 (tpt) cc_final: 0.8912 (tpp) REVERT: Y 429 MET cc_start: 0.9480 (mmt) cc_final: 0.9203 (mmm) REVERT: V 444 GLU cc_start: 0.9145 (tt0) cc_final: 0.8720 (tm-30) REVERT: Z 239 TRP cc_start: 0.9309 (t60) cc_final: 0.9005 (t60) outliers start: 105 outliers final: 70 residues processed: 510 average time/residue: 0.6621 time to fit residues: 591.3771 Evaluate side-chains 474 residues out of total 7506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 399 time to evaluate : 6.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 167 TYR Chi-restraints excluded: chain R residue 264 MET Chi-restraints excluded: chain R residue 296 ARG Chi-restraints excluded: chain R residue 358 VAL Chi-restraints excluded: chain R residue 420 PHE Chi-restraints excluded: chain S residue 52 VAL Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 101 ASN Chi-restraints excluded: chain L residue 114 VAL Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain D residue 21 ASP Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 970 TRP Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1496 MET Chi-restraints excluded: chain A residue 1556 LEU Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 1652 MET Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1677 LEU Chi-restraints excluded: chain A residue 1760 ASN Chi-restraints excluded: chain A residue 1865 ASP Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain N residue 142 MET Chi-restraints excluded: chain N residue 265 LEU Chi-restraints excluded: chain N residue 350 ASP Chi-restraints excluded: chain N residue 545 LEU Chi-restraints excluded: chain N residue 633 ARG Chi-restraints excluded: chain N residue 687 MET Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 548 MET Chi-restraints excluded: chain I residue 651 VAL Chi-restraints excluded: chain I residue 674 VAL Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain O residue 256 LEU Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain O residue 749 VAL Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 549 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 540 SER Chi-restraints excluded: chain J residue 739 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 584 ASP Chi-restraints excluded: chain Q residue 152 SER Chi-restraints excluded: chain Q residue 219 VAL Chi-restraints excluded: chain Y residue 272 ASP Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain V residue 36 LEU Chi-restraints excluded: chain V residue 333 THR Chi-restraints excluded: chain V residue 450 VAL Chi-restraints excluded: chain V residue 542 THR Chi-restraints excluded: chain Z residue 371 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 847 random chunks: chunk 275 optimal weight: 30.0000 chunk 737 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 480 optimal weight: 0.4980 chunk 202 optimal weight: 0.8980 chunk 819 optimal weight: 5.9990 chunk 680 optimal weight: 0.8980 chunk 379 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 271 optimal weight: 10.0000 chunk 430 optimal weight: 0.9980 overall best weight: 1.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1813 GLN ** I 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 595 GLN P 754 HIS ** Q 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 197 HIS V 252 GLN ** Z 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 69609 Z= 0.190 Angle : 0.522 11.978 94280 Z= 0.262 Chirality : 0.038 0.176 10552 Planarity : 0.003 0.063 11989 Dihedral : 4.188 35.154 9320 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.63 % Allowed : 15.09 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.09), residues: 8451 helix: 1.45 (0.07), residues: 5384 sheet: -0.19 (0.22), residues: 572 loop : -1.45 (0.13), residues: 2495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1386 HIS 0.007 0.001 HIS U 321 PHE 0.015 0.001 PHE K 495 TYR 0.012 0.001 TYR Y 140 ARG 0.007 0.000 ARG P 581 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16902 Ramachandran restraints generated. 8451 Oldfield, 0 Emsley, 8451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16902 Ramachandran restraints generated. 8451 Oldfield, 0 Emsley, 8451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 7506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 414 time to evaluate : 6.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 88 MET cc_start: 0.9082 (tpp) cc_final: 0.8875 (tpp) REVERT: R 124 ASP cc_start: 0.8640 (t0) cc_final: 0.8213 (t0) REVERT: R 198 LEU cc_start: 0.9669 (tt) cc_final: 0.9444 (pp) REVERT: R 420 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7809 (m-10) REVERT: L 12 ASP cc_start: 0.9031 (t70) cc_final: 0.8576 (t0) REVERT: L 14 LYS cc_start: 0.9674 (mptt) cc_final: 0.9417 (mmtm) REVERT: L 84 LYS cc_start: 0.9444 (tmtt) cc_final: 0.9164 (tmtt) REVERT: L 136 MET cc_start: 0.9246 (ttt) cc_final: 0.8830 (ptm) REVERT: L 153 MET cc_start: 0.8889 (tpp) cc_final: 0.8605 (tpt) REVERT: L 178 PHE cc_start: 0.9244 (OUTLIER) cc_final: 0.9040 (m-80) REVERT: D 26 GLU cc_start: 0.8538 (mp0) cc_final: 0.8188 (mp0) REVERT: D 29 GLU cc_start: 0.8805 (pt0) cc_final: 0.8436 (tm-30) REVERT: D 31 GLN cc_start: 0.9204 (tm-30) cc_final: 0.8534 (tm-30) REVERT: D 33 GLN cc_start: 0.9158 (mt0) cc_final: 0.7627 (mt0) REVERT: D 34 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8776 (pp20) REVERT: D 36 GLN cc_start: 0.9273 (tm-30) cc_final: 0.8776 (tm-30) REVERT: D 42 GLN cc_start: 0.8181 (pp30) cc_final: 0.7884 (tm-30) REVERT: D 46 GLU cc_start: 0.8511 (pm20) cc_final: 0.8020 (pm20) REVERT: A 11 MET cc_start: 0.8471 (mmm) cc_final: 0.7150 (mmm) REVERT: A 668 MET cc_start: 0.9230 (mtp) cc_final: 0.8981 (mtm) REVERT: A 970 TRP cc_start: 0.5956 (OUTLIER) cc_final: 0.4948 (p90) REVERT: A 1316 MET cc_start: 0.8881 (mtm) cc_final: 0.8275 (mpp) REVERT: A 1550 MET cc_start: 0.8137 (tpp) cc_final: 0.7732 (tpp) REVERT: A 1731 ARG cc_start: 0.8577 (tpp-160) cc_final: 0.7919 (ttp80) REVERT: N 156 MET cc_start: 0.9435 (tmm) cc_final: 0.8996 (tmm) REVERT: N 350 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7557 (p0) REVERT: N 414 MET cc_start: 0.8700 (mtt) cc_final: 0.8459 (ttp) REVERT: N 445 ASP cc_start: 0.8050 (m-30) cc_final: 0.7566 (p0) REVERT: N 554 MET cc_start: 0.1027 (tpt) cc_final: 0.0623 (tpt) REVERT: I 116 MET cc_start: 0.8688 (ppp) cc_final: 0.8390 (ppp) REVERT: I 305 MET cc_start: 0.9021 (mtp) cc_final: 0.8392 (ptm) REVERT: I 322 MET cc_start: 0.8926 (mmm) cc_final: 0.8702 (mmm) REVERT: I 411 MET cc_start: 0.8931 (tmm) cc_final: 0.8542 (tmm) REVERT: I 425 MET cc_start: 0.8758 (mtp) cc_final: 0.8478 (mtp) REVERT: I 598 MET cc_start: 0.7477 (tpp) cc_final: 0.7239 (tpt) REVERT: O 114 ASP cc_start: 0.9307 (OUTLIER) cc_final: 0.8822 (p0) REVERT: O 414 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8352 (pp) REVERT: K 88 GLN cc_start: 0.9167 (mt0) cc_final: 0.8943 (mt0) REVERT: K 249 MET cc_start: 0.8814 (tpp) cc_final: 0.8500 (tpp) REVERT: K 364 MET cc_start: 0.8715 (mtt) cc_final: 0.8512 (mtp) REVERT: M 53 GLN cc_start: 0.8891 (pt0) cc_final: 0.8654 (pp30) REVERT: H 97 LYS cc_start: 0.8878 (ttmt) cc_final: 0.8644 (mtpp) REVERT: J 463 MET cc_start: 0.8906 (tpp) cc_final: 0.8500 (tpp) REVERT: P 463 MET cc_start: 0.9442 (tpp) cc_final: 0.8938 (tpp) REVERT: P 643 MET cc_start: 0.8787 (tpt) cc_final: 0.8514 (tpp) REVERT: P 656 MET cc_start: 0.9147 (tmm) cc_final: 0.8314 (tmm) REVERT: Y 63 MET cc_start: 0.9263 (mmm) cc_final: 0.8777 (mmm) REVERT: Y 91 LYS cc_start: 0.9708 (mttt) cc_final: 0.9029 (ptmm) REVERT: Y 142 MET cc_start: 0.9411 (mmm) cc_final: 0.9117 (mmt) REVERT: Y 386 MET cc_start: 0.8336 (mtm) cc_final: 0.7958 (ptp) REVERT: Y 427 MET cc_start: 0.9157 (tpt) cc_final: 0.8917 (tpp) REVERT: Y 429 MET cc_start: 0.9470 (mmt) cc_final: 0.9196 (mmm) REVERT: V 444 GLU cc_start: 0.9152 (tt0) cc_final: 0.8729 (tm-30) REVERT: Z 239 TRP cc_start: 0.9333 (t60) cc_final: 0.9053 (t60) REVERT: Z 390 GLN cc_start: 0.8840 (tp40) cc_final: 0.8495 (tp40) outliers start: 117 outliers final: 76 residues processed: 508 average time/residue: 0.6249 time to fit residues: 555.8381 Evaluate side-chains 478 residues out of total 7506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 396 time to evaluate : 6.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 167 TYR Chi-restraints excluded: chain R residue 264 MET Chi-restraints excluded: chain R residue 296 ARG Chi-restraints excluded: chain R residue 358 VAL Chi-restraints excluded: chain R residue 420 PHE Chi-restraints excluded: chain S residue 52 VAL Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 94 ILE Chi-restraints excluded: chain L residue 101 ASN Chi-restraints excluded: chain L residue 114 VAL Chi-restraints excluded: chain L residue 177 ASP Chi-restraints excluded: chain L residue 178 PHE Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 970 TRP Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1556 LEU Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1677 LEU Chi-restraints excluded: chain A residue 1760 ASN Chi-restraints excluded: chain A residue 1865 ASP Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain N residue 265 LEU Chi-restraints excluded: chain N residue 326 CYS Chi-restraints excluded: chain N residue 350 ASP Chi-restraints excluded: chain N residue 545 LEU Chi-restraints excluded: chain N residue 687 MET Chi-restraints excluded: chain N residue 692 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 548 MET Chi-restraints excluded: chain I residue 651 VAL Chi-restraints excluded: chain I residue 674 VAL Chi-restraints excluded: chain O residue 64 LEU Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 114 ASP Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain O residue 284 THR Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 436 THR Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 442 ASP Chi-restraints excluded: chain K residue 549 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 540 SER Chi-restraints excluded: chain J residue 739 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 584 ASP Chi-restraints excluded: chain Q residue 152 SER Chi-restraints excluded: chain Q residue 219 VAL Chi-restraints excluded: chain Y residue 168 THR Chi-restraints excluded: chain Y residue 272 ASP Chi-restraints excluded: chain U residue 190 ASP Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain V residue 36 LEU Chi-restraints excluded: chain V residue 333 THR Chi-restraints excluded: chain V residue 450 VAL Chi-restraints excluded: chain V residue 542 THR Chi-restraints excluded: chain Z residue 371 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 847 random chunks: chunk 790 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 466 optimal weight: 4.9990 chunk 598 optimal weight: 0.8980 chunk 463 optimal weight: 5.9990 chunk 689 optimal weight: 4.9990 chunk 457 optimal weight: 7.9990 chunk 816 optimal weight: 2.9990 chunk 510 optimal weight: 5.9990 chunk 497 optimal weight: 0.9980 chunk 376 optimal weight: 2.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1250 GLN A1432 GLN ** A1559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 34 ASN J 595 GLN P 659 GLN ** Q 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 151 GLN ** Z 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 69609 Z= 0.239 Angle : 0.550 11.542 94280 Z= 0.276 Chirality : 0.039 0.181 10552 Planarity : 0.003 0.063 11989 Dihedral : 4.207 36.745 9320 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.66 % Allowed : 15.47 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.10), residues: 8451 helix: 1.57 (0.07), residues: 5386 sheet: -0.15 (0.22), residues: 572 loop : -1.40 (0.13), residues: 2493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A1386 HIS 0.007 0.001 HIS U 321 PHE 0.016 0.001 PHE U 116 TYR 0.012 0.001 TYR K 322 ARG 0.011 0.000 ARG R 296 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16902 Ramachandran restraints generated. 8451 Oldfield, 0 Emsley, 8451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16902 Ramachandran restraints generated. 8451 Oldfield, 0 Emsley, 8451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 7506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 404 time to evaluate : 6.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 88 MET cc_start: 0.9092 (tpp) cc_final: 0.8881 (tpp) REVERT: R 198 LEU cc_start: 0.9658 (tt) cc_final: 0.9450 (pp) REVERT: R 420 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7839 (m-10) REVERT: L 12 ASP cc_start: 0.9039 (t70) cc_final: 0.8615 (t0) REVERT: L 14 LYS cc_start: 0.9679 (mptt) cc_final: 0.9414 (mmtm) REVERT: L 84 LYS cc_start: 0.9458 (tmtt) cc_final: 0.9216 (tmtt) REVERT: L 112 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8043 (tm-30) REVERT: L 136 MET cc_start: 0.9257 (ttt) cc_final: 0.8790 (ptm) REVERT: L 153 MET cc_start: 0.8912 (tpp) cc_final: 0.8679 (tpt) REVERT: D 26 GLU cc_start: 0.8501 (mp0) cc_final: 0.8126 (mp0) REVERT: D 29 GLU cc_start: 0.8801 (pt0) cc_final: 0.8430 (tm-30) REVERT: D 31 GLN cc_start: 0.9222 (tm-30) cc_final: 0.8562 (tm-30) REVERT: D 33 GLN cc_start: 0.9158 (mt0) cc_final: 0.7567 (mt0) REVERT: D 34 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8815 (pp20) REVERT: D 36 GLN cc_start: 0.9282 (tm-30) cc_final: 0.8787 (tm-30) REVERT: D 42 GLN cc_start: 0.8190 (pp30) cc_final: 0.7824 (tm-30) REVERT: D 46 GLU cc_start: 0.8498 (pm20) cc_final: 0.8064 (pm20) REVERT: A 11 MET cc_start: 0.8444 (mmm) cc_final: 0.7114 (mmm) REVERT: A 161 MET cc_start: 0.8436 (mpp) cc_final: 0.8207 (mpp) REVERT: A 970 TRP cc_start: 0.6076 (OUTLIER) cc_final: 0.5046 (p90) REVERT: A 1316 MET cc_start: 0.8853 (mtm) cc_final: 0.8247 (mpp) REVERT: A 1550 MET cc_start: 0.8156 (tpp) cc_final: 0.7726 (tpp) REVERT: N 156 MET cc_start: 0.9426 (tmm) cc_final: 0.8979 (tmm) REVERT: N 350 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.7623 (p0) REVERT: N 414 MET cc_start: 0.8760 (mtt) cc_final: 0.8534 (ttp) REVERT: N 445 ASP cc_start: 0.8027 (m-30) cc_final: 0.7540 (p0) REVERT: N 554 MET cc_start: 0.0946 (tpt) cc_final: 0.0680 (tpt) REVERT: N 560 MET cc_start: 0.1210 (mtt) cc_final: 0.0875 (tpp) REVERT: N 633 ARG cc_start: 0.2483 (OUTLIER) cc_final: 0.1834 (ttp-170) REVERT: I 116 MET cc_start: 0.8705 (ppp) cc_final: 0.8390 (ppp) REVERT: I 305 MET cc_start: 0.9028 (mtp) cc_final: 0.8389 (ptm) REVERT: I 322 MET cc_start: 0.8932 (mmm) cc_final: 0.8721 (mmm) REVERT: I 347 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.8980 (tp) REVERT: I 411 MET cc_start: 0.9024 (tmm) cc_final: 0.8576 (tmm) REVERT: I 425 MET cc_start: 0.8757 (mtp) cc_final: 0.8488 (mtp) REVERT: I 598 MET cc_start: 0.7334 (tpp) cc_final: 0.7109 (tpt) REVERT: I 645 ASP cc_start: 0.9287 (OUTLIER) cc_final: 0.9068 (m-30) REVERT: O 114 ASP cc_start: 0.9335 (OUTLIER) cc_final: 0.8900 (p0) REVERT: O 414 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8436 (pp) REVERT: K 88 GLN cc_start: 0.9155 (mt0) cc_final: 0.8950 (mt0) REVERT: K 249 MET cc_start: 0.8850 (tpp) cc_final: 0.8607 (tpp) REVERT: M 23 LYS cc_start: 0.9296 (mmmm) cc_final: 0.9086 (mmtm) REVERT: M 53 GLN cc_start: 0.8914 (pt0) cc_final: 0.8675 (pp30) REVERT: H 97 LYS cc_start: 0.8904 (ttmt) cc_final: 0.8679 (mtpp) REVERT: P 463 MET cc_start: 0.9438 (tpp) cc_final: 0.8944 (tpp) REVERT: P 643 MET cc_start: 0.8803 (tpt) cc_final: 0.8526 (tpp) REVERT: P 656 MET cc_start: 0.9164 (tmm) cc_final: 0.8312 (tmm) REVERT: Y 63 MET cc_start: 0.9203 (mmm) cc_final: 0.8686 (mmm) REVERT: Y 91 LYS cc_start: 0.9714 (mttt) cc_final: 0.9041 (ptmm) REVERT: Y 142 MET cc_start: 0.9426 (mmm) cc_final: 0.9051 (mmt) REVERT: Y 386 MET cc_start: 0.8379 (mtm) cc_final: 0.7977 (ptp) REVERT: Y 427 MET cc_start: 0.9162 (tpt) cc_final: 0.8922 (tpp) REVERT: Y 429 MET cc_start: 0.9473 (mmt) cc_final: 0.9200 (mmm) REVERT: V 444 GLU cc_start: 0.9144 (tt0) cc_final: 0.8732 (tm-30) REVERT: Z 239 TRP cc_start: 0.9341 (t60) cc_final: 0.9073 (t60) REVERT: Z 390 GLN cc_start: 0.8830 (tp40) cc_final: 0.8467 (tp40) outliers start: 119 outliers final: 90 residues processed: 497 average time/residue: 0.6173 time to fit residues: 544.1079 Evaluate side-chains 491 residues out of total 7506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 393 time to evaluate : 6.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 123 PHE Chi-restraints excluded: chain R residue 167 TYR Chi-restraints excluded: chain R residue 264 MET Chi-restraints excluded: chain R residue 358 VAL Chi-restraints excluded: chain R residue 420 PHE Chi-restraints excluded: chain S residue 52 VAL Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 101 ASN Chi-restraints excluded: chain L residue 177 ASP Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 970 TRP Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1230 ILE Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1358 ILE Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1556 LEU Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 1652 MET Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1677 LEU Chi-restraints excluded: chain A residue 1760 ASN Chi-restraints excluded: chain A residue 1865 ASP Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain N residue 265 LEU Chi-restraints excluded: chain N residue 326 CYS Chi-restraints excluded: chain N residue 350 ASP Chi-restraints excluded: chain N residue 424 ILE Chi-restraints excluded: chain N residue 545 LEU Chi-restraints excluded: chain N residue 633 ARG Chi-restraints excluded: chain N residue 687 MET Chi-restraints excluded: chain N residue 692 LEU Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 347 LEU Chi-restraints excluded: chain I residue 423 VAL Chi-restraints excluded: chain I residue 548 MET Chi-restraints excluded: chain I residue 645 ASP Chi-restraints excluded: chain I residue 651 VAL Chi-restraints excluded: chain I residue 674 VAL Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 114 ASP Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain O residue 284 THR Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 603 MET Chi-restraints excluded: chain O residue 608 LEU Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 439 VAL Chi-restraints excluded: chain K residue 442 ASP Chi-restraints excluded: chain K residue 549 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 540 SER Chi-restraints excluded: chain J residue 595 GLN Chi-restraints excluded: chain J residue 739 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 584 ASP Chi-restraints excluded: chain Q residue 152 SER Chi-restraints excluded: chain Q residue 219 VAL Chi-restraints excluded: chain Y residue 168 THR Chi-restraints excluded: chain Y residue 272 ASP Chi-restraints excluded: chain U residue 190 ASP Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain V residue 36 LEU Chi-restraints excluded: chain V residue 333 THR Chi-restraints excluded: chain V residue 450 VAL Chi-restraints excluded: chain V residue 542 THR Chi-restraints excluded: chain Z residue 234 ASP Chi-restraints excluded: chain Z residue 371 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 847 random chunks: chunk 505 optimal weight: 0.9990 chunk 326 optimal weight: 7.9990 chunk 487 optimal weight: 0.9980 chunk 245 optimal weight: 0.9990 chunk 160 optimal weight: 7.9990 chunk 158 optimal weight: 0.5980 chunk 519 optimal weight: 6.9990 chunk 556 optimal weight: 2.9990 chunk 403 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 641 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1841 ASN N 147 GLN ** I 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 731 ASN ** K 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 69609 Z= 0.141 Angle : 0.514 12.838 94280 Z= 0.256 Chirality : 0.038 0.171 10552 Planarity : 0.003 0.058 11989 Dihedral : 4.140 35.016 9320 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.45 % Allowed : 15.76 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.10), residues: 8451 helix: 1.62 (0.07), residues: 5384 sheet: -0.10 (0.22), residues: 580 loop : -1.31 (0.13), residues: 2487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1386 HIS 0.007 0.000 HIS O 645 PHE 0.018 0.001 PHE U 221 TYR 0.012 0.001 TYR Y 140 ARG 0.007 0.000 ARG R 296 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16902 Ramachandran restraints generated. 8451 Oldfield, 0 Emsley, 8451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16902 Ramachandran restraints generated. 8451 Oldfield, 0 Emsley, 8451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 7506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 416 time to evaluate : 6.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 124 ASP cc_start: 0.8055 (t0) cc_final: 0.7563 (t0) REVERT: R 198 LEU cc_start: 0.9655 (tt) cc_final: 0.9440 (pp) REVERT: R 264 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8350 (mmp) REVERT: R 420 PHE cc_start: 0.8062 (t80) cc_final: 0.7826 (m-10) REVERT: L 12 ASP cc_start: 0.8985 (t70) cc_final: 0.8614 (t0) REVERT: L 14 LYS cc_start: 0.9652 (mptt) cc_final: 0.9449 (mmtm) REVERT: L 75 LYS cc_start: 0.9390 (ttmm) cc_final: 0.9186 (ptmm) REVERT: L 84 LYS cc_start: 0.9435 (tmtt) cc_final: 0.9207 (tmtt) REVERT: L 136 MET cc_start: 0.9236 (ttt) cc_final: 0.8825 (ptm) REVERT: D 26 GLU cc_start: 0.8501 (mp0) cc_final: 0.8146 (mp0) REVERT: D 29 GLU cc_start: 0.8797 (pt0) cc_final: 0.8440 (tm-30) REVERT: D 31 GLN cc_start: 0.9204 (tm-30) cc_final: 0.8530 (tm-30) REVERT: D 33 GLN cc_start: 0.9154 (mt0) cc_final: 0.7631 (mt0) REVERT: D 34 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8811 (pp20) REVERT: D 36 GLN cc_start: 0.9264 (tm-30) cc_final: 0.8936 (tm-30) REVERT: D 42 GLN cc_start: 0.8259 (pp30) cc_final: 0.7892 (tm-30) REVERT: D 46 GLU cc_start: 0.8455 (pm20) cc_final: 0.8091 (pm20) REVERT: A 11 MET cc_start: 0.8440 (mmm) cc_final: 0.7166 (mmm) REVERT: A 48 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8547 (mm) REVERT: A 161 MET cc_start: 0.8357 (mpp) cc_final: 0.8132 (mpp) REVERT: A 604 MET cc_start: 0.8788 (mtp) cc_final: 0.8466 (mtp) REVERT: A 665 MET cc_start: 0.9218 (mmm) cc_final: 0.8674 (mmm) REVERT: A 668 MET cc_start: 0.9227 (mtp) cc_final: 0.8427 (mtp) REVERT: A 970 TRP cc_start: 0.5945 (OUTLIER) cc_final: 0.5009 (p90) REVERT: A 1316 MET cc_start: 0.8824 (mtm) cc_final: 0.8243 (mpp) REVERT: A 1550 MET cc_start: 0.8101 (tpp) cc_final: 0.7776 (tpp) REVERT: A 1840 MET cc_start: 0.8689 (ttm) cc_final: 0.8481 (ttm) REVERT: N 156 MET cc_start: 0.9417 (tmm) cc_final: 0.8972 (tmm) REVERT: N 350 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7508 (p0) REVERT: N 414 MET cc_start: 0.8768 (mtt) cc_final: 0.8567 (ttp) REVERT: N 445 ASP cc_start: 0.8027 (m-30) cc_final: 0.7534 (p0) REVERT: N 554 MET cc_start: 0.1007 (tpt) cc_final: 0.0749 (tpt) REVERT: N 633 ARG cc_start: 0.2637 (OUTLIER) cc_final: 0.1964 (ttp-170) REVERT: I 116 MET cc_start: 0.8704 (ppp) cc_final: 0.8385 (ppp) REVERT: I 305 MET cc_start: 0.9071 (mtp) cc_final: 0.8420 (ptt) REVERT: I 322 MET cc_start: 0.8925 (mmm) cc_final: 0.8660 (mmm) REVERT: I 347 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9079 (tp) REVERT: I 411 MET cc_start: 0.9070 (tmm) cc_final: 0.8638 (tmm) REVERT: I 425 MET cc_start: 0.8773 (mtp) cc_final: 0.8233 (mtp) REVERT: I 645 ASP cc_start: 0.9315 (OUTLIER) cc_final: 0.9112 (m-30) REVERT: O 114 ASP cc_start: 0.9314 (OUTLIER) cc_final: 0.8815 (p0) REVERT: O 414 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8295 (pp) REVERT: K 88 GLN cc_start: 0.9127 (mt0) cc_final: 0.8913 (mt0) REVERT: K 249 MET cc_start: 0.8816 (tpp) cc_final: 0.8581 (tpp) REVERT: H 97 LYS cc_start: 0.8858 (ttmt) cc_final: 0.8635 (mtpp) REVERT: J 463 MET cc_start: 0.8930 (tpp) cc_final: 0.8522 (tpp) REVERT: P 463 MET cc_start: 0.9428 (tpp) cc_final: 0.8927 (tpp) REVERT: P 643 MET cc_start: 0.8763 (tpt) cc_final: 0.8474 (tpp) REVERT: P 656 MET cc_start: 0.9130 (tmm) cc_final: 0.8356 (tmm) REVERT: Y 63 MET cc_start: 0.9196 (mmm) cc_final: 0.8697 (mmm) REVERT: Y 91 LYS cc_start: 0.9705 (mttt) cc_final: 0.9167 (ptmm) REVERT: Y 142 MET cc_start: 0.9398 (mmm) cc_final: 0.9024 (mmt) REVERT: Y 386 MET cc_start: 0.8287 (mtm) cc_final: 0.7980 (ptp) REVERT: Y 427 MET cc_start: 0.9143 (tpt) cc_final: 0.8909 (tpp) REVERT: Y 429 MET cc_start: 0.9470 (mmt) cc_final: 0.9182 (mmm) REVERT: V 444 GLU cc_start: 0.9149 (tt0) cc_final: 0.8728 (tm-30) REVERT: Z 239 TRP cc_start: 0.9319 (t60) cc_final: 0.9051 (t60) REVERT: Z 390 GLN cc_start: 0.8822 (tp40) cc_final: 0.8568 (tp40) outliers start: 104 outliers final: 79 residues processed: 500 average time/residue: 0.6444 time to fit residues: 569.9804 Evaluate side-chains 490 residues out of total 7506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 402 time to evaluate : 6.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 123 PHE Chi-restraints excluded: chain R residue 167 TYR Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 264 MET Chi-restraints excluded: chain R residue 358 VAL Chi-restraints excluded: chain S residue 52 VAL Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 101 ASN Chi-restraints excluded: chain L residue 177 ASP Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 970 TRP Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1556 LEU Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1677 LEU Chi-restraints excluded: chain A residue 1760 ASN Chi-restraints excluded: chain A residue 1865 ASP Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain N residue 147 GLN Chi-restraints excluded: chain N residue 265 LEU Chi-restraints excluded: chain N residue 326 CYS Chi-restraints excluded: chain N residue 350 ASP Chi-restraints excluded: chain N residue 424 ILE Chi-restraints excluded: chain N residue 545 LEU Chi-restraints excluded: chain N residue 633 ARG Chi-restraints excluded: chain N residue 687 MET Chi-restraints excluded: chain N residue 692 LEU Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 347 LEU Chi-restraints excluded: chain I residue 423 VAL Chi-restraints excluded: chain I residue 486 LEU Chi-restraints excluded: chain I residue 548 MET Chi-restraints excluded: chain I residue 645 ASP Chi-restraints excluded: chain I residue 651 VAL Chi-restraints excluded: chain I residue 674 VAL Chi-restraints excluded: chain O residue 64 LEU Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 114 ASP Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain O residue 284 THR Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 351 ASP Chi-restraints excluded: chain K residue 549 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 540 SER Chi-restraints excluded: chain J residue 739 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain Q residue 152 SER Chi-restraints excluded: chain Q residue 219 VAL Chi-restraints excluded: chain Y residue 168 THR Chi-restraints excluded: chain Y residue 272 ASP Chi-restraints excluded: chain U residue 190 ASP Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain V residue 36 LEU Chi-restraints excluded: chain V residue 333 THR Chi-restraints excluded: chain V residue 450 VAL Chi-restraints excluded: chain V residue 542 THR Chi-restraints excluded: chain Z residue 371 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 847 random chunks: chunk 742 optimal weight: 5.9990 chunk 782 optimal weight: 5.9990 chunk 713 optimal weight: 4.9990 chunk 760 optimal weight: 0.0570 chunk 781 optimal weight: 2.9990 chunk 457 optimal weight: 7.9990 chunk 331 optimal weight: 4.9990 chunk 597 optimal weight: 0.8980 chunk 233 optimal weight: 5.9990 chunk 687 optimal weight: 1.9990 chunk 719 optimal weight: 0.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 323 HIS R 369 ASN ** R 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1841 ASN N 586 GLN ** I 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 595 GLN ** Q 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 52 ASN ** Z 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 69609 Z= 0.168 Angle : 0.530 13.439 94280 Z= 0.263 Chirality : 0.038 0.197 10552 Planarity : 0.003 0.056 11989 Dihedral : 4.096 34.988 9320 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.55 % Allowed : 15.99 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.10), residues: 8451 helix: 1.70 (0.07), residues: 5383 sheet: -0.02 (0.22), residues: 565 loop : -1.28 (0.13), residues: 2503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1386 HIS 0.007 0.001 HIS U 321 PHE 0.012 0.001 PHE U 116 TYR 0.014 0.001 TYR A1610 ARG 0.005 0.000 ARG R 296 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16902 Ramachandran restraints generated. 8451 Oldfield, 0 Emsley, 8451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16902 Ramachandran restraints generated. 8451 Oldfield, 0 Emsley, 8451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 7506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 410 time to evaluate : 6.187 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: R 124 ASP cc_start: 0.8093 (t0) cc_final: 0.7584 (t0) REVERT: R 198 LEU cc_start: 0.9641 (tt) cc_final: 0.9436 (pp) REVERT: R 264 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8163 (mmp) REVERT: R 420 PHE cc_start: 0.8074 (t80) cc_final: 0.7836 (m-10) REVERT: L 12 ASP cc_start: 0.8991 (t70) cc_final: 0.8632 (t0) REVERT: L 14 LYS cc_start: 0.9666 (mptt) cc_final: 0.9455 (mmtm) REVERT: L 84 LYS cc_start: 0.9433 (tmtt) cc_final: 0.9205 (tmtt) REVERT: L 136 MET cc_start: 0.9243 (ttt) cc_final: 0.8827 (ptm) REVERT: D 26 GLU cc_start: 0.8508 (mp0) cc_final: 0.8152 (mp0) REVERT: D 29 GLU cc_start: 0.8798 (pt0) cc_final: 0.8491 (tm-30) REVERT: D 31 GLN cc_start: 0.9207 (tm-30) cc_final: 0.8538 (tm-30) REVERT: D 33 GLN cc_start: 0.9154 (mt0) cc_final: 0.7708 (mt0) REVERT: D 34 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8809 (pp20) REVERT: D 36 GLN cc_start: 0.9266 (tm-30) cc_final: 0.8945 (tm-30) REVERT: D 42 GLN cc_start: 0.8282 (pp30) cc_final: 0.7793 (tm-30) REVERT: D 46 GLU cc_start: 0.8526 (pm20) cc_final: 0.8238 (pm20) REVERT: A 11 MET cc_start: 0.8419 (mmm) cc_final: 0.7126 (mmm) REVERT: A 48 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8536 (mm) REVERT: A 161 MET cc_start: 0.8349 (mpp) cc_final: 0.8144 (mpp) REVERT: A 604 MET cc_start: 0.8797 (mtp) cc_final: 0.8461 (mtp) REVERT: A 665 MET cc_start: 0.9218 (mmm) cc_final: 0.8683 (mmm) REVERT: A 668 MET cc_start: 0.9211 (mtp) cc_final: 0.8425 (mtp) REVERT: A 970 TRP cc_start: 0.5980 (OUTLIER) cc_final: 0.5038 (p90) REVERT: A 1316 MET cc_start: 0.8839 (mtm) cc_final: 0.8250 (mpp) REVERT: A 1550 MET cc_start: 0.8108 (tpp) cc_final: 0.7794 (tpp) REVERT: A 1803 ARG cc_start: 0.8913 (tpp80) cc_final: 0.8700 (mmm-85) REVERT: N 156 MET cc_start: 0.9417 (tmm) cc_final: 0.8974 (tmm) REVERT: N 350 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7583 (p0) REVERT: N 414 MET cc_start: 0.8766 (mtt) cc_final: 0.8519 (ttp) REVERT: N 445 ASP cc_start: 0.8021 (m-30) cc_final: 0.7528 (p0) REVERT: I 116 MET cc_start: 0.8699 (ppp) cc_final: 0.8385 (ppp) REVERT: I 305 MET cc_start: 0.9067 (mtp) cc_final: 0.8438 (ptm) REVERT: I 322 MET cc_start: 0.8887 (mmm) cc_final: 0.8644 (mmm) REVERT: I 347 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9071 (tp) REVERT: I 411 MET cc_start: 0.9094 (tmm) cc_final: 0.8626 (tmm) REVERT: I 425 MET cc_start: 0.8752 (mtp) cc_final: 0.8237 (mtp) REVERT: I 645 ASP cc_start: 0.9313 (OUTLIER) cc_final: 0.9112 (m-30) REVERT: O 114 ASP cc_start: 0.9335 (OUTLIER) cc_final: 0.8924 (p0) REVERT: O 414 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8279 (pp) REVERT: K 249 MET cc_start: 0.8835 (tpp) cc_final: 0.8609 (tpp) REVERT: H 97 LYS cc_start: 0.8855 (ttmt) cc_final: 0.8633 (mtpp) REVERT: J 463 MET cc_start: 0.8909 (tpp) cc_final: 0.8481 (tpp) REVERT: P 463 MET cc_start: 0.9423 (tpp) cc_final: 0.8935 (tpp) REVERT: P 643 MET cc_start: 0.8788 (tpt) cc_final: 0.8494 (tpp) REVERT: P 656 MET cc_start: 0.9141 (tmm) cc_final: 0.8372 (tmm) REVERT: Y 63 MET cc_start: 0.9179 (mmm) cc_final: 0.8655 (mmm) REVERT: Y 91 LYS cc_start: 0.9713 (mttt) cc_final: 0.9050 (ptmm) REVERT: Y 142 MET cc_start: 0.9403 (mmm) cc_final: 0.9024 (mmt) REVERT: Y 386 MET cc_start: 0.8262 (mtm) cc_final: 0.7943 (ptp) REVERT: Y 427 MET cc_start: 0.9150 (tpt) cc_final: 0.8912 (tpp) REVERT: Y 429 MET cc_start: 0.9470 (mmt) cc_final: 0.9187 (mmm) REVERT: V 444 GLU cc_start: 0.9157 (tt0) cc_final: 0.8734 (tm-30) REVERT: Z 239 TRP cc_start: 0.9323 (t60) cc_final: 0.9065 (t60) REVERT: Z 390 GLN cc_start: 0.8817 (tp40) cc_final: 0.8562 (tp40) REVERT: Z 427 MET cc_start: 0.8659 (mmm) cc_final: 0.8456 (mmm) outliers start: 111 outliers final: 89 residues processed: 496 average time/residue: 0.6104 time to fit residues: 533.8671 Evaluate side-chains 499 residues out of total 7506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 402 time to evaluate : 6.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 123 PHE Chi-restraints excluded: chain R residue 167 TYR Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 264 MET Chi-restraints excluded: chain R residue 358 VAL Chi-restraints excluded: chain S residue 52 VAL Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 101 ASN Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 970 TRP Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1274 LEU Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1358 ILE Chi-restraints excluded: chain A residue 1392 THR Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1526 VAL Chi-restraints excluded: chain A residue 1556 LEU Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1677 LEU Chi-restraints excluded: chain A residue 1760 ASN Chi-restraints excluded: chain A residue 1865 ASP Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain N residue 265 LEU Chi-restraints excluded: chain N residue 326 CYS Chi-restraints excluded: chain N residue 350 ASP Chi-restraints excluded: chain N residue 424 ILE Chi-restraints excluded: chain N residue 545 LEU Chi-restraints excluded: chain N residue 633 ARG Chi-restraints excluded: chain N residue 687 MET Chi-restraints excluded: chain N residue 692 LEU Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 347 LEU Chi-restraints excluded: chain I residue 423 VAL Chi-restraints excluded: chain I residue 486 LEU Chi-restraints excluded: chain I residue 548 MET Chi-restraints excluded: chain I residue 645 ASP Chi-restraints excluded: chain I residue 651 VAL Chi-restraints excluded: chain I residue 674 VAL Chi-restraints excluded: chain O residue 64 LEU Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 114 ASP Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain O residue 284 THR Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 436 THR Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 351 ASP Chi-restraints excluded: chain K residue 442 ASP Chi-restraints excluded: chain K residue 549 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 540 SER Chi-restraints excluded: chain J residue 739 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain Q residue 152 SER Chi-restraints excluded: chain Q residue 219 VAL Chi-restraints excluded: chain Y residue 168 THR Chi-restraints excluded: chain Y residue 272 ASP Chi-restraints excluded: chain U residue 190 ASP Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain V residue 36 LEU Chi-restraints excluded: chain V residue 333 THR Chi-restraints excluded: chain V residue 450 VAL Chi-restraints excluded: chain V residue 542 THR Chi-restraints excluded: chain Z residue 371 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 847 random chunks: chunk 758 optimal weight: 5.9990 chunk 499 optimal weight: 0.8980 chunk 804 optimal weight: 0.9980 chunk 491 optimal weight: 4.9990 chunk 381 optimal weight: 0.9990 chunk 559 optimal weight: 2.9990 chunk 843 optimal weight: 8.9990 chunk 776 optimal weight: 0.0870 chunk 671 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 519 optimal weight: 0.0870 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 323 HIS ** R 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 725 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1559 HIS ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 276 HIS ** K 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 69609 Z= 0.133 Angle : 0.524 14.148 94280 Z= 0.259 Chirality : 0.038 0.176 10552 Planarity : 0.003 0.055 11989 Dihedral : 4.043 34.178 9320 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.35 % Allowed : 16.27 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.10), residues: 8451 helix: 1.73 (0.07), residues: 5370 sheet: -0.01 (0.22), residues: 580 loop : -1.26 (0.13), residues: 2501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1386 HIS 0.007 0.001 HIS U 321 PHE 0.025 0.001 PHE U 221 TYR 0.013 0.001 TYR R 279 ARG 0.014 0.000 ARG R 296 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16902 Ramachandran restraints generated. 8451 Oldfield, 0 Emsley, 8451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16902 Ramachandran restraints generated. 8451 Oldfield, 0 Emsley, 8451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 7506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 436 time to evaluate : 6.246 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: R 124 ASP cc_start: 0.8131 (t0) cc_final: 0.7590 (t0) REVERT: R 198 LEU cc_start: 0.9648 (tt) cc_final: 0.9445 (pp) REVERT: R 420 PHE cc_start: 0.8027 (t80) cc_final: 0.7806 (m-10) REVERT: L 12 ASP cc_start: 0.8947 (t70) cc_final: 0.8600 (t0) REVERT: L 84 LYS cc_start: 0.9417 (tmtt) cc_final: 0.9184 (tmtt) REVERT: D 26 GLU cc_start: 0.8487 (mp0) cc_final: 0.8160 (mp0) REVERT: D 33 GLN cc_start: 0.9160 (mt0) cc_final: 0.8795 (mm-40) REVERT: D 34 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8843 (mm-30) REVERT: D 36 GLN cc_start: 0.9263 (tm-30) cc_final: 0.8934 (tm-30) REVERT: D 42 GLN cc_start: 0.8317 (pp30) cc_final: 0.8017 (tm-30) REVERT: D 46 GLU cc_start: 0.8447 (pm20) cc_final: 0.8178 (pm20) REVERT: A 11 MET cc_start: 0.8380 (mmm) cc_final: 0.7121 (mmm) REVERT: A 48 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8538 (mm) REVERT: A 604 MET cc_start: 0.8786 (mtp) cc_final: 0.8443 (mtp) REVERT: A 665 MET cc_start: 0.9206 (mmm) cc_final: 0.8678 (mmm) REVERT: A 668 MET cc_start: 0.9218 (mtp) cc_final: 0.8432 (mtp) REVERT: A 857 MET cc_start: 0.6803 (mmm) cc_final: 0.6550 (mmm) REVERT: A 970 TRP cc_start: 0.5923 (OUTLIER) cc_final: 0.4975 (p90) REVERT: A 1307 LEU cc_start: 0.9351 (tp) cc_final: 0.8992 (mt) REVERT: A 1316 MET cc_start: 0.8665 (mtm) cc_final: 0.8121 (mpp) REVERT: A 1550 MET cc_start: 0.8019 (tpp) cc_final: 0.7741 (tpp) REVERT: A 1803 ARG cc_start: 0.8844 (tpp80) cc_final: 0.8601 (mmm-85) REVERT: N 156 MET cc_start: 0.9414 (tmm) cc_final: 0.8971 (tmm) REVERT: N 350 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7499 (p0) REVERT: N 414 MET cc_start: 0.8752 (mtt) cc_final: 0.8484 (ttp) REVERT: N 445 ASP cc_start: 0.7953 (m-30) cc_final: 0.7448 (p0) REVERT: N 696 MET cc_start: -0.0983 (mmp) cc_final: -0.1915 (tpp) REVERT: I 116 MET cc_start: 0.8676 (ppp) cc_final: 0.8362 (ppp) REVERT: I 305 MET cc_start: 0.9063 (mtp) cc_final: 0.8448 (ptm) REVERT: I 411 MET cc_start: 0.9114 (tmm) cc_final: 0.8636 (tmm) REVERT: I 425 MET cc_start: 0.8784 (mtp) cc_final: 0.8285 (mtp) REVERT: I 746 MET cc_start: 0.6162 (mmp) cc_final: 0.5659 (mpp) REVERT: O 114 ASP cc_start: 0.9323 (OUTLIER) cc_final: 0.8829 (p0) REVERT: O 414 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8179 (pp) REVERT: K 249 MET cc_start: 0.8819 (tpp) cc_final: 0.8498 (tpp) REVERT: W 1 MET cc_start: 0.7576 (tpp) cc_final: 0.7122 (tpp) REVERT: M 53 GLN cc_start: 0.9281 (tt0) cc_final: 0.8724 (tm-30) REVERT: H 97 LYS cc_start: 0.8838 (ttmt) cc_final: 0.8611 (mtpp) REVERT: J 463 MET cc_start: 0.8904 (tpp) cc_final: 0.8477 (tpp) REVERT: P 463 MET cc_start: 0.9425 (tpp) cc_final: 0.8931 (tpp) REVERT: P 643 MET cc_start: 0.8782 (tpt) cc_final: 0.8506 (tpp) REVERT: P 656 MET cc_start: 0.9128 (tmm) cc_final: 0.8395 (tmm) REVERT: Y 63 MET cc_start: 0.9152 (mmm) cc_final: 0.8628 (mmm) REVERT: Y 91 LYS cc_start: 0.9710 (mttt) cc_final: 0.9063 (ptmm) REVERT: Y 142 MET cc_start: 0.9399 (mmm) cc_final: 0.9005 (mmt) REVERT: Y 386 MET cc_start: 0.8258 (mtm) cc_final: 0.7960 (ptp) REVERT: Y 427 MET cc_start: 0.9149 (tpt) cc_final: 0.8918 (tpp) REVERT: Y 429 MET cc_start: 0.9462 (mmt) cc_final: 0.9182 (mmm) REVERT: V 444 GLU cc_start: 0.9161 (tt0) cc_final: 0.8729 (tm-30) REVERT: Z 239 TRP cc_start: 0.9309 (t60) cc_final: 0.9055 (t60) REVERT: Z 386 MET cc_start: 0.8973 (mmt) cc_final: 0.8314 (mpp) REVERT: Z 390 GLN cc_start: 0.8855 (tp40) cc_final: 0.8587 (tp40) REVERT: Z 427 MET cc_start: 0.8648 (mmm) cc_final: 0.8436 (mmm) outliers start: 97 outliers final: 79 residues processed: 512 average time/residue: 0.6288 time to fit residues: 565.4635 Evaluate side-chains 494 residues out of total 7506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 410 time to evaluate : 6.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 123 PHE Chi-restraints excluded: chain R residue 167 TYR Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 358 VAL Chi-restraints excluded: chain S residue 52 VAL Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 101 ASN Chi-restraints excluded: chain L residue 177 ASP Chi-restraints excluded: chain L residue 179 MET Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 498 VAL Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 970 TRP Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1330 VAL Chi-restraints excluded: chain A residue 1373 MET Chi-restraints excluded: chain A residue 1404 LEU Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1556 LEU Chi-restraints excluded: chain A residue 1620 VAL Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1676 LEU Chi-restraints excluded: chain A residue 1760 ASN Chi-restraints excluded: chain A residue 1865 ASP Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain N residue 326 CYS Chi-restraints excluded: chain N residue 350 ASP Chi-restraints excluded: chain N residue 633 ARG Chi-restraints excluded: chain N residue 687 MET Chi-restraints excluded: chain N residue 692 LEU Chi-restraints excluded: chain I residue 49 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 423 VAL Chi-restraints excluded: chain I residue 486 LEU Chi-restraints excluded: chain I residue 548 MET Chi-restraints excluded: chain I residue 651 VAL Chi-restraints excluded: chain I residue 674 VAL Chi-restraints excluded: chain O residue 64 LEU Chi-restraints excluded: chain O residue 100 MET Chi-restraints excluded: chain O residue 114 ASP Chi-restraints excluded: chain O residue 232 THR Chi-restraints excluded: chain O residue 256 LEU Chi-restraints excluded: chain O residue 284 THR Chi-restraints excluded: chain O residue 414 LEU Chi-restraints excluded: chain O residue 436 THR Chi-restraints excluded: chain O residue 636 ILE Chi-restraints excluded: chain K residue 50 THR Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 442 ASP Chi-restraints excluded: chain K residue 549 VAL Chi-restraints excluded: chain C residue 17 VAL Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 739 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain Q residue 152 SER Chi-restraints excluded: chain Q residue 219 VAL Chi-restraints excluded: chain Y residue 168 THR Chi-restraints excluded: chain Y residue 272 ASP Chi-restraints excluded: chain U residue 190 ASP Chi-restraints excluded: chain U residue 243 LEU Chi-restraints excluded: chain V residue 333 THR Chi-restraints excluded: chain V residue 450 VAL Chi-restraints excluded: chain V residue 542 THR Chi-restraints excluded: chain Z residue 234 ASP Chi-restraints excluded: chain Z residue 371 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 847 random chunks: chunk 412 optimal weight: 0.9980 chunk 533 optimal weight: 0.0570 chunk 715 optimal weight: 2.9990 chunk 205 optimal weight: 0.9990 chunk 619 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 186 optimal weight: 2.9990 chunk 673 optimal weight: 2.9990 chunk 281 optimal weight: 0.9980 chunk 691 optimal weight: 1.9990 chunk 85 optimal weight: 0.0770 overall best weight: 0.6056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 323 HIS ** R 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 639 HIS ** I 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.067261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.044833 restraints weight = 496628.490| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 5.30 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 69609 Z= 0.135 Angle : 0.529 14.032 94280 Z= 0.260 Chirality : 0.038 0.186 10552 Planarity : 0.003 0.055 11989 Dihedral : 3.995 33.851 9320 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.18 % Allowed : 16.53 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.10), residues: 8451 helix: 1.77 (0.07), residues: 5375 sheet: 0.03 (0.22), residues: 579 loop : -1.26 (0.13), residues: 2497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1386 HIS 0.007 0.000 HIS U 321 PHE 0.012 0.001 PHE A1821 TYR 0.017 0.001 TYR R 279 ARG 0.009 0.000 ARG R 296 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12804.74 seconds wall clock time: 228 minutes 48.59 seconds (13728.59 seconds total)