Starting phenix.real_space_refine (version: dev) on Fri Feb 24 03:50:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w8g_32355/02_2023/7w8g_32355_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w8g_32355/02_2023/7w8g_32355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w8g_32355/02_2023/7w8g_32355.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w8g_32355/02_2023/7w8g_32355.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w8g_32355/02_2023/7w8g_32355_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w8g_32355/02_2023/7w8g_32355_updated.pdb" } resolution = 2.52 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "2 TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 272": "OD1" <-> "OD2" Residue "2 TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 423": "OE1" <-> "OE2" Residue "2 GLU 479": "OE1" <-> "OE2" Residue "2 ASP 490": "OD1" <-> "OD2" Residue "2 PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 583": "OD1" <-> "OD2" Residue "2 GLU 592": "OE1" <-> "OE2" Residue "2 TYR 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 688": "OD1" <-> "OD2" Residue "2 PHE 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 796": "OE1" <-> "OE2" Residue "2 GLU 818": "OE1" <-> "OE2" Residue "2 TYR 832": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 183": "OE1" <-> "OE2" Residue "3 TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 275": "OD1" <-> "OD2" Residue "3 ASP 358": "OD1" <-> "OD2" Residue "3 TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 402": "OD1" <-> "OD2" Residue "3 ASP 410": "OD1" <-> "OD2" Residue "3 TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 578": "OE1" <-> "OE2" Residue "3 PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 665": "OE1" <-> "OE2" Residue "3 GLU 674": "OE1" <-> "OE2" Residue "4 GLU 214": "OE1" <-> "OE2" Residue "4 PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 273": "OD1" <-> "OD2" Residue "4 GLU 367": "OE1" <-> "OE2" Residue "4 ASP 408": "OD1" <-> "OD2" Residue "4 ASP 505": "OD1" <-> "OD2" Residue "4 TYR 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 561": "OD1" <-> "OD2" Residue "4 TYR 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 633": "OE1" <-> "OE2" Residue "4 ASP 693": "OD1" <-> "OD2" Residue "4 ASP 703": "OD1" <-> "OD2" Residue "4 GLU 714": "OE1" <-> "OE2" Residue "4 TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 764": "OE1" <-> "OE2" Residue "4 GLU 824": "OE1" <-> "OE2" Residue "5 TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 21": "OD1" <-> "OD2" Residue "5 PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 152": "OD1" <-> "OD2" Residue "5 PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 218": "OE1" <-> "OE2" Residue "5 GLU 246": "OE1" <-> "OE2" Residue "5 GLU 353": "OE1" <-> "OE2" Residue "5 PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 461": "OE1" <-> "OE2" Residue "5 PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 465": "OE1" <-> "OE2" Residue "5 GLU 488": "OE1" <-> "OE2" Residue "5 ASP 489": "OD1" <-> "OD2" Residue "5 TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 565": "OD1" <-> "OD2" Residue "6 ASP 121": "OD1" <-> "OD2" Residue "6 PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 278": "OD1" <-> "OD2" Residue "6 GLU 299": "OE1" <-> "OE2" Residue "6 TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 355": "OD1" <-> "OD2" Residue "6 ASP 406": "OD1" <-> "OD2" Residue "6 PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 620": "OD1" <-> "OD2" Residue "6 ASP 718": "OD1" <-> "OD2" Residue "6 TYR 754": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 817": "OD1" <-> "OD2" Residue "7 PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 122": "OD1" <-> "OD2" Residue "7 TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 156": "OD1" <-> "OD2" Residue "7 GLU 256": "OE1" <-> "OE2" Residue "7 TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 272": "OE1" <-> "OE2" Residue "7 PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 377": "OE1" <-> "OE2" Residue "7 GLU 421": "OE1" <-> "OE2" Residue "7 ASP 441": "OD1" <-> "OD2" Residue "7 TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 609": "OD1" <-> "OD2" Residue "7 ASP 627": "OD1" <-> "OD2" Residue "7 TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 674": "OE1" <-> "OE2" Residue "7 PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 706": "OD1" <-> "OD2" Residue "7 ASP 711": "OD1" <-> "OD2" Residue "7 ASP 712": "OD1" <-> "OD2" Residue "B TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "B ASP 272": "OD1" <-> "OD2" Residue "B TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 423": "OE1" <-> "OE2" Residue "B GLU 479": "OE1" <-> "OE2" Residue "B ASP 490": "OD1" <-> "OD2" Residue "B ASP 510": "OD1" <-> "OD2" Residue "B PHE 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 688": "OD1" <-> "OD2" Residue "B PHE 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 796": "OE1" <-> "OE2" Residue "B ASP 835": "OD1" <-> "OD2" Residue "C ASP 40": "OD1" <-> "OD2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "C PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 183": "OE1" <-> "OE2" Residue "C TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 216": "OD1" <-> "OD2" Residue "C ASP 235": "OD1" <-> "OD2" Residue "C GLU 237": "OE1" <-> "OE2" Residue "C TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 275": "OD1" <-> "OD2" Residue "C ASP 358": "OD1" <-> "OD2" Residue "C ASP 375": "OD1" <-> "OD2" Residue "C ASP 402": "OD1" <-> "OD2" Residue "C ASP 410": "OD1" <-> "OD2" Residue "C TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 685": "OD1" <-> "OD2" Residue "C GLU 703": "OE1" <-> "OE2" Residue "C PHE 735": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D GLU 222": "OE1" <-> "OE2" Residue "D GLU 223": "OE1" <-> "OE2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "D ASP 273": "OD1" <-> "OD2" Residue "D ASP 278": "OD1" <-> "OD2" Residue "D ASP 361": "OD1" <-> "OD2" Residue "D ASP 408": "OD1" <-> "OD2" Residue "D ASP 475": "OD1" <-> "OD2" Residue "D ASP 505": "OD1" <-> "OD2" Residue "D TYR 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 633": "OE1" <-> "OE2" Residue "D ASP 703": "OD1" <-> "OD2" Residue "D ASP 713": "OD1" <-> "OD2" Residue "D GLU 714": "OE1" <-> "OE2" Residue "D TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 764": "OE1" <-> "OE2" Residue "D GLU 799": "OE1" <-> "OE2" Residue "D GLU 820": "OE1" <-> "OE2" Residue "E TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 21": "OD1" <-> "OD2" Residue "E ASP 23": "OD1" <-> "OD2" Residue "E PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 85": "OD1" <-> "OD2" Residue "E ASP 152": "OD1" <-> "OD2" Residue "E PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 218": "OE1" <-> "OE2" Residue "E GLU 246": "OE1" <-> "OE2" Residue "E GLU 356": "OE1" <-> "OE2" Residue "E ASP 456": "OD1" <-> "OD2" Residue "E GLU 461": "OE1" <-> "OE2" Residue "E PHE 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 498": "OE1" <-> "OE2" Residue "E TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 113": "OE1" <-> "OE2" Residue "F ASP 121": "OD1" <-> "OD2" Residue "F PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 378": "OD1" <-> "OD2" Residue "F ASP 406": "OD1" <-> "OD2" Residue "F PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 541": "OE1" <-> "OE2" Residue "F GLU 640": "OE1" <-> "OE2" Residue "F ASP 645": "OD1" <-> "OD2" Residue "F GLU 654": "OE1" <-> "OE2" Residue "F ASP 717": "OD1" <-> "OD2" Residue "F ASP 718": "OD1" <-> "OD2" Residue "F GLU 726": "OE1" <-> "OE2" Residue "F ASP 733": "OD1" <-> "OD2" Residue "F TYR 754": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 817": "OD1" <-> "OD2" Residue "F GLU 818": "OE1" <-> "OE2" Residue "G GLU 91": "OE1" <-> "OE2" Residue "G PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 122": "OD1" <-> "OD2" Residue "G GLU 131": "OE1" <-> "OE2" Residue "G GLU 164": "OE1" <-> "OE2" Residue "G ASP 179": "OD1" <-> "OD2" Residue "G ASP 187": "OD1" <-> "OD2" Residue "G GLU 190": "OE1" <-> "OE2" Residue "G ASP 250": "OD1" <-> "OD2" Residue "G TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 505": "OE1" <-> "OE2" Residue "G GLU 542": "OE1" <-> "OE2" Residue "G TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 609": "OD1" <-> "OD2" Residue "G ASP 627": "OD1" <-> "OD2" Residue "G TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 674": "OE1" <-> "OE2" Residue "G PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 706": "OD1" <-> "OD2" Residue "G ASP 711": "OD1" <-> "OD2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 62460 Number of models: 1 Model: "" Number of chains: 24 Chain: "2" Number of atoms: 4970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 4970 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 25, 'TRANS': 602} Chain breaks: 2 Chain: "3" Number of atoms: 4987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 4987 Classifications: {'peptide': 637} Link IDs: {'PTRANS': 28, 'TRANS': 608} Chain breaks: 4 Chain: "4" Number of atoms: 5323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5323 Classifications: {'peptide': 670} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 645} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "5" Number of atoms: 5143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5143 Classifications: {'peptide': 658} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 629} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "6" Number of atoms: 5109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5109 Classifications: {'peptide': 646} Link IDs: {'PTRANS': 22, 'TRANS': 623} Chain breaks: 3 Chain: "7" Number of atoms: 5505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 5505 Classifications: {'peptide': 699} Link IDs: {'PTRANS': 32, 'TRANS': 666} Chain breaks: 2 Chain: "B" Number of atoms: 4970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 4970 Classifications: {'peptide': 628} Link IDs: {'PTRANS': 25, 'TRANS': 602} Chain breaks: 2 Chain: "C" Number of atoms: 4987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 4987 Classifications: {'peptide': 637} Link IDs: {'PTRANS': 28, 'TRANS': 608} Chain breaks: 4 Chain: "D" Number of atoms: 5323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5323 Classifications: {'peptide': 670} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 645} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 5143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5143 Classifications: {'peptide': 658} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 629} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 5109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 646, 5109 Classifications: {'peptide': 646} Link IDs: {'PTRANS': 22, 'TRANS': 623} Chain breaks: 3 Chain: "G" Number of atoms: 5505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 5505 Classifications: {'peptide': 699} Link IDs: {'PTRANS': 32, 'TRANS': 666} Chain breaks: 2 Chain: "2" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "5" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "7" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1302 SG CYS 2 341 93.937 112.773 65.494 1.00 41.70 S ATOM 1325 SG CYS 2 344 97.487 111.810 65.292 1.00 48.39 S ATOM 1483 SG CYS 2 364 95.189 111.375 62.182 1.00 41.74 S ATOM 1504 SG CYS 2 367 95.184 109.051 65.315 1.00 47.57 S ATOM 11400 SG CYS 4 349 52.511 121.934 46.820 1.00 32.99 S ATOM 11421 SG CYS 4 352 50.433 121.108 43.938 1.00 36.68 S ATOM 11568 SG CYS 4 371 48.936 120.575 47.416 1.00 45.62 S ATOM 11610 SG CYS 4 376 51.734 118.271 46.061 1.00 50.96 S ATOM 16593 SG CYS 5 183 85.652 110.748 88.012 1.00 20.28 S ATOM 16618 SG CYS 5 186 87.098 107.038 88.854 1.00 18.51 S ATOM 16805 SG CYS 5 211 88.120 108.926 85.961 1.00 16.94 S ATOM 16923 SG CYS 5 236 84.449 107.869 86.053 1.00 22.39 S ATOM 21671 SG CYS 6 311 71.186 116.912 48.394 1.00 58.41 S ATOM 21693 SG CYS 6 314 71.714 113.877 46.228 1.00 59.59 S ATOM 21850 SG CYS 6 333 68.393 116.244 45.539 1.00 63.23 S ATOM 21884 SG CYS 6 338 68.431 114.006 47.507 1.00 63.25 S ATOM 27404 SG CYS 7 262 41.041 122.709 72.986 1.00 13.73 S ATOM 27427 SG CYS 7 265 39.143 120.848 75.675 1.00 12.99 S ATOM 27581 SG CYS 7 284 42.976 121.416 75.939 1.00 15.58 S ATOM 27618 SG CYS 7 289 41.508 118.877 73.633 1.00 14.86 S ATOM 32339 SG CYS B 341 61.756 112.340 65.511 1.00 39.92 S ATOM 32362 SG CYS B 344 58.204 113.326 65.271 1.00 48.20 S ATOM 32520 SG CYS B 364 60.555 113.775 62.203 1.00 41.24 S ATOM 32541 SG CYS B 367 60.546 116.070 65.348 1.00 46.86 S ATOM 42437 SG CYS D 349 103.267 103.177 46.815 1.00 32.94 S ATOM 42458 SG CYS D 352 105.307 103.974 43.924 1.00 36.84 S ATOM 42605 SG CYS D 371 106.871 104.514 47.414 1.00 45.59 S ATOM 42647 SG CYS D 376 104.063 106.811 46.025 1.00 51.86 S ATOM 47630 SG CYS E 183 70.016 114.400 88.017 1.00 20.09 S ATOM 47655 SG CYS E 186 68.561 118.107 88.849 1.00 17.73 S ATOM 47842 SG CYS E 211 67.592 116.193 85.937 1.00 16.89 S ATOM 47960 SG CYS E 236 71.252 117.267 86.065 1.00 20.40 S ATOM 52708 SG CYS F 311 84.532 108.247 48.394 1.00 58.09 S ATOM 52730 SG CYS F 314 83.995 111.283 46.234 1.00 59.59 S ATOM 52887 SG CYS F 333 87.262 108.882 45.491 1.00 62.93 S ATOM 52921 SG CYS F 338 87.295 111.139 47.520 1.00 61.93 S ATOM 58441 SG CYS G 262 114.667 102.413 72.953 1.00 15.56 S ATOM 58464 SG CYS G 265 116.476 104.272 75.668 1.00 20.28 S ATOM 58618 SG CYS G 284 112.571 103.681 75.746 1.00 14.47 S ATOM 58655 SG CYS G 289 114.126 106.249 73.585 1.00 16.57 S Time building chain proxies: 25.12, per 1000 atoms: 0.40 Number of scatterers: 62460 At special positions: 0 Unit cell: (156.748, 226.18, 149.384, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 10 29.99 S 296 16.00 P 34 15.00 Mg 12 11.99 O 12060 8.00 N 10892 7.00 C 39156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS 7 474 " - pdb=" SG CYS 7 522 " distance=2.05 Simple disulfide: pdb=" SG CYS G 474 " - pdb=" SG CYS G 522 " distance=2.05 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: 17.77 Conformation dependent library (CDL) restraints added in 7.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 22003 " pdb="ZN ZN 22003 " - pdb=" SG CYS 2 344 " pdb="ZN ZN 22003 " - pdb=" SG CYS 2 367 " pdb="ZN ZN 22003 " - pdb=" SG CYS 2 341 " pdb="ZN ZN 22003 " - pdb=" SG CYS 2 364 " pdb=" ZN 42003 " pdb="ZN ZN 42003 " - pdb=" SG CYS 4 352 " pdb="ZN ZN 42003 " - pdb=" SG CYS 4 349 " pdb="ZN ZN 42003 " - pdb=" SG CYS 4 376 " pdb="ZN ZN 42003 " - pdb=" SG CYS 4 371 " pdb=" ZN 52003 " pdb="ZN ZN 52003 " - pdb=" SG CYS 5 211 " pdb="ZN ZN 52003 " - pdb=" SG CYS 5 236 " pdb="ZN ZN 52003 " - pdb=" SG CYS 5 183 " pdb="ZN ZN 52003 " - pdb=" SG CYS 5 186 " pdb=" ZN 62003 " pdb="ZN ZN 62003 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 62003 " - pdb=" SG CYS 6 314 " pdb="ZN ZN 62003 " - pdb=" SG CYS 6 333 " pdb="ZN ZN 62003 " - pdb=" SG CYS 6 311 " pdb=" ZN 72003 " pdb="ZN ZN 72003 " - pdb=" SG CYS 7 265 " pdb="ZN ZN 72003 " - pdb=" SG CYS 7 289 " pdb="ZN ZN 72003 " - pdb=" SG CYS 7 284 " pdb="ZN ZN 72003 " - pdb=" SG CYS 7 262 " pdb=" ZN B2003 " pdb="ZN ZN B2003 " - pdb=" SG CYS B 344 " pdb="ZN ZN B2003 " - pdb=" SG CYS B 367 " pdb="ZN ZN B2003 " - pdb=" SG CYS B 341 " pdb="ZN ZN B2003 " - pdb=" SG CYS B 364 " pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 352 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 349 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 376 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 371 " pdb=" ZN E2003 " pdb="ZN ZN E2003 " - pdb=" SG CYS E 211 " pdb="ZN ZN E2003 " - pdb=" SG CYS E 236 " pdb="ZN ZN E2003 " - pdb=" SG CYS E 183 " pdb="ZN ZN E2003 " - pdb=" SG CYS E 186 " pdb=" ZN F2003 " pdb="ZN ZN F2003 " - pdb=" SG CYS F 338 " pdb="ZN ZN F2003 " - pdb=" SG CYS F 314 " pdb="ZN ZN F2003 " - pdb=" SG CYS F 333 " pdb="ZN ZN F2003 " - pdb=" SG CYS F 311 " pdb=" ZN G2003 " pdb="ZN ZN G2003 " - pdb=" SG CYS G 265 " pdb="ZN ZN G2003 " - pdb=" SG CYS G 289 " pdb="ZN ZN G2003 " - pdb=" SG CYS G 284 " pdb="ZN ZN G2003 " - pdb=" SG CYS G 262 " Number of angles added : 60 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14952 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 309 helices and 88 sheets defined 39.1% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.30 Creating SS restraints... Processing helix chain '2' and resid 183 through 187 Processing helix chain '2' and resid 194 through 199 Processing helix chain '2' and resid 201 through 217 Processing helix chain '2' and resid 226 through 236 Processing helix chain '2' and resid 246 through 252 Processing helix chain '2' and resid 254 through 262 Processing helix chain '2' and resid 264 through 282 Processing helix chain '2' and resid 284 through 289 removed outlier: 4.057A pdb=" N ALA 2 287 " --> pdb=" O PRO 2 284 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG 2 288 " --> pdb=" O ASP 2 285 " (cutoff:3.500A) Processing helix chain '2' and resid 306 through 308 No H-bonds generated for 'chain '2' and resid 306 through 308' Processing helix chain '2' and resid 311 through 313 No H-bonds generated for 'chain '2' and resid 311 through 313' Processing helix chain '2' and resid 412 through 414 No H-bonds generated for 'chain '2' and resid 412 through 414' Processing helix chain '2' and resid 478 through 488 Processing helix chain '2' and resid 491 through 500 removed outlier: 4.705A pdb=" N ILE 2 494 " --> pdb=" O ARG 2 491 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP 2 495 " --> pdb=" O GLY 2 492 " (cutoff:3.500A) Processing helix chain '2' and resid 509 through 520 Processing helix chain '2' and resid 549 through 559 Processing helix chain '2' and resid 594 through 598 Processing helix chain '2' and resid 609 through 611 No H-bonds generated for 'chain '2' and resid 609 through 611' Processing helix chain '2' and resid 614 through 626 Processing helix chain '2' and resid 653 through 655 No H-bonds generated for 'chain '2' and resid 653 through 655' Processing helix chain '2' and resid 663 through 666 No H-bonds generated for 'chain '2' and resid 663 through 666' Processing helix chain '2' and resid 671 through 675 Processing helix chain '2' and resid 689 through 705 Processing helix chain '2' and resid 760 through 773 removed outlier: 3.687A pdb=" N LYS 2 765 " --> pdb=" O GLU 2 761 " (cutoff:3.500A) Processing helix chain '2' and resid 780 through 800 removed outlier: 4.342A pdb=" N ASP 2 784 " --> pdb=" O MET 2 781 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS 2 785 " --> pdb=" O ASP 2 782 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N SER 2 787 " --> pdb=" O ASP 2 784 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR 2 790 " --> pdb=" O SER 2 787 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA 2 791 " --> pdb=" O ARG 2 788 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG 2 794 " --> pdb=" O ALA 2 791 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ARG 2 795 " --> pdb=" O ASP 2 792 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR 2 800 " --> pdb=" O SER 2 797 " (cutoff:3.500A) Processing helix chain '2' and resid 807 through 823 removed outlier: 3.721A pdb=" N GLU 2 818 " --> pdb=" O LEU 2 814 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS 2 822 " --> pdb=" O GLU 2 818 " (cutoff:3.500A) Processing helix chain '2' and resid 831 through 847 Processing helix chain '2' and resid 851 through 860 removed outlier: 3.511A pdb=" N ARG 2 855 " --> pdb=" O VAL 2 851 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN 2 856 " --> pdb=" O SER 2 852 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG 2 859 " --> pdb=" O ARG 2 855 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER 2 860 " --> pdb=" O GLN 2 856 " (cutoff:3.500A) Processing helix chain '2' and resid 862 through 865 No H-bonds generated for 'chain '2' and resid 862 through 865' Processing helix chain '3' and resid 19 through 34 Processing helix chain '3' and resid 36 through 58 Processing helix chain '3' and resid 100 through 106 Processing helix chain '3' and resid 108 through 116 Processing helix chain '3' and resid 118 through 136 Proline residue: 3 123 - end of helix Processing helix chain '3' and resid 162 through 164 No H-bonds generated for 'chain '3' and resid 162 through 164' Processing helix chain '3' and resid 173 through 175 No H-bonds generated for 'chain '3' and resid 173 through 175' Processing helix chain '3' and resid 280 through 282 No H-bonds generated for 'chain '3' and resid 280 through 282' Processing helix chain '3' and resid 344 through 354 Processing helix chain '3' and resid 359 through 363 Processing helix chain '3' and resid 375 through 386 Processing helix chain '3' and resid 415 through 425 Processing helix chain '3' and resid 439 through 442 No H-bonds generated for 'chain '3' and resid 439 through 442' Processing helix chain '3' and resid 461 through 464 No H-bonds generated for 'chain '3' and resid 461 through 464' Processing helix chain '3' and resid 475 through 477 No H-bonds generated for 'chain '3' and resid 475 through 477' Processing helix chain '3' and resid 480 through 491 removed outlier: 3.960A pdb=" N GLU 3 488 " --> pdb=" O VAL 3 484 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL 3 489 " --> pdb=" O ALA 3 485 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU 3 491 " --> pdb=" O HIS 3 487 " (cutoff:3.500A) Processing helix chain '3' and resid 529 through 533 Processing helix chain '3' and resid 537 through 542 Processing helix chain '3' and resid 555 through 568 Processing helix chain '3' and resid 653 through 666 removed outlier: 3.508A pdb=" N LYS 3 658 " --> pdb=" O PRO 3 654 " (cutoff:3.500A) Processing helix chain '3' and resid 673 through 687 removed outlier: 3.819A pdb=" N VAL 3 678 " --> pdb=" O GLU 3 674 " (cutoff:3.500A) Processing helix chain '3' and resid 700 through 715 Processing helix chain '3' and resid 723 through 737 removed outlier: 3.670A pdb=" N PHE 3 735 " --> pdb=" O ASN 3 731 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA 3 736 " --> pdb=" O LEU 3 732 " (cutoff:3.500A) Processing helix chain '4' and resid 187 through 200 Processing helix chain '4' and resid 203 through 209 Processing helix chain '4' and resid 218 through 221 No H-bonds generated for 'chain '4' and resid 218 through 221' Processing helix chain '4' and resid 225 through 236 Processing helix chain '4' and resid 245 through 250 Processing helix chain '4' and resid 255 through 263 removed outlier: 3.765A pdb=" N HIS 4 259 " --> pdb=" O GLU 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 265 through 286 removed outlier: 3.766A pdb=" N SER 4 270 " --> pdb=" O GLN 4 266 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE 4 284 " --> pdb=" O MET 4 280 " (cutoff:3.500A) Processing helix chain '4' and resid 293 through 298 Processing helix chain '4' and resid 319 through 321 No H-bonds generated for 'chain '4' and resid 319 through 321' Processing helix chain '4' and resid 421 through 423 No H-bonds generated for 'chain '4' and resid 421 through 423' Processing helix chain '4' and resid 478 through 480 No H-bonds generated for 'chain '4' and resid 478 through 480' Processing helix chain '4' and resid 482 through 491 Processing helix chain '4' and resid 503 through 514 removed outlier: 3.508A pdb=" N ALA 4 514 " --> pdb=" O ARG 4 510 " (cutoff:3.500A) Processing helix chain '4' and resid 518 through 524 Processing helix chain '4' and resid 534 through 545 Processing helix chain '4' and resid 574 through 584 Processing helix chain '4' and resid 598 through 602 Processing helix chain '4' and resid 620 through 623 No H-bonds generated for 'chain '4' and resid 620 through 623' Processing helix chain '4' and resid 634 through 636 No H-bonds generated for 'chain '4' and resid 634 through 636' Processing helix chain '4' and resid 639 through 651 removed outlier: 3.880A pdb=" N VAL 4 644 " --> pdb=" O SER 4 640 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU 4 645 " --> pdb=" O THR 4 641 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N HIS 4 646 " --> pdb=" O ARG 4 642 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLU 4 647 " --> pdb=" O SER 4 643 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL 4 648 " --> pdb=" O VAL 4 644 " (cutoff:3.500A) Processing helix chain '4' and resid 688 through 692 Processing helix chain '4' and resid 696 through 701 removed outlier: 3.885A pdb=" N ARG 4 701 " --> pdb=" O PRO 4 697 " (cutoff:3.500A) Processing helix chain '4' and resid 714 through 729 removed outlier: 3.882A pdb=" N LEU 4 727 " --> pdb=" O HIS 4 723 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TYR 4 728 " --> pdb=" O LEU 4 724 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU 4 729 " --> pdb=" O THR 4 725 " (cutoff:3.500A) Processing helix chain '4' and resid 744 through 757 Processing helix chain '4' and resid 764 through 782 Processing helix chain '4' and resid 795 through 811 Processing helix chain '4' and resid 819 through 832 Processing helix chain '5' and resid 24 through 37 Processing helix chain '5' and resid 45 through 55 Processing helix chain '5' and resid 65 through 71 removed outlier: 3.534A pdb=" N ILE 5 69 " --> pdb=" O MET 5 65 " (cutoff:3.500A) Processing helix chain '5' and resid 73 through 81 Processing helix chain '5' and resid 83 through 104 Proline residue: 5 88 - end of helix removed outlier: 3.722A pdb=" N ARG 5 100 " --> pdb=" O GLN 5 96 " (cutoff:3.500A) Processing helix chain '5' and resid 148 through 150 No H-bonds generated for 'chain '5' and resid 148 through 150' Processing helix chain '5' and resid 153 through 155 No H-bonds generated for 'chain '5' and resid 153 through 155' Processing helix chain '5' and resid 213 through 216 No H-bonds generated for 'chain '5' and resid 213 through 216' Processing helix chain '5' and resid 245 through 247 No H-bonds generated for 'chain '5' and resid 245 through 247' Processing helix chain '5' and resid 280 through 282 No H-bonds generated for 'chain '5' and resid 280 through 282' Processing helix chain '5' and resid 351 through 361 Processing helix chain '5' and resid 366 through 373 Processing helix chain '5' and resid 382 through 393 Processing helix chain '5' and resid 422 through 432 Processing helix chain '5' and resid 468 through 471 No H-bonds generated for 'chain '5' and resid 468 through 471' Processing helix chain '5' and resid 487 through 498 Processing helix chain '5' and resid 536 through 539 No H-bonds generated for 'chain '5' and resid 536 through 539' Processing helix chain '5' and resid 544 through 549 removed outlier: 3.865A pdb=" N SER 5 548 " --> pdb=" O THR 5 544 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG 5 549 " --> pdb=" O THR 5 545 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 544 through 549' Processing helix chain '5' and resid 562 through 577 Processing helix chain '5' and resid 579 through 590 Processing helix chain '5' and resid 596 through 609 Processing helix chain '5' and resid 616 through 640 removed outlier: 4.450A pdb=" N GLU 5 620 " --> pdb=" O GLN 5 617 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS 5 621 " --> pdb=" O ALA 5 618 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE 5 626 " --> pdb=" O SER 5 623 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N THR 5 628 " --> pdb=" O ASN 5 625 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE 5 629 " --> pdb=" O PHE 5 626 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU 5 634 " --> pdb=" O LYS 5 631 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER 5 640 " --> pdb=" O GLU 5 637 " (cutoff:3.500A) Processing helix chain '5' and resid 650 through 666 removed outlier: 3.639A pdb=" N LEU 5 666 " --> pdb=" O SER 5 662 " (cutoff:3.500A) Processing helix chain '5' and resid 674 through 694 removed outlier: 3.588A pdb=" N GLU 5 679 " --> pdb=" O ARG 5 675 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET 5 689 " --> pdb=" O GLN 5 685 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ASP 5 690 " --> pdb=" O ALA 5 686 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA 5 691 " --> pdb=" O SER 5 687 " (cutoff:3.500A) Processing helix chain '6' and resid 106 through 121 removed outlier: 3.781A pdb=" N GLU 6 120 " --> pdb=" O GLU 6 116 " (cutoff:3.500A) Processing helix chain '6' and resid 135 through 146 removed outlier: 3.772A pdb=" N ILE 6 145 " --> pdb=" O GLU 6 141 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR 6 146 " --> pdb=" O PHE 6 142 " (cutoff:3.500A) Processing helix chain '6' and resid 155 through 159 Processing helix chain '6' and resid 165 through 172 Processing helix chain '6' and resid 174 through 192 Proline residue: 6 179 - end of helix Processing helix chain '6' and resid 194 through 197 Processing helix chain '6' and resid 276 through 278 No H-bonds generated for 'chain '6' and resid 276 through 278' Processing helix chain '6' and resid 281 through 283 No H-bonds generated for 'chain '6' and resid 281 through 283' Processing helix chain '6' and resid 383 through 385 No H-bonds generated for 'chain '6' and resid 383 through 385' Processing helix chain '6' and resid 407 through 411 removed outlier: 3.598A pdb=" N LEU 6 410 " --> pdb=" O VAL 6 407 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY 6 411 " --> pdb=" O THR 6 408 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 407 through 411' Processing helix chain '6' and resid 501 through 507 removed outlier: 3.595A pdb=" N SER 6 507 " --> pdb=" O VAL 6 503 " (cutoff:3.500A) Processing helix chain '6' and resid 510 through 520 Processing helix chain '6' and resid 525 through 532 Processing helix chain '6' and resid 541 through 552 Processing helix chain '6' and resid 581 through 591 removed outlier: 3.663A pdb=" N LEU 6 585 " --> pdb=" O LYS 6 581 " (cutoff:3.500A) Processing helix chain '6' and resid 605 through 608 No H-bonds generated for 'chain '6' and resid 605 through 608' Processing helix chain '6' and resid 627 through 630 No H-bonds generated for 'chain '6' and resid 627 through 630' Processing helix chain '6' and resid 641 through 643 No H-bonds generated for 'chain '6' and resid 641 through 643' Processing helix chain '6' and resid 646 through 658 removed outlier: 3.950A pdb=" N ALA 6 655 " --> pdb=" O ALA 6 651 " (cutoff:3.500A) Processing helix chain '6' and resid 695 through 698 No H-bonds generated for 'chain '6' and resid 695 through 698' Processing helix chain '6' and resid 703 through 708 removed outlier: 3.910A pdb=" N ARG 6 708 " --> pdb=" O PRO 6 704 " (cutoff:3.500A) Processing helix chain '6' and resid 721 through 741 removed outlier: 7.934A pdb=" N ASP 6 739 " --> pdb=" O HIS 6 735 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N GLU 6 740 " --> pdb=" O MET 6 736 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA 6 741 " --> pdb=" O LYS 6 737 " (cutoff:3.500A) Processing helix chain '6' and resid 748 through 760 removed outlier: 4.008A pdb=" N THR 6 760 " --> pdb=" O LYS 6 756 " (cutoff:3.500A) Processing helix chain '6' and resid 767 through 790 removed outlier: 3.720A pdb=" N SER 6 771 " --> pdb=" O LYS 6 767 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N SER 6 789 " --> pdb=" O ALA 6 785 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ARG 6 790 " --> pdb=" O GLN 6 786 " (cutoff:3.500A) Processing helix chain '6' and resid 797 through 813 Processing helix chain '6' and resid 821 through 834 Processing helix chain '7' and resid 14 through 27 removed outlier: 3.504A pdb=" N PHE 7 18 " --> pdb=" O TYR 7 14 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL 7 26 " --> pdb=" O THR 7 22 " (cutoff:3.500A) Processing helix chain '7' and resid 62 through 71 Processing helix chain '7' and resid 82 through 95 Processing helix chain '7' and resid 102 through 108 Processing helix chain '7' and resid 110 through 123 removed outlier: 3.994A pdb=" N GLU 7 115 " --> pdb=" O ASN 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 138 through 164 Processing helix chain '7' and resid 174 through 188 Processing helix chain '7' and resid 194 through 196 No H-bonds generated for 'chain '7' and resid 194 through 196' Processing helix chain '7' and resid 209 through 214 removed outlier: 3.525A pdb=" N ARG 7 214 " --> pdb=" O ASN 7 210 " (cutoff:3.500A) Processing helix chain '7' and resid 227 through 229 No H-bonds generated for 'chain '7' and resid 227 through 229' Processing helix chain '7' and resid 232 through 234 No H-bonds generated for 'chain '7' and resid 232 through 234' Processing helix chain '7' and resid 287 through 291 removed outlier: 3.742A pdb=" N GLN 7 291 " --> pdb=" O GLU 7 287 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 287 through 291' Processing helix chain '7' and resid 337 through 339 No H-bonds generated for 'chain '7' and resid 337 through 339' Processing helix chain '7' and resid 395 through 407 removed outlier: 3.752A pdb=" N GLU 7 399 " --> pdb=" O SER 7 395 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG 7 400 " --> pdb=" O ASP 7 396 " (cutoff:3.500A) Processing helix chain '7' and resid 410 through 416 Processing helix chain '7' and resid 426 through 437 Processing helix chain '7' and resid 466 through 476 Processing helix chain '7' and resid 512 through 515 No H-bonds generated for 'chain '7' and resid 512 through 515' Processing helix chain '7' and resid 526 through 528 No H-bonds generated for 'chain '7' and resid 526 through 528' Processing helix chain '7' and resid 531 through 543 removed outlier: 4.166A pdb=" N GLU 7 542 " --> pdb=" O HIS 7 538 " (cutoff:3.500A) Processing helix chain '7' and resid 588 through 593 Processing helix chain '7' and resid 606 through 622 removed outlier: 3.738A pdb=" N GLU 7 610 " --> pdb=" O ARG 7 606 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS 7 611 " --> pdb=" O ASP 7 607 " (cutoff:3.500A) Processing helix chain '7' and resid 635 through 647 Processing helix chain '7' and resid 654 through 674 Processing helix chain '7' and resid 686 through 702 Processing helix chain '7' and resid 710 through 729 removed outlier: 3.944A pdb=" N LYS 7 724 " --> pdb=" O VAL 7 720 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N SER 7 726 " --> pdb=" O VAL 7 722 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LEU 7 727 " --> pdb=" O SER 7 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 201 through 217 Processing helix chain 'B' and resid 226 through 237 Processing helix chain 'B' and resid 246 through 252 Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 264 through 282 Processing helix chain 'B' and resid 284 through 289 removed outlier: 4.075A pdb=" N ALA B 287 " --> pdb=" O PRO B 284 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG B 288 " --> pdb=" O ASP B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 311 through 313 No H-bonds generated for 'chain 'B' and resid 311 through 313' Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 478 through 488 Processing helix chain 'B' and resid 491 through 500 removed outlier: 4.700A pdb=" N ILE B 494 " --> pdb=" O ARG B 491 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP B 495 " --> pdb=" O GLY B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 520 Processing helix chain 'B' and resid 549 through 559 Processing helix chain 'B' and resid 594 through 598 Processing helix chain 'B' and resid 609 through 611 No H-bonds generated for 'chain 'B' and resid 609 through 611' Processing helix chain 'B' and resid 614 through 626 Processing helix chain 'B' and resid 653 through 655 No H-bonds generated for 'chain 'B' and resid 653 through 655' Processing helix chain 'B' and resid 663 through 666 No H-bonds generated for 'chain 'B' and resid 663 through 666' Processing helix chain 'B' and resid 671 through 675 Processing helix chain 'B' and resid 689 through 705 Processing helix chain 'B' and resid 760 through 773 removed outlier: 3.612A pdb=" N LYS B 765 " --> pdb=" O GLU B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 780 through 800 removed outlier: 3.616A pdb=" N MET B 783 " --> pdb=" O GLN B 780 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP B 784 " --> pdb=" O MET B 781 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS B 785 " --> pdb=" O ASP B 782 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N SER B 787 " --> pdb=" O ASP B 784 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B 789 " --> pdb=" O VAL B 786 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR B 790 " --> pdb=" O SER B 787 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA B 791 " --> pdb=" O ARG B 788 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG B 794 " --> pdb=" O ALA B 791 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ARG B 795 " --> pdb=" O ASP B 792 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR B 800 " --> pdb=" O SER B 797 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 823 removed outlier: 3.998A pdb=" N GLU B 818 " --> pdb=" O LEU B 814 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS B 822 " --> pdb=" O GLU B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 847 Processing helix chain 'B' and resid 851 through 860 removed outlier: 3.508A pdb=" N ARG B 855 " --> pdb=" O VAL B 851 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN B 856 " --> pdb=" O SER B 852 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG B 859 " --> pdb=" O ARG B 855 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER B 860 " --> pdb=" O GLN B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 865 No H-bonds generated for 'chain 'B' and resid 862 through 865' Processing helix chain 'C' and resid 19 through 34 Processing helix chain 'C' and resid 36 through 58 removed outlier: 3.513A pdb=" N ARG C 43 " --> pdb=" O ARG C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 106 Processing helix chain 'C' and resid 108 through 116 Processing helix chain 'C' and resid 118 through 137 Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 162 through 164 No H-bonds generated for 'chain 'C' and resid 162 through 164' Processing helix chain 'C' and resid 173 through 175 No H-bonds generated for 'chain 'C' and resid 173 through 175' Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 344 through 354 Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 375 through 386 Processing helix chain 'C' and resid 415 through 425 Processing helix chain 'C' and resid 439 through 442 No H-bonds generated for 'chain 'C' and resid 439 through 442' Processing helix chain 'C' and resid 461 through 464 No H-bonds generated for 'chain 'C' and resid 461 through 464' Processing helix chain 'C' and resid 475 through 477 No H-bonds generated for 'chain 'C' and resid 475 through 477' Processing helix chain 'C' and resid 480 through 491 removed outlier: 4.052A pdb=" N GLU C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU C 491 " --> pdb=" O HIS C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 533 Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 555 through 568 Processing helix chain 'C' and resid 653 through 666 removed outlier: 3.537A pdb=" N LYS C 658 " --> pdb=" O PRO C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 687 removed outlier: 3.866A pdb=" N VAL C 678 " --> pdb=" O GLU C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 715 Processing helix chain 'C' and resid 723 through 737 removed outlier: 3.670A pdb=" N PHE C 735 " --> pdb=" O ASN C 731 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA C 736 " --> pdb=" O LEU C 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 200 Processing helix chain 'D' and resid 203 through 209 Processing helix chain 'D' and resid 218 through 221 No H-bonds generated for 'chain 'D' and resid 218 through 221' Processing helix chain 'D' and resid 225 through 236 Processing helix chain 'D' and resid 245 through 250 Processing helix chain 'D' and resid 255 through 263 removed outlier: 3.755A pdb=" N HIS D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 286 removed outlier: 3.764A pdb=" N SER D 270 " --> pdb=" O GLN D 266 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE D 284 " --> pdb=" O MET D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 298 Processing helix chain 'D' and resid 314 through 316 No H-bonds generated for 'chain 'D' and resid 314 through 316' Processing helix chain 'D' and resid 319 through 321 No H-bonds generated for 'chain 'D' and resid 319 through 321' Processing helix chain 'D' and resid 421 through 423 No H-bonds generated for 'chain 'D' and resid 421 through 423' Processing helix chain 'D' and resid 478 through 480 No H-bonds generated for 'chain 'D' and resid 478 through 480' Processing helix chain 'D' and resid 482 through 491 Processing helix chain 'D' and resid 503 through 514 removed outlier: 3.500A pdb=" N ALA D 514 " --> pdb=" O ARG D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 524 Processing helix chain 'D' and resid 534 through 545 Processing helix chain 'D' and resid 574 through 584 Processing helix chain 'D' and resid 598 through 602 Processing helix chain 'D' and resid 620 through 623 No H-bonds generated for 'chain 'D' and resid 620 through 623' Processing helix chain 'D' and resid 634 through 636 No H-bonds generated for 'chain 'D' and resid 634 through 636' Processing helix chain 'D' and resid 639 through 651 removed outlier: 3.747A pdb=" N VAL D 644 " --> pdb=" O SER D 640 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU D 645 " --> pdb=" O THR D 641 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N HIS D 646 " --> pdb=" O ARG D 642 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N GLU D 647 " --> pdb=" O SER D 643 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL D 648 " --> pdb=" O VAL D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 692 Processing helix chain 'D' and resid 696 through 701 removed outlier: 3.914A pdb=" N ARG D 701 " --> pdb=" O PRO D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 729 removed outlier: 3.866A pdb=" N LEU D 727 " --> pdb=" O HIS D 723 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TYR D 728 " --> pdb=" O LEU D 724 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU D 729 " --> pdb=" O THR D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 744 through 757 Processing helix chain 'D' and resid 764 through 782 removed outlier: 3.536A pdb=" N GLU D 769 " --> pdb=" O ALA D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 795 through 811 Processing helix chain 'D' and resid 819 through 832 Processing helix chain 'E' and resid 24 through 37 Processing helix chain 'E' and resid 45 through 55 Processing helix chain 'E' and resid 65 through 71 removed outlier: 3.597A pdb=" N ILE E 69 " --> pdb=" O MET E 65 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY E 70 " --> pdb=" O GLU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 81 Processing helix chain 'E' and resid 83 through 104 Proline residue: E 88 - end of helix removed outlier: 3.786A pdb=" N ARG E 100 " --> pdb=" O GLN E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 150 No H-bonds generated for 'chain 'E' and resid 148 through 150' Processing helix chain 'E' and resid 153 through 155 No H-bonds generated for 'chain 'E' and resid 153 through 155' Processing helix chain 'E' and resid 213 through 216 No H-bonds generated for 'chain 'E' and resid 213 through 216' Processing helix chain 'E' and resid 245 through 247 No H-bonds generated for 'chain 'E' and resid 245 through 247' Processing helix chain 'E' and resid 280 through 282 No H-bonds generated for 'chain 'E' and resid 280 through 282' Processing helix chain 'E' and resid 351 through 361 Processing helix chain 'E' and resid 366 through 373 Processing helix chain 'E' and resid 382 through 393 removed outlier: 3.511A pdb=" N MET E 393 " --> pdb=" O VAL E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 432 Processing helix chain 'E' and resid 468 through 471 No H-bonds generated for 'chain 'E' and resid 468 through 471' Processing helix chain 'E' and resid 487 through 498 Processing helix chain 'E' and resid 536 through 539 No H-bonds generated for 'chain 'E' and resid 536 through 539' Processing helix chain 'E' and resid 544 through 549 Processing helix chain 'E' and resid 562 through 577 Processing helix chain 'E' and resid 579 through 590 Processing helix chain 'E' and resid 596 through 609 Processing helix chain 'E' and resid 616 through 640 removed outlier: 4.473A pdb=" N GLU E 620 " --> pdb=" O GLN E 617 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS E 621 " --> pdb=" O ALA E 618 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N PHE E 626 " --> pdb=" O SER E 623 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR E 628 " --> pdb=" O ASN E 625 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE E 629 " --> pdb=" O PHE E 626 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU E 634 " --> pdb=" O LYS E 631 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER E 640 " --> pdb=" O GLU E 637 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 666 Processing helix chain 'E' and resid 674 through 694 removed outlier: 3.667A pdb=" N GLU E 679 " --> pdb=" O ARG E 675 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET E 689 " --> pdb=" O GLN E 685 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ASP E 690 " --> pdb=" O ALA E 686 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA E 691 " --> pdb=" O SER E 687 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 121 removed outlier: 3.721A pdb=" N GLU F 120 " --> pdb=" O GLU F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 146 removed outlier: 3.608A pdb=" N ILE F 145 " --> pdb=" O GLU F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 160 Processing helix chain 'F' and resid 165 through 172 Processing helix chain 'F' and resid 174 through 192 Proline residue: F 179 - end of helix Processing helix chain 'F' and resid 194 through 197 Processing helix chain 'F' and resid 276 through 278 No H-bonds generated for 'chain 'F' and resid 276 through 278' Processing helix chain 'F' and resid 281 through 283 No H-bonds generated for 'chain 'F' and resid 281 through 283' Processing helix chain 'F' and resid 365 through 367 No H-bonds generated for 'chain 'F' and resid 365 through 367' Processing helix chain 'F' and resid 383 through 385 No H-bonds generated for 'chain 'F' and resid 383 through 385' Processing helix chain 'F' and resid 407 through 411 removed outlier: 3.618A pdb=" N LEU F 410 " --> pdb=" O VAL F 407 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY F 411 " --> pdb=" O THR F 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 407 through 411' Processing helix chain 'F' and resid 501 through 507 removed outlier: 3.593A pdb=" N SER F 507 " --> pdb=" O VAL F 503 " (cutoff:3.500A) Processing helix chain 'F' and resid 510 through 521 Processing helix chain 'F' and resid 525 through 532 Processing helix chain 'F' and resid 541 through 552 Processing helix chain 'F' and resid 581 through 591 removed outlier: 3.675A pdb=" N LEU F 585 " --> pdb=" O LYS F 581 " (cutoff:3.500A) Processing helix chain 'F' and resid 605 through 608 No H-bonds generated for 'chain 'F' and resid 605 through 608' Processing helix chain 'F' and resid 627 through 630 No H-bonds generated for 'chain 'F' and resid 627 through 630' Processing helix chain 'F' and resid 641 through 643 No H-bonds generated for 'chain 'F' and resid 641 through 643' Processing helix chain 'F' and resid 646 through 658 removed outlier: 3.974A pdb=" N ALA F 655 " --> pdb=" O ALA F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 695 through 698 No H-bonds generated for 'chain 'F' and resid 695 through 698' Processing helix chain 'F' and resid 703 through 708 removed outlier: 3.836A pdb=" N ARG F 708 " --> pdb=" O PRO F 704 " (cutoff:3.500A) Processing helix chain 'F' and resid 721 through 741 removed outlier: 8.012A pdb=" N ASP F 739 " --> pdb=" O HIS F 735 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N GLU F 740 " --> pdb=" O MET F 736 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA F 741 " --> pdb=" O LYS F 737 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 760 removed outlier: 4.016A pdb=" N THR F 760 " --> pdb=" O LYS F 756 " (cutoff:3.500A) Processing helix chain 'F' and resid 767 through 790 removed outlier: 3.720A pdb=" N SER F 771 " --> pdb=" O LYS F 767 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N SER F 789 " --> pdb=" O ALA F 785 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ARG F 790 " --> pdb=" O GLN F 786 " (cutoff:3.500A) Processing helix chain 'F' and resid 797 through 813 Processing helix chain 'F' and resid 821 through 834 Processing helix chain 'G' and resid 14 through 27 removed outlier: 3.546A pdb=" N VAL G 26 " --> pdb=" O THR G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 71 Processing helix chain 'G' and resid 82 through 95 Processing helix chain 'G' and resid 102 through 108 Processing helix chain 'G' and resid 110 through 123 removed outlier: 4.000A pdb=" N GLU G 115 " --> pdb=" O ASN G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 164 Processing helix chain 'G' and resid 174 through 188 Processing helix chain 'G' and resid 194 through 196 No H-bonds generated for 'chain 'G' and resid 194 through 196' Processing helix chain 'G' and resid 209 through 214 removed outlier: 3.520A pdb=" N ARG G 214 " --> pdb=" O ASN G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 234 No H-bonds generated for 'chain 'G' and resid 232 through 234' Processing helix chain 'G' and resid 287 through 291 Processing helix chain 'G' and resid 337 through 339 No H-bonds generated for 'chain 'G' and resid 337 through 339' Processing helix chain 'G' and resid 395 through 407 removed outlier: 3.730A pdb=" N GLU G 399 " --> pdb=" O SER G 395 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG G 400 " --> pdb=" O ASP G 396 " (cutoff:3.500A) Processing helix chain 'G' and resid 410 through 416 Processing helix chain 'G' and resid 426 through 437 Processing helix chain 'G' and resid 466 through 476 Processing helix chain 'G' and resid 512 through 515 No H-bonds generated for 'chain 'G' and resid 512 through 515' Processing helix chain 'G' and resid 526 through 528 No H-bonds generated for 'chain 'G' and resid 526 through 528' Processing helix chain 'G' and resid 531 through 543 removed outlier: 4.244A pdb=" N GLU G 542 " --> pdb=" O HIS G 538 " (cutoff:3.500A) Processing helix chain 'G' and resid 588 through 593 Processing helix chain 'G' and resid 606 through 622 removed outlier: 3.618A pdb=" N GLU G 610 " --> pdb=" O ARG G 606 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS G 611 " --> pdb=" O ASP G 607 " (cutoff:3.500A) Processing helix chain 'G' and resid 635 through 647 removed outlier: 3.563A pdb=" N THR G 647 " --> pdb=" O ALA G 643 " (cutoff:3.500A) Processing helix chain 'G' and resid 654 through 674 Processing helix chain 'G' and resid 686 through 702 Processing helix chain 'G' and resid 710 through 729 removed outlier: 3.888A pdb=" N LYS G 724 " --> pdb=" O VAL G 720 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N SER G 726 " --> pdb=" O VAL G 722 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N LEU G 727 " --> pdb=" O SER G 723 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '2' and resid 241 through 245 removed outlier: 6.506A pdb=" N HIS 2 294 " --> pdb=" O LEU 2 242 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL 2 244 " --> pdb=" O HIS 2 294 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ARG 2 296 " --> pdb=" O VAL 2 244 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain '2' and resid 423 through 430 removed outlier: 3.774A pdb=" N SER 2 316 " --> pdb=" O TYR 2 430 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR 2 389 " --> pdb=" O THR 2 325 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ARG 2 327 " --> pdb=" O ARG 2 387 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ARG 2 387 " --> pdb=" O ARG 2 327 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N THR 2 449 " --> pdb=" O HIS 2 405 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLU 2 407 " --> pdb=" O THR 2 449 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR 2 427 " --> pdb=" O ASN 2 454 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ILE 2 456 " --> pdb=" O GLU 2 425 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLU 2 425 " --> pdb=" O ILE 2 456 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '2' and resid 339 through 341 Processing sheet with id= D, first strand: chain '2' and resid 525 through 527 Processing sheet with id= E, first strand: chain '2' and resid 679 through 683 removed outlier: 6.375A pdb=" N GLY 2 602 " --> pdb=" O SER 2 645 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE 2 647 " --> pdb=" O GLY 2 602 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N CYS 2 604 " --> pdb=" O ILE 2 647 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ALA 2 649 " --> pdb=" O CYS 2 604 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE 2 606 " --> pdb=" O ALA 2 649 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '2' and resid 579 through 582 Processing sheet with id= G, first strand: chain '2' and resid 628 through 633 Processing sheet with id= H, first strand: chain '2' and resid 331 through 336 removed outlier: 6.720A pdb=" N VAL 2 381 " --> pdb=" O LYS 2 335 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '3' and resid 95 through 99 removed outlier: 6.941A pdb=" N LYS 3 154 " --> pdb=" O ILE 3 96 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ILE 3 98 " --> pdb=" O LYS 3 154 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N SER 3 156 " --> pdb=" O ILE 3 98 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain '3' and resid 273 through 278 removed outlier: 3.931A pdb=" N LYS 3 188 " --> pdb=" O THR 3 257 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLN 3 259 " --> pdb=" O VAL 3 186 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N VAL 3 186 " --> pdb=" O GLN 3 259 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS 3 178 " --> pdb=" O PHE 3 298 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG 3 291 " --> pdb=" O LEU 3 329 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL 3 297 " --> pdb=" O GLY 3 323 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLY 3 323 " --> pdb=" O VAL 3 297 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LYS 3 299 " --> pdb=" O ILE 3 321 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ILE 3 321 " --> pdb=" O LYS 3 299 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU 3 301 " --> pdb=" O THR 3 319 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N THR 3 319 " --> pdb=" O LEU 3 301 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '3' and resid 208 through 213 Processing sheet with id= L, first strand: chain '3' and resid 545 through 549 removed outlier: 3.528A pdb=" N GLY 3 409 " --> pdb=" O ALA 3 516 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N GLY 3 468 " --> pdb=" O SER 3 511 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ILE 3 513 " --> pdb=" O GLY 3 468 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL 3 470 " --> pdb=" O ILE 3 513 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ALA 3 515 " --> pdb=" O VAL 3 470 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ILE 3 472 " --> pdb=" O ALA 3 515 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '3' and resid 444 through 448 Processing sheet with id= N, first strand: chain '3' and resid 494 through 498 Processing sheet with id= O, first strand: chain '3' and resid 193 through 198 removed outlier: 6.762A pdb=" N THR 3 249 " --> pdb=" O ILE 3 197 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '4' and resid 240 through 244 removed outlier: 6.965A pdb=" N LYS 4 302 " --> pdb=" O LEU 4 241 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N LEU 4 243 " --> pdb=" O LYS 4 302 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ARG 4 304 " --> pdb=" O LEU 4 243 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain '4' and resid 414 through 420 removed outlier: 3.786A pdb=" N ARG 4 334 " --> pdb=" O LYS 4 398 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLN 4 400 " --> pdb=" O VAL 4 332 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N VAL 4 332 " --> pdb=" O GLN 4 400 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N THR 4 438 " --> pdb=" O VAL 4 463 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL 4 463 " --> pdb=" O THR 4 438 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ARG 4 440 " --> pdb=" O VAL 4 461 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N VAL 4 461 " --> pdb=" O ARG 4 440 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE 4 442 " --> pdb=" O THR 4 459 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N THR 4 459 " --> pdb=" O ILE 4 442 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain '4' and resid 355 through 359 Processing sheet with id= S, first strand: chain '4' and resid 704 through 708 Processing sheet with id= T, first strand: chain '4' and resid 603 through 607 Processing sheet with id= U, first strand: chain '4' and resid 653 through 657 Processing sheet with id= V, first strand: chain '4' and resid 339 through 344 removed outlier: 7.046A pdb=" N SER 4 390 " --> pdb=" O LYS 4 343 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain '5' and resid 60 through 64 removed outlier: 6.386A pdb=" N GLN 5 136 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL 5 63 " --> pdb=" O GLN 5 136 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE 5 138 " --> pdb=" O VAL 5 63 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain '5' and resid 291 through 297 removed outlier: 6.752A pdb=" N LYS 5 257 " --> pdb=" O ILE 5 167 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N THR 5 169 " --> pdb=" O PHE 5 255 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N PHE 5 255 " --> pdb=" O THR 5 169 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N THR 5 275 " --> pdb=" O PRO 5 326 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ASP 5 279 " --> pdb=" O ILE 5 330 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N GLY 5 332 " --> pdb=" O ASP 5 279 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL 5 295 " --> pdb=" O LEU 5 331 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE 5 333 " --> pdb=" O THR 5 293 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR 5 293 " --> pdb=" O ILE 5 333 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain '5' and resid 173 through 176 Processing sheet with id= Z, first strand: chain '5' and resid 189 through 193 removed outlier: 4.521A pdb=" N SER 5 180 " --> pdb=" O ILE 5 244 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain '5' and resid 552 through 556 Processing sheet with id= AB, first strand: chain '5' and resid 501 through 505 Processing sheet with id= AC, first strand: chain '5' and resid 452 through 455 removed outlier: 3.696A pdb=" N GLY 5 466 " --> pdb=" O SER 5 452 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLN 5 454 " --> pdb=" O LEU 5 464 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU 5 464 " --> pdb=" O GLN 5 454 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain '6' and resid 150 through 154 removed outlier: 6.406A pdb=" N GLN 6 264 " --> pdb=" O ILE 6 151 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ILE 6 153 " --> pdb=" O GLN 6 264 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N SER 6 266 " --> pdb=" O ILE 6 153 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain '6' and resid 394 through 400 removed outlier: 6.753A pdb=" N ARG 6 360 " --> pdb=" O THR 6 295 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N THR 6 297 " --> pdb=" O LYS 6 358 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LYS 6 358 " --> pdb=" O THR 6 297 " (cutoff:3.500A) removed outlier: 14.269A pdb=" N TYR 6 450 " --> pdb=" O THR 6 376 " (cutoff:3.500A) removed outlier: 12.225A pdb=" N ASP 6 378 " --> pdb=" O TYR 6 450 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ILE 6 452 " --> pdb=" O ASP 6 378 " (cutoff:3.500A) removed outlier: 9.258A pdb=" N ILE 6 380 " --> pdb=" O ILE 6 452 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE 6 454 " --> pdb=" O ILE 6 380 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ARG 6 382 " --> pdb=" O PHE 6 454 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ALA 6 456 " --> pdb=" O ARG 6 382 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR 6 398 " --> pdb=" O CYS 6 457 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL 6 459 " --> pdb=" O LYS 6 396 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LYS 6 396 " --> pdb=" O VAL 6 459 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N SER 6 461 " --> pdb=" O ARG 6 394 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ARG 6 394 " --> pdb=" O SER 6 461 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain '6' and resid 308 through 311 removed outlier: 4.838A pdb=" N SER 6 308 " --> pdb=" O ASN 6 347 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain '6' and resid 418 through 420 Processing sheet with id= AH, first strand: chain '6' and resid 711 through 715 removed outlier: 3.925A pdb=" N GLY 6 575 " --> pdb=" O ALA 6 682 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL 6 596 " --> pdb=" O CYS 6 637 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ASP 6 639 " --> pdb=" O VAL 6 596 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR 6 598 " --> pdb=" O ASP 6 639 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain '6' and resid 610 through 614 Processing sheet with id= AJ, first strand: chain '6' and resid 660 through 663 Processing sheet with id= AK, first strand: chain '6' and resid 301 through 306 removed outlier: 6.828A pdb=" N ARG 6 352 " --> pdb=" O TYR 6 305 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain '7' and resid 77 through 81 removed outlier: 6.150A pdb=" N PHE 7 201 " --> pdb=" O VAL 7 78 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ILE 7 80 " --> pdb=" O PHE 7 201 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR 7 203 " --> pdb=" O ILE 7 80 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain '7' and resid 330 through 336 removed outlier: 3.825A pdb=" N ARG 7 247 " --> pdb=" O LYS 7 314 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLN 7 316 " --> pdb=" O ILE 7 245 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ILE 7 245 " --> pdb=" O GLN 7 316 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE 7 354 " --> pdb=" O ALA 7 378 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ALA 7 378 " --> pdb=" O ILE 7 354 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU 7 356 " --> pdb=" O LEU 7 376 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU 7 376 " --> pdb=" O LEU 7 356 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ALA 7 358 " --> pdb=" O THR 7 374 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N THR 7 374 " --> pdb=" O ALA 7 358 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain '7' and resid 268 through 272 removed outlier: 4.466A pdb=" N ALA 7 259 " --> pdb=" O SER 7 301 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain '7' and resid 596 through 600 Processing sheet with id= AP, first strand: chain '7' and resid 495 through 500 Processing sheet with id= AQ, first strand: chain '7' and resid 545 through 549 Processing sheet with id= AR, first strand: chain '7' and resid 252 through 257 removed outlier: 6.972A pdb=" N LYS 7 306 " --> pdb=" O GLU 7 256 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'B' and resid 241 through 245 removed outlier: 6.502A pdb=" N HIS B 294 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL B 244 " --> pdb=" O HIS B 294 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ARG B 296 " --> pdb=" O VAL B 244 " (cutoff:3.500A) No H-bonds generated for sheet with id= AS Processing sheet with id= AT, first strand: chain 'B' and resid 423 through 430 removed outlier: 3.773A pdb=" N SER B 316 " --> pdb=" O TYR B 430 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR B 389 " --> pdb=" O THR B 325 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG B 327 " --> pdb=" O ARG B 387 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ARG B 387 " --> pdb=" O ARG B 327 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N THR B 449 " --> pdb=" O HIS B 405 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLU B 407 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR B 427 " --> pdb=" O ASN B 454 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ILE B 456 " --> pdb=" O GLU B 425 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLU B 425 " --> pdb=" O ILE B 456 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'B' and resid 339 through 341 Processing sheet with id= AV, first strand: chain 'B' and resid 525 through 527 Processing sheet with id= AW, first strand: chain 'B' and resid 679 through 683 removed outlier: 6.347A pdb=" N GLY B 602 " --> pdb=" O SER B 645 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE B 647 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N CYS B 604 " --> pdb=" O ILE B 647 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ALA B 649 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE B 606 " --> pdb=" O ALA B 649 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'B' and resid 579 through 582 Processing sheet with id= AY, first strand: chain 'B' and resid 628 through 633 Processing sheet with id= AZ, first strand: chain 'B' and resid 331 through 336 removed outlier: 6.722A pdb=" N VAL B 381 " --> pdb=" O LYS B 335 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'C' and resid 95 through 99 removed outlier: 6.930A pdb=" N LYS C 154 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE C 98 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N SER C 156 " --> pdb=" O ILE C 98 " (cutoff:3.500A) No H-bonds generated for sheet with id= BA Processing sheet with id= BB, first strand: chain 'C' and resid 273 through 278 removed outlier: 4.037A pdb=" N LYS C 188 " --> pdb=" O THR C 257 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN C 259 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N VAL C 186 " --> pdb=" O GLN C 259 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS C 178 " --> pdb=" O PHE C 298 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG C 291 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL C 297 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N GLY C 323 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LYS C 299 " --> pdb=" O ILE C 321 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ILE C 321 " --> pdb=" O LYS C 299 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LEU C 301 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N THR C 319 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'C' and resid 208 through 213 Processing sheet with id= BD, first strand: chain 'C' and resid 545 through 549 removed outlier: 6.536A pdb=" N GLY C 468 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ILE C 513 " --> pdb=" O GLY C 468 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL C 470 " --> pdb=" O ILE C 513 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ALA C 515 " --> pdb=" O VAL C 470 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE C 472 " --> pdb=" O ALA C 515 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'C' and resid 444 through 448 Processing sheet with id= BF, first strand: chain 'C' and resid 494 through 498 Processing sheet with id= BG, first strand: chain 'C' and resid 193 through 198 removed outlier: 6.762A pdb=" N THR C 249 " --> pdb=" O ILE C 197 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'D' and resid 240 through 244 removed outlier: 6.959A pdb=" N LYS D 302 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N LEU D 243 " --> pdb=" O LYS D 302 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ARG D 304 " --> pdb=" O LEU D 243 " (cutoff:3.500A) No H-bonds generated for sheet with id= BH Processing sheet with id= BI, first strand: chain 'D' and resid 414 through 420 removed outlier: 3.775A pdb=" N ARG D 334 " --> pdb=" O LYS D 398 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLN D 400 " --> pdb=" O VAL D 332 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N VAL D 332 " --> pdb=" O GLN D 400 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR D 438 " --> pdb=" O VAL D 463 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N VAL D 463 " --> pdb=" O THR D 438 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ARG D 440 " --> pdb=" O VAL D 461 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N VAL D 461 " --> pdb=" O ARG D 440 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE D 442 " --> pdb=" O THR D 459 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N THR D 459 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'D' and resid 355 through 359 Processing sheet with id= BK, first strand: chain 'D' and resid 704 through 708 Processing sheet with id= BL, first strand: chain 'D' and resid 603 through 607 Processing sheet with id= BM, first strand: chain 'D' and resid 653 through 657 Processing sheet with id= BN, first strand: chain 'D' and resid 339 through 344 removed outlier: 7.023A pdb=" N SER D 390 " --> pdb=" O LYS D 343 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'E' and resid 60 through 64 removed outlier: 6.477A pdb=" N GLN E 136 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N VAL E 63 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE E 138 " --> pdb=" O VAL E 63 " (cutoff:3.500A) No H-bonds generated for sheet with id= BO Processing sheet with id= BP, first strand: chain 'E' and resid 291 through 297 removed outlier: 6.656A pdb=" N LYS E 257 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR E 169 " --> pdb=" O PHE E 255 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE E 255 " --> pdb=" O THR E 169 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N THR E 275 " --> pdb=" O PRO E 326 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ASP E 279 " --> pdb=" O ILE E 330 " (cutoff:3.500A) removed outlier: 8.802A pdb=" N GLY E 332 " --> pdb=" O ASP E 279 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL E 295 " --> pdb=" O LEU E 331 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE E 333 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR E 293 " --> pdb=" O ILE E 333 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'E' and resid 173 through 176 Processing sheet with id= BR, first strand: chain 'E' and resid 189 through 193 removed outlier: 4.521A pdb=" N SER E 180 " --> pdb=" O ILE E 244 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'E' and resid 552 through 556 Processing sheet with id= BT, first strand: chain 'E' and resid 501 through 505 Processing sheet with id= BU, first strand: chain 'E' and resid 452 through 455 removed outlier: 3.648A pdb=" N GLY E 466 " --> pdb=" O SER E 452 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLN E 454 " --> pdb=" O LEU E 464 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N LEU E 464 " --> pdb=" O GLN E 454 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'F' and resid 150 through 154 removed outlier: 6.413A pdb=" N GLN F 264 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ILE F 153 " --> pdb=" O GLN F 264 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N SER F 266 " --> pdb=" O ILE F 153 " (cutoff:3.500A) No H-bonds generated for sheet with id= BV Processing sheet with id= BW, first strand: chain 'F' and resid 394 through 400 removed outlier: 6.748A pdb=" N ARG F 360 " --> pdb=" O THR F 295 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N THR F 297 " --> pdb=" O LYS F 358 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LYS F 358 " --> pdb=" O THR F 297 " (cutoff:3.500A) removed outlier: 14.294A pdb=" N TYR F 450 " --> pdb=" O THR F 376 " (cutoff:3.500A) removed outlier: 12.253A pdb=" N ASP F 378 " --> pdb=" O TYR F 450 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ILE F 452 " --> pdb=" O ASP F 378 " (cutoff:3.500A) removed outlier: 9.256A pdb=" N ILE F 380 " --> pdb=" O ILE F 452 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE F 454 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N ARG F 382 " --> pdb=" O PHE F 454 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ALA F 456 " --> pdb=" O ARG F 382 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N THR F 398 " --> pdb=" O CYS F 457 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N VAL F 459 " --> pdb=" O LYS F 396 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LYS F 396 " --> pdb=" O VAL F 459 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N SER F 461 " --> pdb=" O ARG F 394 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ARG F 394 " --> pdb=" O SER F 461 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'F' and resid 308 through 311 removed outlier: 4.820A pdb=" N SER F 308 " --> pdb=" O ASN F 347 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'F' and resid 418 through 420 Processing sheet with id= BZ, first strand: chain 'F' and resid 711 through 715 removed outlier: 3.896A pdb=" N GLY F 575 " --> pdb=" O ALA F 682 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL F 596 " --> pdb=" O CYS F 637 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASP F 639 " --> pdb=" O VAL F 596 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR F 598 " --> pdb=" O ASP F 639 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'F' and resid 610 through 614 Processing sheet with id= CB, first strand: chain 'F' and resid 660 through 663 Processing sheet with id= CC, first strand: chain 'F' and resid 301 through 306 removed outlier: 6.824A pdb=" N ARG F 352 " --> pdb=" O TYR F 305 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'G' and resid 77 through 81 removed outlier: 6.143A pdb=" N PHE G 201 " --> pdb=" O VAL G 78 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ILE G 80 " --> pdb=" O PHE G 201 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N TYR G 203 " --> pdb=" O ILE G 80 " (cutoff:3.500A) No H-bonds generated for sheet with id= CD Processing sheet with id= CE, first strand: chain 'G' and resid 330 through 336 removed outlier: 3.795A pdb=" N ARG G 247 " --> pdb=" O LYS G 314 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLN G 316 " --> pdb=" O ILE G 245 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ILE G 245 " --> pdb=" O GLN G 316 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE G 354 " --> pdb=" O ALA G 378 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ALA G 378 " --> pdb=" O ILE G 354 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU G 356 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU G 376 " --> pdb=" O LEU G 356 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ALA G 358 " --> pdb=" O THR G 374 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N THR G 374 " --> pdb=" O ALA G 358 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'G' and resid 268 through 272 removed outlier: 4.441A pdb=" N ALA G 259 " --> pdb=" O SER G 301 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain 'G' and resid 596 through 600 Processing sheet with id= CH, first strand: chain 'G' and resid 495 through 500 Processing sheet with id= CI, first strand: chain 'G' and resid 545 through 549 Processing sheet with id= CJ, first strand: chain 'G' and resid 252 through 257 removed outlier: 6.956A pdb=" N LYS G 306 " --> pdb=" O GLU G 256 " (cutoff:3.500A) 2375 hydrogen bonds defined for protein. 6750 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: 24.47 Time building geometry restraints manager: 19.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 20953 1.35 - 1.50: 15433 1.50 - 1.65: 26584 1.65 - 1.80: 241 1.80 - 1.95: 231 Bond restraints: 63442 Sorted by residual: bond pdb=" CG PRO F 745 " pdb=" CD PRO F 745 " ideal model delta sigma weight residual 1.503 1.388 0.115 3.40e-02 8.65e+02 1.15e+01 bond pdb=" CB CYS 7 474 " pdb=" SG CYS 7 474 " ideal model delta sigma weight residual 1.808 1.731 0.077 3.30e-02 9.18e+02 5.38e+00 bond pdb=" CB CYS G 474 " pdb=" SG CYS G 474 " ideal model delta sigma weight residual 1.808 1.734 0.074 3.30e-02 9.18e+02 4.98e+00 bond pdb=" CB PRO G 632 " pdb=" CG PRO G 632 " ideal model delta sigma weight residual 1.492 1.603 -0.111 5.00e-02 4.00e+02 4.96e+00 bond pdb=" CB PRO F 745 " pdb=" CG PRO F 745 " ideal model delta sigma weight residual 1.492 1.603 -0.111 5.00e-02 4.00e+02 4.90e+00 ... (remaining 63437 not shown) Histogram of bond angle deviations from ideal: 94.23 - 102.64: 283 102.64 - 111.06: 23491 111.06 - 119.47: 30896 119.47 - 127.89: 30853 127.89 - 136.30: 333 Bond angle restraints: 85856 Sorted by residual: angle pdb=" N PRO F 745 " pdb=" CD PRO F 745 " pdb=" CG PRO F 745 " ideal model delta sigma weight residual 103.20 94.23 8.97 1.50e+00 4.44e-01 3.58e+01 angle pdb=" CA PRO G 632 " pdb=" N PRO G 632 " pdb=" CD PRO G 632 " ideal model delta sigma weight residual 112.00 104.40 7.60 1.40e+00 5.10e-01 2.95e+01 angle pdb=" CA PRO F 745 " pdb=" N PRO F 745 " pdb=" CD PRO F 745 " ideal model delta sigma weight residual 112.00 105.05 6.95 1.40e+00 5.10e-01 2.46e+01 angle pdb=" N GLN F 833 " pdb=" CA GLN F 833 " pdb=" CB GLN F 833 " ideal model delta sigma weight residual 110.42 117.76 -7.34 1.62e+00 3.81e-01 2.05e+01 angle pdb=" CA GLN F 833 " pdb=" CB GLN F 833 " pdb=" CG GLN F 833 " ideal model delta sigma weight residual 114.10 123.15 -9.05 2.00e+00 2.50e-01 2.05e+01 ... (remaining 85851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 38404 35.44 - 70.87: 585 70.87 - 106.31: 59 106.31 - 141.74: 2 141.74 - 177.18: 2 Dihedral angle restraints: 39052 sinusoidal: 16016 harmonic: 23036 Sorted by residual: dihedral pdb=" O2A ADP 32001 " pdb=" O3A ADP 32001 " pdb=" PA ADP 32001 " pdb=" PB ADP 32001 " ideal model delta sinusoidal sigma weight residual -60.00 67.61 -127.61 1 2.00e+01 2.50e-03 3.86e+01 dihedral pdb=" O2A ADP C2001 " pdb=" O3A ADP C2001 " pdb=" PA ADP C2001 " pdb=" PB ADP C2001 " ideal model delta sinusoidal sigma weight residual -60.00 67.00 -127.00 1 2.00e+01 2.50e-03 3.84e+01 dihedral pdb=" CA ARG E 5 " pdb=" C ARG E 5 " pdb=" N PRO E 6 " pdb=" CA PRO E 6 " ideal model delta harmonic sigma weight residual 180.00 152.59 27.41 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 39049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 9034 0.085 - 0.170: 906 0.170 - 0.255: 21 0.255 - 0.340: 1 0.340 - 0.425: 2 Chirality restraints: 9964 Sorted by residual: chirality pdb=" CB VAL F 403 " pdb=" CA VAL F 403 " pdb=" CG1 VAL F 403 " pdb=" CG2 VAL F 403 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" CB VAL 6 403 " pdb=" CA VAL 6 403 " pdb=" CG1 VAL 6 403 " pdb=" CG2 VAL 6 403 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" CB ILE E 646 " pdb=" CA ILE E 646 " pdb=" CG1 ILE E 646 " pdb=" CG2 ILE E 646 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.89e+00 ... (remaining 9961 not shown) Planarity restraints: 11040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 631 " -0.081 5.00e-02 4.00e+02 1.18e-01 2.23e+01 pdb=" N PRO G 632 " 0.204 5.00e-02 4.00e+02 pdb=" CA PRO G 632 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO G 632 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO F 744 " 0.073 5.00e-02 4.00e+02 1.06e-01 1.79e+01 pdb=" N PRO F 745 " -0.183 5.00e-02 4.00e+02 pdb=" CA PRO F 745 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO F 745 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR 7 631 " 0.062 5.00e-02 4.00e+02 9.24e-02 1.37e+01 pdb=" N PRO 7 632 " -0.160 5.00e-02 4.00e+02 pdb=" CA PRO 7 632 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO 7 632 " 0.050 5.00e-02 4.00e+02 ... (remaining 11037 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 598 2.61 - 3.19: 52198 3.19 - 3.76: 99579 3.76 - 4.33: 140412 4.33 - 4.90: 227041 Nonbonded interactions: 519828 Sorted by model distance: nonbonded pdb=" O2G AGS 62001 " pdb="MG MG 62002 " model vdw 2.042 2.170 nonbonded pdb=" O2G AGS F2001 " pdb="MG MG F2002 " model vdw 2.052 2.170 nonbonded pdb=" O2G AGS G2001 " pdb="MG MG G2002 " model vdw 2.053 2.170 nonbonded pdb=" OG SER D 575 " pdb="MG MG D2002 " model vdw 2.054 2.170 nonbonded pdb=" OG SER B 550 " pdb="MG MG B2002 " model vdw 2.065 2.170 ... (remaining 519823 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '2' selection = chain 'B' } ncs_group { reference = chain '3' selection = chain 'C' } ncs_group { reference = chain '4' selection = chain 'D' } ncs_group { reference = chain '5' selection = chain 'E' } ncs_group { reference = chain '6' selection = chain 'F' } ncs_group { reference = chain '7' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 10 6.06 5 P 34 5.49 5 Mg 12 5.21 5 S 296 5.16 5 C 39156 2.51 5 N 10892 2.21 5 O 12060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 12.890 Check model and map are aligned: 0.680 Process input model: 131.310 Find NCS groups from input model: 6.220 Set up NCS constraints: 0.610 Set refine NCS operators: 0.000 Set scattering table: 0.600 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 165.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 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 : 0.004 0.115 63442 Z= 0.261 Angle : 0.773 14.399 85856 Z= 0.431 Chirality : 0.048 0.425 9964 Planarity : 0.006 0.118 11040 Dihedral : 13.850 177.179 24094 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.09), residues: 7788 helix: -0.16 (0.09), residues: 3164 sheet: 0.28 (0.13), residues: 1496 loop : -0.24 (0.10), residues: 3128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1159 residues out of total 6964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1156 time to evaluate : 5.557 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 5 residues processed: 1159 average time/residue: 1.6420 time to fit residues: 2378.9669 Evaluate side-chains 773 residues out of total 6964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 768 time to evaluate : 5.616 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 1 average time/residue: 0.4664 time to fit residues: 8.5315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 658 optimal weight: 7.9990 chunk 591 optimal weight: 0.7980 chunk 328 optimal weight: 0.5980 chunk 201 optimal weight: 0.6980 chunk 398 optimal weight: 3.9990 chunk 315 optimal weight: 7.9990 chunk 611 optimal weight: 2.9990 chunk 236 optimal weight: 4.9990 chunk 371 optimal weight: 1.9990 chunk 455 optimal weight: 7.9990 chunk 708 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 433 ASN 2 626 GLN 2 710 ASN ** 3 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 365 GLN 3 417 GLN ** 3 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 380 ASN 4 465 HIS 5 334 GLN 5 363 ASN 5 454 GLN 5 499 GLN 5 560 HIS 5 561 ASN 5 574 ASN 6 182 GLN 6 556 HIS ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 271 GLN 7 538 HIS 7 554 ASN 7 558 ASN B 391 GLN B 433 ASN C 239 ASN ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 GLN ** C 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 ASN D 465 HIS E 363 ASN E 454 GLN E 524 ASN E 560 HIS F 156 GLN F 514 ASN F 556 HIS ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 GLN G 271 GLN G 554 ASN ** G 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 63442 Z= 0.245 Angle : 0.584 12.787 85856 Z= 0.301 Chirality : 0.044 0.277 9964 Planarity : 0.005 0.065 11040 Dihedral : 6.851 173.777 8718 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer Outliers : 2.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.09), residues: 7788 helix: 0.60 (0.09), residues: 3160 sheet: 0.24 (0.13), residues: 1482 loop : -0.10 (0.10), residues: 3146 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1011 residues out of total 6964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 833 time to evaluate : 5.626 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 178 outliers final: 76 residues processed: 929 average time/residue: 1.5937 time to fit residues: 1882.8591 Evaluate side-chains 823 residues out of total 6964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 747 time to evaluate : 5.590 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 45 residues processed: 31 average time/residue: 0.8652 time to fit residues: 47.7811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 393 optimal weight: 0.6980 chunk 219 optimal weight: 1.9990 chunk 589 optimal weight: 3.9990 chunk 482 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 709 optimal weight: 8.9990 chunk 766 optimal weight: 0.0000 chunk 631 optimal weight: 8.9990 chunk 703 optimal weight: 0.8980 chunk 241 optimal weight: 20.0000 chunk 569 optimal weight: 4.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 200 GLN 3 52 ASN ** 3 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 365 GLN ** 3 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 670 GLN ** 3 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 380 ASN 5 363 ASN 5 454 GLN 5 499 GLN 5 524 ASN 6 156 GLN 6 335 ASN 6 514 ASN 6 556 HIS ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 700 ASN B 710 ASN C 52 ASN ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 GLN C 487 HIS D 380 ASN D 483 GLN E 195 ASN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 ASN E 499 GLN E 524 ASN F 156 GLN F 182 GLN F 335 ASN F 514 ASN F 556 HIS ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 271 GLN G 558 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 63442 Z= 0.225 Angle : 0.562 12.582 85856 Z= 0.290 Chirality : 0.043 0.215 9964 Planarity : 0.004 0.056 11040 Dihedral : 6.644 167.196 8718 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer Outliers : 3.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.09), residues: 7788 helix: 0.92 (0.09), residues: 3154 sheet: 0.10 (0.13), residues: 1520 loop : -0.01 (0.10), residues: 3114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1022 residues out of total 6964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 802 time to evaluate : 5.926 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 220 outliers final: 104 residues processed: 939 average time/residue: 1.5836 time to fit residues: 1885.8558 Evaluate side-chains 845 residues out of total 6964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 741 time to evaluate : 5.568 Switching outliers to nearest non-outliers outliers start: 104 outliers final: 65 residues processed: 41 average time/residue: 0.8907 time to fit residues: 60.9303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 701 optimal weight: 0.0770 chunk 533 optimal weight: 2.9990 chunk 368 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 338 optimal weight: 0.8980 chunk 476 optimal weight: 5.9990 chunk 712 optimal weight: 0.6980 chunk 753 optimal weight: 9.9990 chunk 372 optimal weight: 0.4980 chunk 674 optimal weight: 0.0770 chunk 203 optimal weight: 1.9990 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 365 GLN ** 3 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 731 ASN 4 483 GLN 5 363 ASN ** 5 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 524 ASN 6 156 GLN 6 514 ASN 6 556 HIS ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 316 GLN 7 669 GLN B 760 GLN ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 GLN C 487 HIS D 483 GLN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 ASN F 156 GLN F 514 ASN F 556 HIS ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 833 GLN G 297 GLN G 316 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.071 63442 Z= 0.142 Angle : 0.500 11.018 85856 Z= 0.257 Chirality : 0.041 0.166 9964 Planarity : 0.004 0.050 11040 Dihedral : 6.364 167.935 8718 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer Outliers : 2.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.09), residues: 7788 helix: 1.21 (0.09), residues: 3156 sheet: 0.16 (0.13), residues: 1506 loop : 0.10 (0.11), residues: 3126 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 6964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 781 time to evaluate : 5.641 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 183 outliers final: 88 residues processed: 898 average time/residue: 1.5712 time to fit residues: 1795.6734 Evaluate side-chains 814 residues out of total 6964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 726 time to evaluate : 5.647 Switching outliers to nearest non-outliers outliers start: 88 outliers final: 73 residues processed: 16 average time/residue: 0.8412 time to fit residues: 28.4229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 627 optimal weight: 1.9990 chunk 427 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 561 optimal weight: 1.9990 chunk 311 optimal weight: 4.9990 chunk 643 optimal weight: 5.9990 chunk 521 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 384 optimal weight: 3.9990 chunk 676 optimal weight: 0.7980 chunk 190 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 239 ASN 3 293 ASN ** 3 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 365 GLN 3 487 HIS 4 483 GLN ** 5 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 524 ASN 6 156 GLN 6 514 ASN 6 556 HIS ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 558 ASN ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 GLN C 487 HIS D 193 ASN D 380 ASN D 483 GLN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 636 ASN F 156 GLN F 514 ASN F 556 HIS ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 291 GLN G 297 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.074 63442 Z= 0.370 Angle : 0.650 14.368 85856 Z= 0.337 Chirality : 0.047 0.239 9964 Planarity : 0.005 0.091 11040 Dihedral : 6.781 161.008 8718 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 3.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.09), residues: 7788 helix: 0.94 (0.09), residues: 3156 sheet: 0.07 (0.13), residues: 1522 loop : -0.08 (0.10), residues: 3110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1039 residues out of total 6964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 778 time to evaluate : 5.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 261 outliers final: 137 residues processed: 949 average time/residue: 1.5860 time to fit residues: 1916.6427 Evaluate side-chains 877 residues out of total 6964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 740 time to evaluate : 5.602 Switching outliers to nearest non-outliers outliers start: 137 outliers final: 103 residues processed: 36 average time/residue: 0.8129 time to fit residues: 52.5412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 253 optimal weight: 0.9990 chunk 678 optimal weight: 10.0000 chunk 149 optimal weight: 0.3980 chunk 442 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 754 optimal weight: 0.7980 chunk 626 optimal weight: 0.6980 chunk 349 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 249 optimal weight: 1.9990 chunk 396 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 293 ASN ** 3 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 365 GLN 3 487 HIS 4 483 GLN 5 235 ASN ** 5 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 617 GLN 6 156 GLN 6 514 ASN 6 556 HIS ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 124 ASN ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 GLN C 487 HIS D 483 GLN E 108 GLN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 156 GLN F 514 ASN F 556 HIS ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 ASN G 291 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 63442 Z= 0.190 Angle : 0.544 12.329 85856 Z= 0.280 Chirality : 0.043 0.190 9964 Planarity : 0.004 0.055 11040 Dihedral : 6.496 160.350 8718 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer Outliers : 3.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.09), residues: 7788 helix: 1.13 (0.09), residues: 3166 sheet: 0.04 (0.13), residues: 1522 loop : -0.01 (0.11), residues: 3100 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 976 residues out of total 6964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 764 time to evaluate : 5.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 212 outliers final: 127 residues processed: 909 average time/residue: 1.6262 time to fit residues: 1878.1434 Evaluate side-chains 855 residues out of total 6964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 728 time to evaluate : 5.604 Switching outliers to nearest non-outliers outliers start: 127 outliers final: 101 residues processed: 28 average time/residue: 0.7054 time to fit residues: 39.3519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 727 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 429 optimal weight: 0.7980 chunk 551 optimal weight: 2.9990 chunk 427 optimal weight: 4.9990 chunk 635 optimal weight: 3.9990 chunk 421 optimal weight: 9.9990 chunk 751 optimal weight: 6.9990 chunk 470 optimal weight: 3.9990 chunk 458 optimal weight: 3.9990 chunk 347 optimal weight: 4.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 365 GLN 3 487 HIS 4 483 GLN 5 235 ASN ** 5 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 617 GLN 6 156 GLN 6 514 ASN 6 556 HIS ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 GLN B 856 GLN ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 GLN C 487 HIS D 483 GLN E 145 GLN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 156 GLN F 514 ASN F 556 HIS ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 297 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.088 63442 Z= 0.293 Angle : 0.608 13.695 85856 Z= 0.314 Chirality : 0.045 0.214 9964 Planarity : 0.005 0.067 11040 Dihedral : 6.653 157.787 8718 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 3.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.09), residues: 7788 helix: 1.04 (0.09), residues: 3158 sheet: 0.04 (0.13), residues: 1498 loop : -0.07 (0.10), residues: 3132 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 999 residues out of total 6964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 757 time to evaluate : 6.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 242 outliers final: 142 residues processed: 922 average time/residue: 1.6034 time to fit residues: 1906.1640 Evaluate side-chains 880 residues out of total 6964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 738 time to evaluate : 5.664 Switching outliers to nearest non-outliers outliers start: 142 outliers final: 111 residues processed: 33 average time/residue: 0.9162 time to fit residues: 53.3600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 465 optimal weight: 3.9990 chunk 300 optimal weight: 4.9990 chunk 449 optimal weight: 4.9990 chunk 226 optimal weight: 0.8980 chunk 147 optimal weight: 0.7980 chunk 145 optimal weight: 5.9990 chunk 477 optimal weight: 0.6980 chunk 512 optimal weight: 1.9990 chunk 371 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 590 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 365 GLN 3 487 HIS ** 5 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 524 ASN 5 617 GLN 6 156 GLN 6 514 ASN 6 556 HIS ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 GLN ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 365 GLN C 487 HIS D 483 GLN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 617 GLN F 156 GLN F 514 ASN F 556 HIS ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 63442 Z= 0.200 Angle : 0.551 12.387 85856 Z= 0.284 Chirality : 0.043 0.222 9964 Planarity : 0.004 0.056 11040 Dihedral : 6.474 155.633 8718 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer Outliers : 2.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.09), residues: 7788 helix: 1.16 (0.09), residues: 3170 sheet: -0.01 (0.13), residues: 1516 loop : -0.02 (0.11), residues: 3102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 948 residues out of total 6964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 762 time to evaluate : 5.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 186 outliers final: 124 residues processed: 898 average time/residue: 1.5863 time to fit residues: 1822.0601 Evaluate side-chains 859 residues out of total 6964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 735 time to evaluate : 5.636 Switching outliers to nearest non-outliers outliers start: 124 outliers final: 107 residues processed: 18 average time/residue: 0.7097 time to fit residues: 28.5519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 683 optimal weight: 0.7980 chunk 720 optimal weight: 0.6980 chunk 657 optimal weight: 5.9990 chunk 700 optimal weight: 9.9990 chunk 421 optimal weight: 8.9990 chunk 305 optimal weight: 0.7980 chunk 550 optimal weight: 0.3980 chunk 214 optimal weight: 1.9990 chunk 633 optimal weight: 5.9990 chunk 662 optimal weight: 5.9990 chunk 698 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 487 HIS ** 5 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 617 GLN 6 156 GLN 6 514 ASN 6 556 HIS ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 GLN ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 HIS D 483 GLN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 617 GLN F 156 GLN F 514 ASN F 556 HIS ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 720 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 63442 Z= 0.167 Angle : 0.526 11.858 85856 Z= 0.270 Chirality : 0.042 0.183 9964 Planarity : 0.004 0.055 11040 Dihedral : 6.305 155.723 8718 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 2.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.09), residues: 7788 helix: 1.27 (0.09), residues: 3170 sheet: -0.00 (0.13), residues: 1526 loop : 0.03 (0.11), residues: 3092 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 6964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 764 time to evaluate : 5.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 164 outliers final: 119 residues processed: 889 average time/residue: 1.6260 time to fit residues: 1843.2891 Evaluate side-chains 855 residues out of total 6964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 736 time to evaluate : 5.597 Switching outliers to nearest non-outliers outliers start: 119 outliers final: 103 residues processed: 16 average time/residue: 0.6172 time to fit residues: 24.3981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 460 optimal weight: 3.9990 chunk 740 optimal weight: 0.8980 chunk 452 optimal weight: 0.8980 chunk 351 optimal weight: 1.9990 chunk 514 optimal weight: 2.9990 chunk 777 optimal weight: 3.9990 chunk 715 optimal weight: 0.2980 chunk 618 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 477 optimal weight: 7.9990 chunk 379 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 200 GLN 2 626 GLN ** 3 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 487 HIS 5 145 GLN ** 5 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 524 ASN 5 617 GLN 6 156 GLN 6 514 ASN 6 556 HIS ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 GLN ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 HIS D 380 ASN D 483 GLN E 145 GLN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 617 GLN F 156 GLN F 514 ASN F 556 HIS ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 720 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 63442 Z= 0.176 Angle : 0.536 15.941 85856 Z= 0.275 Chirality : 0.042 0.183 9964 Planarity : 0.004 0.056 11040 Dihedral : 6.276 155.645 8718 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer Outliers : 2.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.76 (0.09), residues: 7788 helix: 1.31 (0.09), residues: 3166 sheet: 0.02 (0.13), residues: 1528 loop : 0.06 (0.11), residues: 3094 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15576 Ramachandran restraints generated. 7788 Oldfield, 0 Emsley, 7788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 892 residues out of total 6964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 749 time to evaluate : 5.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 143 outliers final: 116 residues processed: 864 average time/residue: 1.6196 time to fit residues: 1786.8027 Evaluate side-chains 835 residues out of total 6964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 719 time to evaluate : 5.522 Switching outliers to nearest non-outliers outliers start: 116 outliers final: 107 residues processed: 10 average time/residue: 0.7740 time to fit residues: 19.8968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 491 optimal weight: 0.9990 chunk 659 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 570 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 171 optimal weight: 0.0370 chunk 619 optimal weight: 7.9990 chunk 259 optimal weight: 8.9990 chunk 636 optimal weight: 2.9990 chunk 78 optimal weight: 0.0970 chunk 114 optimal weight: 6.9990 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 528 ASN ** 3 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 487 HIS 5 145 GLN ** 5 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 584 GLN ** 5 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 156 GLN 6 556 HIS ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 HIS B 856 GLN ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 HIS D 483 GLN E 145 GLN ** E 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 617 GLN F 156 GLN F 514 ASN F 556 HIS ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 720 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.174055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.133761 restraints weight = 65291.333| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.62 r_work: 0.3333 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 63442 Z= 0.192 Angle : 0.547 15.735 85856 Z= 0.280 Chirality : 0.042 0.186 9964 Planarity : 0.004 0.055 11040 Dihedral : 6.302 155.445 8718 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 2.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.73 (0.09), residues: 7788 helix: 1.28 (0.09), residues: 3182 sheet: -0.02 (0.13), residues: 1530 loop : 0.06 (0.11), residues: 3076 =============================================================================== Job complete usr+sys time: 25454.32 seconds wall clock time: 441 minutes 1.51 seconds (26461.51 seconds total)