Starting phenix.real_space_refine on Sat Feb 17 06:47:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v3v_31685/02_2024/7v3v_31685_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v3v_31685/02_2024/7v3v_31685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v3v_31685/02_2024/7v3v_31685.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v3v_31685/02_2024/7v3v_31685.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v3v_31685/02_2024/7v3v_31685_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v3v_31685/02_2024/7v3v_31685_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 11 6.06 5 P 37 5.49 5 Mg 12 5.21 5 S 322 5.16 5 C 42942 2.51 5 N 11897 2.21 5 O 13135 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 510": "OD1" <-> "OD2" Residue "2 ASP 544": "OD1" <-> "OD2" Residue "2 TYR 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 476": "OD1" <-> "OD2" Residue "3 TYR 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 735": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 223": "OE1" <-> "OE2" Residue "4 GLU 297": "OE1" <-> "OE2" Residue "4 ASP 341": "OD1" <-> "OD2" Residue "4 PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 401": "OE1" <-> "OE2" Residue "4 ASP 404": "OD1" <-> "OD2" Residue "4 PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 639": "OD1" <-> "OD2" Residue "4 ASP 703": "OD1" <-> "OD2" Residue "4 ASP 713": "OD1" <-> "OD2" Residue "4 TYR 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 806": "OE1" <-> "OE2" Residue "4 GLU 818": "OE1" <-> "OE2" Residue "5 TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 551": "OD1" <-> "OD2" Residue "6 TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 154": "OD1" <-> "OD2" Residue "6 TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 278": "OD1" <-> "OD2" Residue "6 TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 355": "OD1" <-> "OD2" Residue "6 GLU 363": "OE1" <-> "OE2" Residue "6 GLU 367": "OE1" <-> "OE2" Residue "6 GLU 387": "OE1" <-> "OE2" Residue "6 ASP 393": "OD1" <-> "OD2" Residue "6 ASP 447": "OD1" <-> "OD2" Residue "6 PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 576": "OD1" <-> "OD2" Residue "6 PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 777": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 13": "OD1" <-> "OD2" Residue "7 TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 133": "OD1" <-> "OD2" Residue "7 ASP 140": "OD1" <-> "OD2" Residue "7 ASP 156": "OD1" <-> "OD2" Residue "7 PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 268": "OE1" <-> "OE2" Residue "7 PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 272": "OE1" <-> "OE2" Residue "7 PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ASP 461": "OD1" <-> "OD2" Residue "7 TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 614": "OE1" <-> "OE2" Residue "7 TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 TYR 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 715": "OE1" <-> "OE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 607": "OD1" <-> "OD2" Residue "B ASP 610": "OD1" <-> "OD2" Residue "B ASP 616": "OD1" <-> "OD2" Residue "B PHE 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 782": "OD1" <-> "OD2" Residue "B PHE 803": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 828": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 213": "OD1" <-> "OD2" Residue "C ASP 252": "OD1" <-> "OD2" Residue "C ASP 346": "OD1" <-> "OD2" Residue "C TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 375": "OD1" <-> "OD2" Residue "C ASP 410": "OD1" <-> "OD2" Residue "C ASP 473": "OD1" <-> "OD2" Residue "C ASP 476": "OD1" <-> "OD2" Residue "C GLU 491": "OE1" <-> "OE2" Residue "C ASP 537": "OD1" <-> "OD2" Residue "C TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 735": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 341": "OD1" <-> "OD2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 475": "OD1" <-> "OD2" Residue "D ASP 503": "OD1" <-> "OD2" Residue "D TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 580": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 682": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 693": "OD1" <-> "OD2" Residue "D GLU 745": "OE1" <-> "OE2" Residue "D GLU 806": "OE1" <-> "OE2" Residue "D GLU 820": "OE1" <-> "OE2" Residue "D TYR 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 4": "OD1" <-> "OD2" Residue "E TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 402": "OD1" <-> "OD2" Residue "E ASP 417": "OD1" <-> "OD2" Residue "E GLU 461": "OE1" <-> "OE2" Residue "E ASP 480": "OD1" <-> "OD2" Residue "E ASP 483": "OD1" <-> "OD2" Residue "E TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 141": "OE1" <-> "OE2" Residue "F TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 154": "OD1" <-> "OD2" Residue "F PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 355": "OD1" <-> "OD2" Residue "F ASP 393": "OD1" <-> "OD2" Residue "F ASP 522": "OD1" <-> "OD2" Residue "F ASP 576": "OD1" <-> "OD2" Residue "F ASP 642": "OD1" <-> "OD2" Residue "F TYR 777": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 793": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 20": "OE1" <-> "OE2" Residue "G TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 595": "OD1" <-> "OD2" Residue "G ASP 602": "OD1" <-> "OD2" Residue "G ASP 609": "OD1" <-> "OD2" Residue "G TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 250": "OD1" <-> "OD2" Residue "I TYR 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 330": "OD1" <-> "OD2" Residue "I PHE 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 68356 Number of models: 1 Model: "" Number of chains: 28 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: 5148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5148 Classifications: {'peptide': 659} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 630} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 6 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: 5148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5148 Classifications: {'peptide': 659} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 28, 'TRANS': 630} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 6 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: "H" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3109 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 365} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 2745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2745 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 316} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 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: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 2, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 2, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1302 SG CYS 2 341 137.797 113.558 73.619 1.00 94.42 S ATOM 1325 SG CYS 2 344 141.133 111.696 73.670 1.00 98.04 S ATOM 1483 SG CYS 2 364 139.291 112.361 70.393 1.00 97.74 S ATOM 1504 SG CYS 2 367 138.059 109.733 72.714 1.00100.50 S ATOM 11400 SG CYS 4 349 96.380 119.953 55.220 1.00 56.74 S ATOM 11421 SG CYS 4 352 94.257 118.925 52.404 1.00 58.76 S ATOM 11568 SG CYS 4 371 93.102 118.386 56.084 1.00 64.59 S ATOM 11610 SG CYS 4 376 95.851 116.230 54.313 1.00 69.30 S ATOM 16593 SG CYS 5 183 129.654 111.174 96.201 1.00 44.37 S ATOM 16618 SG CYS 5 186 131.494 107.637 96.994 1.00 46.69 S ATOM 16805 SG CYS 5 211 132.158 109.351 93.970 1.00 46.84 S ATOM 16923 SG CYS 5 236 128.644 108.127 94.330 1.00 56.79 S ATOM 21676 SG CYS 6 311 115.560 116.604 56.697 1.00 99.73 S ATOM 21698 SG CYS 6 314 116.666 114.886 53.859 1.00105.70 S ATOM 21855 SG CYS 6 333 112.718 115.515 54.216 1.00104.73 S ATOM 21889 SG CYS 6 338 114.369 112.889 56.090 1.00112.86 S ATOM 27409 SG CYS 7 262 84.631 120.447 81.144 1.00 37.89 S ATOM 27432 SG CYS 7 265 82.753 118.417 83.695 1.00 37.48 S ATOM 27586 SG CYS 7 284 86.461 119.363 84.201 1.00 41.21 S ATOM 27623 SG CYS 7 289 85.597 116.749 81.680 1.00 44.53 S ATOM 32344 SG CYS B 341 106.128 111.135 73.606 1.00 93.86 S ATOM 32367 SG CYS B 344 102.879 113.184 73.663 1.00 97.46 S ATOM 32525 SG CYS B 364 104.697 112.351 70.388 1.00 97.25 S ATOM 32546 SG CYS B 367 106.022 114.962 72.698 1.00 99.41 S ATOM 42442 SG CYS D 349 147.910 104.545 55.435 1.00 66.80 S ATOM 42463 SG CYS D 352 150.040 105.275 52.442 1.00 69.48 S ATOM 42610 SG CYS D 371 151.282 106.074 56.036 1.00 75.09 S ATOM 42652 SG CYS D 376 148.474 108.113 54.313 1.00 81.78 S ATOM 47635 SG CYS E 183 114.148 113.602 96.155 1.00 45.37 S ATOM 47660 SG CYS E 186 112.298 117.200 96.808 1.00 48.21 S ATOM 47847 SG CYS E 211 111.622 115.407 93.919 1.00 47.15 S ATOM 47965 SG CYS E 236 115.185 116.612 94.262 1.00 57.75 S ATOM 52718 SG CYS F 311 128.771 108.263 56.324 1.00103.79 S ATOM 52740 SG CYS F 314 128.072 111.327 54.284 1.00108.09 S ATOM 52897 SG CYS F 333 131.253 109.050 53.392 1.00108.22 S ATOM 52931 SG CYS F 338 131.359 111.347 55.886 1.00115.91 S ATOM 58451 SG CYS G 262 159.163 104.268 81.323 1.00 40.67 S ATOM 58474 SG CYS G 265 161.083 106.434 83.740 1.00 40.59 S ATOM 58628 SG CYS G 284 157.415 105.501 84.431 1.00 44.82 S ATOM 58665 SG CYS G 289 158.223 108.010 81.780 1.00 47.87 S ATOM 67586 SG CYS I 661 44.578 143.924 74.226 1.00 72.35 S ATOM 67609 SG CYS I 664 45.833 147.532 75.166 1.00 73.65 S Time building chain proxies: 25.68, per 1000 atoms: 0.38 Number of scatterers: 68356 At special positions: 0 Unit cell: (204.58, 225.78, 157.94, 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 11 29.99 S 322 16.00 P 37 15.00 Mg 12 11.99 O 13135 8.00 N 11897 7.00 C 42942 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=2.04 Simple disulfide: pdb=" SG CYS G 474 " - pdb=" SG CYS G 522 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 21.73 Conformation dependent library (CDL) restraints added in 9.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 22003 " pdb="ZN ZN 22003 " - pdb=" SG CYS 2 364 " 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 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 62002 " pdb="ZN ZN 62002 " - pdb=" SG CYS 6 338 " pdb="ZN ZN 62002 " - pdb=" SG CYS 6 314 " pdb="ZN ZN 62002 " - pdb=" SG CYS 6 311 " pdb="ZN ZN 62002 " - pdb=" SG CYS 6 333 " pdb=" ZN 72003 " pdb="ZN ZN 72003 " - pdb=" SG CYS 7 262 " pdb="ZN ZN 72003 " - pdb=" SG CYS 7 284 " pdb="ZN ZN 72003 " - pdb=" SG CYS 7 265 " pdb="ZN ZN 72003 " - pdb=" SG CYS 7 289 " pdb=" ZN B2003 " pdb="ZN ZN B2003 " - pdb=" SG CYS B 364 " 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 D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 349 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 352 " 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 F2002 " pdb="ZN ZN F2002 " - pdb=" SG CYS F 338 " pdb="ZN ZN F2002 " - pdb=" SG CYS F 314 " pdb="ZN ZN F2002 " - pdb=" SG CYS F 333 " pdb="ZN ZN F2002 " - pdb=" SG CYS F 311 " pdb=" ZN G2003 " pdb="ZN ZN G2003 " - pdb=" SG CYS G 262 " pdb="ZN ZN G2003 " - pdb=" SG CYS G 265 " pdb="ZN ZN G2003 " - pdb=" SG CYS G 284 " pdb="ZN ZN G2003 " - pdb=" SG CYS G 289 " pdb=" ZN I 801 " pdb="ZN ZN I 801 " - pdb=" NE2 HIS I 674 " pdb="ZN ZN I 801 " - pdb=" ND1 HIS I 680 " pdb="ZN ZN I 801 " - pdb=" SG CYS I 661 " pdb="ZN ZN I 801 " - pdb=" SG CYS I 664 " Number of angles added : 61 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16304 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 332 helices and 94 sheets defined 38.9% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.18 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 removed outlier: 3.734A pdb=" N HIS 2 282 " --> pdb=" O ALA 2 278 " (cutoff:3.500A) Processing helix chain '2' and resid 286 through 289 No H-bonds generated for 'chain '2' and resid 286 through 289' 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 394 through 396 No H-bonds generated for 'chain '2' and resid 394 through 396' Processing helix chain '2' and resid 478 through 488 removed outlier: 3.670A pdb=" N ARG 2 482 " --> pdb=" O GLU 2 478 " (cutoff:3.500A) Processing helix chain '2' and resid 493 through 500 Processing helix chain '2' and resid 509 through 520 Processing helix chain '2' and resid 527 through 529 No H-bonds generated for 'chain '2' and resid 527 through 529' Processing helix chain '2' and resid 549 through 559 Processing helix chain '2' and resid 594 through 598 Processing helix chain '2' and resid 614 through 625 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: 3.698A pdb=" N LYS 2 765 " --> pdb=" O GLU 2 761 " (cutoff:3.500A) Processing helix chain '2' and resid 780 through 800 removed outlier: 3.516A pdb=" N MET 2 783 " --> pdb=" O GLN 2 780 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASP 2 784 " --> pdb=" O MET 2 781 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS 2 785 " --> pdb=" O ASP 2 782 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL 2 786 " --> pdb=" O MET 2 783 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N SER 2 787 " --> pdb=" O ASP 2 784 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR 2 790 " --> pdb=" O SER 2 787 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG 2 795 " --> pdb=" O ASP 2 792 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR 2 800 " --> pdb=" O SER 2 797 " (cutoff:3.500A) Processing helix chain '2' and resid 807 through 823 removed outlier: 3.689A pdb=" N MET 2 823 " --> pdb=" O SER 2 819 " (cutoff:3.500A) Processing helix chain '2' and resid 831 through 846 Processing helix chain '2' and resid 851 through 860 removed outlier: 3.619A pdb=" N GLN 2 856 " --> pdb=" O SER 2 852 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG 2 859 " --> pdb=" O ARG 2 855 " (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 removed outlier: 3.657A pdb=" N MET 3 136 " --> pdb=" O LEU 3 132 " (cutoff:3.500A) 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 365 removed outlier: 3.514A pdb=" N GLN 3 365 " --> pdb=" O ASP 3 361 " (cutoff:3.500A) 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 492 removed outlier: 3.797A pdb=" N GLU 3 488 " --> pdb=" O VAL 3 484 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL 3 489 " --> pdb=" O ALA 3 485 " (cutoff:3.500A) removed outlier: 3.679A 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 Processing helix chain '3' and resid 673 through 687 removed outlier: 3.761A pdb=" N VAL 3 678 " --> pdb=" O GLU 3 674 " (cutoff:3.500A) Processing helix chain '3' and resid 699 through 715 removed outlier: 3.734A pdb=" N GLU 3 703 " --> pdb=" O ALA 3 699 " (cutoff:3.500A) Processing helix chain '3' and resid 723 through 737 Processing helix chain '4' and resid 187 through 199 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: 3.796A pdb=" N HIS 4 259 " --> pdb=" O GLU 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 265 through 285 removed outlier: 3.958A pdb=" N SER 4 270 " --> pdb=" O GLN 4 266 " (cutoff:3.500A) removed outlier: 4.022A 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 504 through 513 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 639 through 651 removed outlier: 4.204A pdb=" N VAL 4 644 " --> pdb=" O SER 4 640 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LEU 4 645 " --> pdb=" O THR 4 641 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N HIS 4 646 " --> pdb=" O ARG 4 642 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N GLU 4 647 " --> pdb=" O SER 4 643 " (cutoff:3.500A) removed outlier: 3.943A 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: 4.592A pdb=" N ARG 4 701 " --> pdb=" O PRO 4 697 " (cutoff:3.500A) Processing helix chain '4' and resid 715 through 728 removed outlier: 3.871A pdb=" N LEU 4 727 " --> pdb=" O HIS 4 723 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N TYR 4 728 " --> pdb=" O LEU 4 724 " (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 Processing helix chain '5' and resid 73 through 81 Processing helix chain '5' and resid 83 through 106 Proline residue: 5 88 - end of helix removed outlier: 3.607A pdb=" N ARG 5 100 " --> pdb=" O GLN 5 96 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU 5 104 " --> pdb=" O ARG 5 100 " (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 545 through 549 Processing helix chain '5' and resid 562 through 577 removed outlier: 4.255A pdb=" N SER 5 567 " --> pdb=" O GLU 5 563 " (cutoff:3.500A) 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: 4.381A pdb=" N GLU 5 620 " --> pdb=" O GLN 5 617 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LYS 5 621 " --> pdb=" O ALA 5 618 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR 5 628 " --> pdb=" O ASN 5 625 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE 5 629 " --> pdb=" O PHE 5 626 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU 5 633 " --> pdb=" O ARG 5 630 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN 5 636 " --> pdb=" O LEU 5 633 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER 5 640 " --> pdb=" O GLU 5 637 " (cutoff:3.500A) Processing helix chain '5' and resid 650 through 666 Processing helix chain '5' and resid 674 through 694 removed outlier: 3.773A pdb=" N MET 5 689 " --> pdb=" O GLN 5 685 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ASP 5 690 " --> pdb=" O ALA 5 686 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA 5 691 " --> pdb=" O SER 5 687 " (cutoff:3.500A) Processing helix chain '6' and resid 106 through 121 removed outlier: 3.707A pdb=" N GLU 6 120 " --> pdb=" O GLU 6 116 " (cutoff:3.500A) Processing helix chain '6' and resid 135 through 146 removed outlier: 3.542A pdb=" N ILE 6 145 " --> pdb=" O GLU 6 141 " (cutoff:3.500A) removed outlier: 3.541A 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 198 removed outlier: 3.767A pdb=" N ASN 6 198 " --> pdb=" O GLU 6 195 " (cutoff:3.500A) 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 408 through 410 No H-bonds generated for 'chain '6' and resid 408 through 410' Processing helix chain '6' and resid 501 through 507 Processing helix chain '6' and resid 510 through 521 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: 4.010A 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 646 through 657 removed outlier: 3.837A 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: 3.963A pdb=" N ARG 6 708 " --> pdb=" O PRO 6 704 " (cutoff:3.500A) Processing helix chain '6' and resid 721 through 737 Processing helix chain '6' and resid 748 through 760 removed outlier: 3.973A pdb=" N THR 6 760 " --> pdb=" O LYS 6 756 " (cutoff:3.500A) Processing helix chain '6' and resid 767 through 790 removed outlier: 3.856A pdb=" N SER 6 771 " --> pdb=" O LYS 6 767 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N SER 6 789 " --> pdb=" O ALA 6 785 " (cutoff:3.500A) removed outlier: 6.928A 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 3 through 5 No H-bonds generated for 'chain '7' and resid 3 through 5' Processing helix chain '7' and resid 16 through 27 Processing helix chain '7' and resid 62 through 71 removed outlier: 3.748A pdb=" N LEU 7 67 " --> pdb=" O TYR 7 63 " (cutoff:3.500A) 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: 4.077A 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 197 Processing helix chain '7' and resid 209 through 214 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 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 406 removed outlier: 3.912A pdb=" N GLU 7 399 " --> pdb=" O SER 7 395 " (cutoff:3.500A) removed outlier: 3.929A 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: 4.141A pdb=" N GLU 7 542 " --> pdb=" O HIS 7 538 " (cutoff:3.500A) Processing helix chain '7' and resid 580 through 583 No H-bonds generated for 'chain '7' and resid 580 through 583' Processing helix chain '7' and resid 588 through 593 Processing helix chain '7' and resid 606 through 622 removed outlier: 3.687A pdb=" N GLU 7 610 " --> pdb=" O ARG 7 606 " (cutoff:3.500A) Processing helix chain '7' and resid 635 through 646 Processing helix chain '7' and resid 654 through 673 Processing helix chain '7' and resid 686 through 702 Processing helix chain '7' and resid 710 through 729 removed outlier: 3.762A pdb=" N LYS 7 724 " --> pdb=" O VAL 7 720 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER 7 726 " --> pdb=" O VAL 7 722 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N LEU 7 727 " --> pdb=" O SER 7 723 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR 7 728 " --> pdb=" O LYS 7 724 " (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 236 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 281 removed outlier: 3.742A pdb=" N LEU B 273 " --> pdb=" O LYS B 269 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 289 removed outlier: 3.994A pdb=" N ALA B 287 " --> pdb=" O PRO B 284 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE B 289 " --> pdb=" O TYR B 286 " (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 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' 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 493 through 500 Processing helix chain 'B' and resid 509 through 520 Processing helix chain 'B' and resid 527 through 529 No H-bonds generated for 'chain 'B' and resid 527 through 529' Processing helix chain 'B' and resid 549 through 559 Processing helix chain 'B' and resid 594 through 598 Processing helix chain 'B' and resid 614 through 625 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 671 through 674 No H-bonds generated for 'chain 'B' and resid 671 through 674' Processing helix chain 'B' and resid 689 through 705 Processing helix chain 'B' and resid 760 through 773 removed outlier: 4.276A pdb=" N LYS B 765 " --> pdb=" O GLU B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 780 through 800 removed outlier: 3.742A pdb=" N MET B 783 " --> pdb=" O GLN B 780 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ASP B 784 " --> pdb=" O MET B 781 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS B 785 " --> pdb=" O ASP B 782 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B 786 " --> pdb=" O MET B 783 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N SER B 787 " --> pdb=" O ASP B 784 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR B 790 " --> pdb=" O SER B 787 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG B 795 " --> pdb=" O ASP B 792 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR B 800 " --> pdb=" O SER B 797 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 823 Processing helix chain 'B' and resid 831 through 848 removed outlier: 4.364A pdb=" N ALA B 848 " --> pdb=" O SER B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 860 removed outlier: 3.844A pdb=" N GLN B 856 " --> pdb=" O SER B 852 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG B 859 " --> pdb=" O ARG B 855 " (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 37 through 58 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 135 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 344 through 355 removed outlier: 3.608A pdb=" N LYS C 355 " --> pdb=" O ASN C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 365 removed outlier: 3.630A pdb=" N SER C 364 " --> pdb=" O PHE C 360 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN C 365 " --> pdb=" O ASP C 361 " (cutoff:3.500A) 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 492 removed outlier: 3.792A pdb=" N GLU C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) removed outlier: 3.755A 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 570 Processing helix chain 'C' and resid 653 through 666 Processing helix chain 'C' and resid 673 through 688 removed outlier: 4.019A pdb=" N VAL C 678 " --> pdb=" O GLU C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 715 removed outlier: 3.619A pdb=" N GLU C 703 " --> pdb=" O ALA C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 737 Processing helix chain 'D' and resid 187 through 200 Processing helix chain 'D' and resid 203 through 209 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: 3.798A pdb=" N HIS D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 286 removed outlier: 3.901A pdb=" N SER D 270 " --> pdb=" O GLN D 266 " (cutoff:3.500A) removed outlier: 3.776A 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 482 through 491 Processing helix chain 'D' and resid 503 through 513 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 639 through 642 No H-bonds generated for 'chain 'D' and resid 639 through 642' Processing helix chain 'D' and resid 644 through 650 removed outlier: 3.601A pdb=" N GLU D 647 " --> 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: 3.867A pdb=" N ARG D 701 " --> pdb=" O PRO D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 728 removed outlier: 3.940A pdb=" N LEU D 727 " --> pdb=" O HIS D 723 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N TYR D 728 " --> pdb=" O LEU D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 744 through 757 Processing helix chain 'D' and resid 764 through 782 removed outlier: 3.671A pdb=" N ASP D 782 " --> pdb=" O ARG D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 795 through 811 Processing helix chain 'D' and resid 819 through 833 removed outlier: 3.717A pdb=" N ILE D 833 " --> pdb=" O ILE D 829 " (cutoff:3.500A) 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 Processing helix chain 'E' and resid 73 through 81 Processing helix chain 'E' and resid 83 through 106 Proline residue: E 88 - end of helix removed outlier: 3.569A 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 removed outlier: 3.542A pdb=" N SER E 361 " --> pdb=" O PHE E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 373 Processing helix chain 'E' and resid 382 through 393 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 548 Processing helix chain 'E' and resid 562 through 577 removed outlier: 3.958A pdb=" N SER E 567 " --> pdb=" O GLU E 563 " (cutoff:3.500A) 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: 4.443A pdb=" N GLU E 620 " --> pdb=" O PRO E 616 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LYS E 621 " --> pdb=" O GLN E 617 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU E 622 " --> pdb=" O ALA E 618 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG E 630 " --> pdb=" O PHE E 626 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 666 Processing helix chain 'E' and resid 674 through 694 removed outlier: 3.554A pdb=" N MET E 689 " --> pdb=" O GLN E 685 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ASP E 690 " --> pdb=" O ALA E 686 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA E 691 " --> pdb=" O SER E 687 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 121 Processing helix chain 'F' and resid 135 through 146 removed outlier: 3.878A pdb=" N ILE F 145 " --> pdb=" O GLU F 141 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR F 146 " --> pdb=" O PHE F 142 " (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 198 removed outlier: 3.794A pdb=" N ASN F 198 " --> pdb=" O GLU F 195 " (cutoff:3.500A) 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 383 through 385 No H-bonds generated for 'chain 'F' and resid 383 through 385' Processing helix chain 'F' and resid 408 through 410 No H-bonds generated for 'chain 'F' and resid 408 through 410' Processing helix chain 'F' and resid 501 through 507 removed outlier: 3.710A 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 531 Processing helix chain 'F' and resid 541 through 552 Processing helix chain 'F' and resid 581 through 591 removed outlier: 3.792A 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 646 through 657 removed outlier: 3.910A 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: 3.857A pdb=" N ARG F 708 " --> pdb=" O PRO F 704 " (cutoff:3.500A) Processing helix chain 'F' and resid 721 through 737 Processing helix chain 'F' and resid 748 through 760 removed outlier: 3.942A pdb=" N THR F 760 " --> pdb=" O LYS F 756 " (cutoff:3.500A) Processing helix chain 'F' and resid 767 through 790 removed outlier: 3.883A pdb=" N SER F 771 " --> pdb=" O LYS F 767 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER F 789 " --> pdb=" O ALA F 785 " (cutoff:3.500A) removed outlier: 6.919A 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 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: 3.958A 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 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: 3.861A pdb=" N GLU G 399 " --> pdb=" O SER G 395 " (cutoff:3.500A) removed outlier: 3.974A 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 467 through 476 Processing helix chain 'G' and resid 490 through 493 No H-bonds generated for 'chain 'G' and resid 490 through 493' 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: 4.425A pdb=" N GLU G 542 " --> pdb=" O HIS G 538 " (cutoff:3.500A) Processing helix chain 'G' and resid 580 through 583 No H-bonds generated for 'chain 'G' and resid 580 through 583' Processing helix chain 'G' and resid 588 through 593 Processing helix chain 'G' and resid 606 through 622 removed outlier: 3.770A pdb=" N GLU G 610 " --> pdb=" O ARG G 606 " (cutoff:3.500A) Processing helix chain 'G' and resid 635 through 647 removed outlier: 3.663A 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: 4.077A pdb=" N LYS G 724 " --> pdb=" O VAL G 720 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N SER G 726 " --> pdb=" O VAL G 722 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N LEU G 727 " --> pdb=" O SER G 723 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 25 Processing helix chain 'H' and resid 29 through 32 No H-bonds generated for 'chain 'H' and resid 29 through 32' Processing helix chain 'H' and resid 56 through 64 removed outlier: 6.443A pdb=" N SER H 63 " --> pdb=" O LYS H 59 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N HIS H 64 " --> pdb=" O LYS H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 97 removed outlier: 3.531A pdb=" N MET H 97 " --> pdb=" O LEU H 93 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 103 No H-bonds generated for 'chain 'H' and resid 101 through 103' Processing helix chain 'H' and resid 137 through 156 Processing helix chain 'H' and resid 261 through 263 No H-bonds generated for 'chain 'H' and resid 261 through 263' Processing helix chain 'H' and resid 287 through 290 No H-bonds generated for 'chain 'H' and resid 287 through 290' Processing helix chain 'H' and resid 300 through 314 Processing helix chain 'H' and resid 325 through 336 removed outlier: 3.847A pdb=" N ILE H 335 " --> pdb=" O GLU H 331 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 348 removed outlier: 3.666A pdb=" N LEU H 347 " --> pdb=" O LYS H 343 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HIS H 348 " --> pdb=" O CYS H 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 383 removed outlier: 3.852A pdb=" N GLU H 380 " --> pdb=" O LEU H 376 " (cutoff:3.500A) Processing helix chain 'H' and resid 394 through 404 Processing helix chain 'H' and resid 426 through 450 removed outlier: 3.803A pdb=" N PHE H 443 " --> pdb=" O HIS H 439 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN H 448 " --> pdb=" O GLN H 444 " (cutoff:3.500A) Processing helix chain 'H' and resid 460 through 464 Processing helix chain 'H' and resid 467 through 469 No H-bonds generated for 'chain 'H' and resid 467 through 469' Processing helix chain 'I' and resid 107 through 122 Processing helix chain 'I' and resid 138 through 158 removed outlier: 3.613A pdb=" N LYS I 143 " --> pdb=" O TYR I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 182 No H-bonds generated for 'chain 'I' and resid 180 through 182' Processing helix chain 'I' and resid 190 through 196 Processing helix chain 'I' and resid 204 through 213 Processing helix chain 'I' and resid 234 through 244 Processing helix chain 'I' and resid 285 through 288 No H-bonds generated for 'chain 'I' and resid 285 through 288' Processing helix chain 'I' and resid 320 through 343 removed outlier: 4.630A pdb=" N LYS I 335 " --> pdb=" O LYS I 331 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR I 336 " --> pdb=" O ALA I 332 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN I 339 " --> pdb=" O LYS I 335 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU I 340 " --> pdb=" O TYR I 336 " (cutoff:3.500A) Processing helix chain 'I' and resid 374 through 385 Processing helix chain 'I' and resid 522 through 530 removed outlier: 3.772A pdb=" N SER I 528 " --> pdb=" O MET I 524 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ARG I 529 " --> pdb=" O LYS I 525 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU I 530 " --> pdb=" O SER I 526 " (cutoff:3.500A) Processing helix chain 'I' and resid 671 through 675 Processing helix chain 'I' and resid 678 through 685 Processing helix chain 'I' and resid 691 through 702 Processing sheet with id= A, first strand: chain '2' and resid 241 through 245 removed outlier: 6.571A pdb=" N HIS 2 294 " --> pdb=" O LEU 2 242 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL 2 244 " --> pdb=" O HIS 2 294 " (cutoff:3.500A) removed outlier: 5.903A 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 405 through 410 removed outlier: 4.065A pdb=" N ARG 2 326 " --> pdb=" O THR 2 389 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLN 2 391 " --> pdb=" O VAL 2 324 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N VAL 2 324 " --> pdb=" O GLN 2 391 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER 2 316 " --> pdb=" O TYR 2 430 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE 2 429 " --> pdb=" O ALA 2 453 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ALA 2 453 " --> pdb=" O ILE 2 429 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LYS 2 431 " --> pdb=" O ILE 2 451 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ILE 2 451 " --> pdb=" O LYS 2 431 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ASN 2 433 " --> pdb=" O THR 2 449 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N THR 2 449 " --> pdb=" O ASN 2 433 " (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: 6.500A pdb=" N GLY 2 602 " --> pdb=" O SER 2 645 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE 2 647 " --> pdb=" O GLY 2 602 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N CYS 2 604 " --> pdb=" O ILE 2 647 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ALA 2 649 " --> pdb=" O CYS 2 604 " (cutoff:3.500A) removed outlier: 6.851A 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: 6.757A 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: 7.118A pdb=" N LYS 3 154 " --> pdb=" O ILE 3 96 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ILE 3 98 " --> pdb=" O LYS 3 154 " (cutoff:3.500A) removed outlier: 6.261A 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 165 through 167 removed outlier: 7.892A pdb=" N LEU 3 166 " --> pdb=" O LEU 3 179 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N SER 3 181 " --> pdb=" O LEU 3 166 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS 3 178 " --> pdb=" O PHE 3 298 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ARG 3 291 " --> pdb=" O LEU 3 329 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL 3 297 " --> pdb=" O GLY 3 323 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLY 3 323 " --> pdb=" O VAL 3 297 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LYS 3 299 " --> pdb=" O ILE 3 321 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ILE 3 321 " --> pdb=" O LYS 3 299 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU 3 301 " --> pdb=" O THR 3 319 " (cutoff:3.500A) removed outlier: 6.194A 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 273 through 278 removed outlier: 3.775A pdb=" N LYS 3 188 " --> pdb=" O THR 3 257 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLN 3 259 " --> pdb=" O VAL 3 186 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N VAL 3 186 " --> pdb=" O GLN 3 259 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '3' and resid 545 through 549 removed outlier: 3.548A pdb=" N GLY 3 409 " --> pdb=" O ALA 3 516 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLY 3 468 " --> pdb=" O SER 3 511 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ILE 3 513 " --> pdb=" O GLY 3 468 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL 3 470 " --> pdb=" O ILE 3 513 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ALA 3 515 " --> pdb=" O VAL 3 470 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE 3 472 " --> pdb=" O ALA 3 515 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '3' and resid 444 through 448 Processing sheet with id= O, first strand: chain '3' and resid 494 through 498 Processing sheet with id= P, first strand: chain '3' and resid 193 through 198 removed outlier: 6.786A pdb=" N THR 3 249 " --> pdb=" O ILE 3 197 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '4' and resid 240 through 244 removed outlier: 6.995A pdb=" N LYS 4 302 " --> pdb=" O LEU 4 241 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N LEU 4 243 " --> pdb=" O LYS 4 302 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ARG 4 304 " --> pdb=" O LEU 4 243 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain '4' and resid 414 through 420 removed outlier: 3.690A pdb=" N ARG 4 334 " --> pdb=" O LYS 4 398 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLN 4 400 " --> pdb=" O VAL 4 332 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N VAL 4 332 " --> pdb=" O GLN 4 400 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N THR 4 438 " --> pdb=" O VAL 4 463 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N VAL 4 463 " --> pdb=" O THR 4 438 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ARG 4 440 " --> pdb=" O VAL 4 461 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N VAL 4 461 " --> pdb=" O ARG 4 440 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE 4 442 " --> pdb=" O THR 4 459 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N THR 4 459 " --> pdb=" O ILE 4 442 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain '4' and resid 339 through 342 Processing sheet with id= T, first strand: chain '4' and resid 355 through 359 Processing sheet with id= U, first strand: chain '4' and resid 704 through 708 removed outlier: 6.272A pdb=" N VAL 4 589 " --> pdb=" O CYS 4 630 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ASP 4 632 " --> pdb=" O VAL 4 589 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N THR 4 591 " --> pdb=" O ASP 4 632 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain '4' and resid 603 through 607 Processing sheet with id= W, first strand: chain '4' and resid 653 through 657 Processing sheet with id= X, first strand: chain '5' and resid 60 through 64 removed outlier: 6.500A pdb=" N GLN 5 136 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL 5 63 " --> pdb=" O GLN 5 136 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE 5 138 " --> pdb=" O VAL 5 63 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain '5' and resid 291 through 298 removed outlier: 4.007A pdb=" N LYS 5 158 " --> pdb=" O TYR 5 298 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LYS 5 257 " --> pdb=" O ILE 5 167 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR 5 169 " --> pdb=" O PHE 5 255 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE 5 255 " --> pdb=" O THR 5 169 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N THR 5 275 " --> pdb=" O PRO 5 326 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ASP 5 279 " --> pdb=" O ILE 5 330 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N GLY 5 332 " --> pdb=" O ASP 5 279 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL 5 295 " --> pdb=" O LEU 5 331 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ILE 5 333 " --> pdb=" O THR 5 293 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR 5 293 " --> pdb=" O ILE 5 333 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain '5' and resid 189 through 193 removed outlier: 4.594A 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 removed outlier: 6.520A pdb=" N GLY 5 475 " --> pdb=" O SER 5 518 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU 5 520 " --> pdb=" O GLY 5 475 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL 5 477 " --> pdb=" O LEU 5 520 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ALA 5 522 " --> pdb=" O VAL 5 477 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE 5 479 " --> pdb=" O ALA 5 522 " (cutoff:3.500A) 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 173 through 178 removed outlier: 6.608A pdb=" N LYS 5 249 " --> pdb=" O THR 5 177 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain '5' and resid 452 through 455 removed outlier: 6.179A pdb=" N GLN 5 454 " --> pdb=" O LEU 5 464 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N LEU 5 464 " --> pdb=" O GLN 5 454 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain '6' and resid 150 through 154 removed outlier: 6.433A pdb=" N GLN 6 264 " --> pdb=" O ILE 6 151 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ILE 6 153 " --> pdb=" O GLN 6 264 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N SER 6 266 " --> pdb=" O ILE 6 153 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain '6' and resid 394 through 400 removed outlier: 6.656A pdb=" N ARG 6 360 " --> pdb=" O THR 6 295 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N THR 6 297 " --> pdb=" O LYS 6 358 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LYS 6 358 " --> pdb=" O THR 6 297 " (cutoff:3.500A) removed outlier: 14.194A pdb=" N TYR 6 450 " --> pdb=" O THR 6 376 " (cutoff:3.500A) removed outlier: 12.173A pdb=" N ASP 6 378 " --> pdb=" O TYR 6 450 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ILE 6 452 " --> pdb=" O ASP 6 378 " (cutoff:3.500A) removed outlier: 9.307A pdb=" N ILE 6 380 " --> pdb=" O ILE 6 452 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N PHE 6 454 " --> pdb=" O ILE 6 380 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N ARG 6 382 " --> pdb=" O PHE 6 454 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ALA 6 456 " --> pdb=" O ARG 6 382 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N THR 6 398 " --> pdb=" O CYS 6 457 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL 6 459 " --> pdb=" O LYS 6 396 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LYS 6 396 " --> pdb=" O VAL 6 459 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain '6' and resid 309 through 311 Processing sheet with id= AH, first strand: chain '6' and resid 418 through 420 Processing sheet with id= AI, first strand: chain '6' and resid 711 through 715 removed outlier: 3.778A pdb=" N GLY 6 575 " --> pdb=" O ALA 6 682 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain '6' and resid 610 through 614 Processing sheet with id= AK, first strand: chain '6' and resid 660 through 663 Processing sheet with id= AL, first strand: chain '6' and resid 301 through 306 removed outlier: 6.595A pdb=" N ARG 6 352 " --> pdb=" O TYR 6 305 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain '7' and resid 77 through 81 removed outlier: 6.182A pdb=" N PHE 7 201 " --> pdb=" O VAL 7 78 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ILE 7 80 " --> pdb=" O PHE 7 201 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TYR 7 203 " --> pdb=" O ILE 7 80 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain '7' and resid 330 through 336 removed outlier: 3.766A pdb=" N ARG 7 247 " --> pdb=" O LYS 7 314 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN 7 316 " --> pdb=" O ILE 7 245 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ILE 7 245 " --> pdb=" O GLN 7 316 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ILE 7 354 " --> pdb=" O ALA 7 378 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ALA 7 378 " --> pdb=" O ILE 7 354 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU 7 356 " --> pdb=" O LEU 7 376 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LEU 7 376 " --> pdb=" O LEU 7 356 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ALA 7 358 " --> pdb=" O THR 7 374 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N THR 7 374 " --> pdb=" O ALA 7 358 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain '7' and resid 268 through 272 Processing sheet with id= AP, first strand: chain '7' and resid 596 through 600 removed outlier: 6.234A pdb=" N VAL 7 481 " --> pdb=" O CYS 7 522 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ASP 7 524 " --> pdb=" O VAL 7 481 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR 7 483 " --> pdb=" O ASP 7 524 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain '7' and resid 495 through 500 Processing sheet with id= AR, first strand: chain '7' and resid 545 through 549 Processing sheet with id= AS, first strand: chain '7' and resid 252 through 257 removed outlier: 6.982A pdb=" N LYS 7 306 " --> pdb=" O GLU 7 256 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'B' and resid 241 through 245 removed outlier: 6.900A pdb=" N HIS B 294 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N VAL B 244 " --> pdb=" O HIS B 294 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ARG B 296 " --> pdb=" O VAL B 244 " (cutoff:3.500A) No H-bonds generated for sheet with id= AT Processing sheet with id= AU, first strand: chain 'B' and resid 423 through 430 removed outlier: 4.015A pdb=" N SER B 316 " --> pdb=" O TYR B 430 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR B 389 " --> pdb=" O THR B 325 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ARG B 327 " --> pdb=" O ARG B 387 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ARG B 387 " --> pdb=" O ARG B 327 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N THR B 449 " --> pdb=" O HIS B 405 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLU B 407 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA B 448 " --> pdb=" O ASN B 433 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N THR B 427 " --> pdb=" O ASN B 454 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ILE B 456 " --> pdb=" O GLU B 425 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLU B 425 " --> pdb=" O ILE B 456 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'B' and resid 339 through 341 Processing sheet with id= AW, first strand: chain 'B' and resid 525 through 527 Processing sheet with id= AX, first strand: chain 'B' and resid 679 through 683 removed outlier: 6.728A pdb=" N GLY B 602 " --> pdb=" O SER B 645 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE B 647 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N CYS B 604 " --> pdb=" O ILE B 647 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ALA B 649 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE B 606 " --> pdb=" O ALA B 649 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'B' and resid 579 through 582 Processing sheet with id= AZ, first strand: chain 'B' and resid 628 through 633 Processing sheet with id= BA, first strand: chain 'B' and resid 331 through 336 removed outlier: 6.711A pdb=" N VAL B 381 " --> pdb=" O LYS B 335 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'C' and resid 95 through 99 removed outlier: 6.988A pdb=" N LYS C 154 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE C 98 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N SER C 156 " --> pdb=" O ILE C 98 " (cutoff:3.500A) No H-bonds generated for sheet with id= BB Processing sheet with id= BC, first strand: chain 'C' and resid 165 through 167 removed outlier: 7.819A pdb=" N LEU C 166 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N SER C 181 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS C 178 " --> pdb=" O PHE C 298 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG C 291 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL C 297 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLY C 323 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LYS C 299 " --> pdb=" O ILE C 321 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ILE C 321 " --> pdb=" O LYS C 299 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N LEU C 301 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N THR C 319 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'C' and resid 208 through 213 Processing sheet with id= BE, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.808A pdb=" N LYS C 188 " --> pdb=" O THR C 257 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLN C 259 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N VAL C 186 " --> pdb=" O GLN C 259 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'C' and resid 545 through 549 removed outlier: 3.562A pdb=" N GLY C 409 " --> pdb=" O ALA C 516 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY C 468 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ILE C 513 " --> pdb=" O GLY C 468 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N VAL C 470 " --> pdb=" O ILE C 513 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ALA C 515 " --> pdb=" O VAL C 470 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE C 472 " --> pdb=" O ALA C 515 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'C' and resid 444 through 448 Processing sheet with id= BH, first strand: chain 'C' and resid 494 through 498 Processing sheet with id= BI, first strand: chain 'C' and resid 193 through 198 removed outlier: 6.761A pdb=" N THR C 249 " --> pdb=" O ILE C 197 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'D' and resid 240 through 244 removed outlier: 7.012A pdb=" N LYS D 302 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N LEU D 243 " --> pdb=" O LYS D 302 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ARG D 304 " --> pdb=" O LEU D 243 " (cutoff:3.500A) No H-bonds generated for sheet with id= BJ Processing sheet with id= BK, first strand: chain 'D' and resid 414 through 420 removed outlier: 3.768A pdb=" N ARG D 334 " --> pdb=" O LYS D 398 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLN D 400 " --> pdb=" O VAL D 332 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N VAL D 332 " --> pdb=" O GLN D 400 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR D 438 " --> pdb=" O VAL D 463 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL D 463 " --> pdb=" O THR D 438 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG D 440 " --> pdb=" O VAL D 461 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N VAL D 461 " --> pdb=" O ARG D 440 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE D 442 " --> pdb=" O THR D 459 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N THR D 459 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'D' and resid 339 through 342 Processing sheet with id= BM, first strand: chain 'D' and resid 355 through 359 Processing sheet with id= BN, first strand: chain 'D' and resid 704 through 708 removed outlier: 6.312A pdb=" N VAL D 589 " --> pdb=" O CYS D 630 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ASP D 632 " --> pdb=" O VAL D 589 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR D 591 " --> pdb=" O ASP D 632 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'D' and resid 603 through 607 Processing sheet with id= BP, first strand: chain 'D' and resid 653 through 657 Processing sheet with id= BQ, first strand: chain 'E' and resid 60 through 64 removed outlier: 6.315A pdb=" N GLN E 136 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N VAL E 63 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE E 138 " --> pdb=" O VAL E 63 " (cutoff:3.500A) No H-bonds generated for sheet with id= BQ Processing sheet with id= BR, first strand: chain 'E' and resid 291 through 298 removed outlier: 4.057A pdb=" N LYS E 158 " --> pdb=" O TYR E 298 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LYS E 257 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR E 169 " --> pdb=" O PHE E 255 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE E 255 " --> pdb=" O THR E 169 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N THR E 275 " --> pdb=" O PRO E 326 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASP E 279 " --> pdb=" O ILE E 330 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N GLY E 332 " --> pdb=" O ASP E 279 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL E 295 " --> pdb=" O LEU E 331 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ILE E 333 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR E 293 " --> pdb=" O ILE E 333 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'E' and resid 189 through 193 removed outlier: 4.644A pdb=" N SER E 180 " --> pdb=" O ILE E 244 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'E' and resid 552 through 556 removed outlier: 3.517A pdb=" N GLY E 416 " --> pdb=" O ALA E 523 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY E 475 " --> pdb=" O SER E 518 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LEU E 520 " --> pdb=" O GLY E 475 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL E 477 " --> pdb=" O LEU E 520 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ALA E 522 " --> pdb=" O VAL E 477 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE E 479 " --> pdb=" O ALA E 522 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'E' and resid 501 through 505 Processing sheet with id= BV, first strand: chain 'E' and resid 173 through 178 removed outlier: 6.552A pdb=" N LYS E 249 " --> pdb=" O THR E 177 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'E' and resid 452 through 455 removed outlier: 3.748A pdb=" N GLY E 466 " --> pdb=" O SER E 452 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLN E 454 " --> pdb=" O LEU E 464 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LEU E 464 " --> pdb=" O GLN E 454 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'F' and resid 150 through 154 removed outlier: 6.443A pdb=" N GLN F 264 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE F 153 " --> pdb=" O GLN F 264 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N SER F 266 " --> pdb=" O ILE F 153 " (cutoff:3.500A) No H-bonds generated for sheet with id= BX Processing sheet with id= BY, first strand: chain 'F' and resid 394 through 400 removed outlier: 6.699A pdb=" N ARG F 360 " --> pdb=" O THR F 295 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N THR F 297 " --> pdb=" O LYS F 358 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LYS F 358 " --> pdb=" O THR F 297 " (cutoff:3.500A) removed outlier: 14.252A pdb=" N TYR F 450 " --> pdb=" O THR F 376 " (cutoff:3.500A) removed outlier: 12.276A pdb=" N ASP F 378 " --> pdb=" O TYR F 450 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ILE F 452 " --> pdb=" O ASP F 378 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N ILE F 380 " --> pdb=" O ILE F 452 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N PHE F 454 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ARG F 382 " --> pdb=" O PHE F 454 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ALA F 456 " --> pdb=" O ARG F 382 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR F 398 " --> pdb=" O CYS F 457 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL F 459 " --> pdb=" O LYS F 396 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LYS F 396 " --> pdb=" O VAL F 459 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'F' and resid 309 through 311 Processing sheet with id= CA, first strand: chain 'F' and resid 711 through 715 removed outlier: 3.879A pdb=" N GLY F 575 " --> pdb=" O ALA F 682 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'F' and resid 610 through 614 Processing sheet with id= CC, first strand: chain 'F' and resid 660 through 663 Processing sheet with id= CD, first strand: chain 'F' and resid 301 through 306 removed outlier: 6.689A pdb=" N ARG F 352 " --> pdb=" O TYR F 305 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'G' and resid 77 through 81 removed outlier: 6.218A pdb=" N PHE G 201 " --> pdb=" O VAL G 78 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ILE G 80 " --> pdb=" O PHE G 201 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TYR G 203 " --> pdb=" O ILE G 80 " (cutoff:3.500A) No H-bonds generated for sheet with id= CE Processing sheet with id= CF, first strand: chain 'G' and resid 330 through 336 removed outlier: 3.806A pdb=" N ARG G 247 " --> pdb=" O LYS G 314 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLN G 316 " --> pdb=" O ILE G 245 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ILE G 245 " --> pdb=" O GLN G 316 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE G 354 " --> pdb=" O ALA G 378 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ALA G 378 " --> pdb=" O ILE G 354 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU G 356 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU G 376 " --> pdb=" O LEU G 356 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ALA G 358 " --> pdb=" O THR G 374 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N THR G 374 " --> pdb=" O ALA G 358 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain 'G' and resid 268 through 272 Processing sheet with id= CH, first strand: chain 'G' and resid 596 through 600 Processing sheet with id= CI, first strand: chain 'G' and resid 495 through 500 Processing sheet with id= CJ, first strand: chain 'G' and resid 545 through 549 Processing sheet with id= CK, 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) Processing sheet with id= CL, first strand: chain 'H' and resid 106 through 111 removed outlier: 6.897A pdb=" N VAL H 119 " --> pdb=" O CYS H 107 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA H 109 " --> pdb=" O ILE H 117 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE H 117 " --> pdb=" O ALA H 109 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N VAL H 116 " --> pdb=" O ILE H 78 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE H 78 " --> pdb=" O VAL H 116 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LYS H 51 " --> pdb=" O LEU H 35 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LEU H 35 " --> pdb=" O LYS H 51 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain 'H' and resid 169 through 172 Processing sheet with id= CN, first strand: chain 'I' and resid 126 through 128 removed outlier: 6.566A pdb=" N ILE I 172 " --> pdb=" O TYR I 127 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LYS I 200 " --> pdb=" O VAL I 173 " (cutoff:3.500A) No H-bonds generated for sheet with id= CN Processing sheet with id= CO, first strand: chain 'I' and resid 265 through 268 Processing sheet with id= CP, first strand: chain 'I' and resid 659 through 661 2568 hydrogen bonds defined for protein. 7419 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: 28.45 Time building geometry restraints manager: 23.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 23017 1.36 - 1.51: 18116 1.51 - 1.65: 27831 1.65 - 1.80: 349 1.80 - 1.95: 163 Bond restraints: 69476 Sorted by residual: bond pdb=" CA ASN G 575 " pdb=" CB ASN G 575 " ideal model delta sigma weight residual 1.534 1.568 -0.035 1.57e-02 4.06e+03 4.87e+00 bond pdb=" CB PRO G 359 " pdb=" CG PRO G 359 " ideal model delta sigma weight residual 1.492 1.598 -0.106 5.00e-02 4.00e+02 4.50e+00 bond pdb=" CG LEU H 147 " pdb=" CD1 LEU H 147 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.93e+00 bond pdb=" C SER D 414 " pdb=" N ILE D 415 " ideal model delta sigma weight residual 1.331 1.308 0.023 1.20e-02 6.94e+03 3.83e+00 bond pdb=" CB ASP D 693 " pdb=" CG ASP D 693 " ideal model delta sigma weight residual 1.516 1.563 -0.047 2.50e-02 1.60e+03 3.60e+00 ... (remaining 69471 not shown) Histogram of bond angle deviations from ideal: 96.18 - 104.17: 970 104.17 - 112.17: 34808 112.17 - 120.16: 28597 120.16 - 128.16: 29301 128.16 - 136.15: 320 Bond angle restraints: 93996 Sorted by residual: angle pdb=" CB ARG H 316 " pdb=" CG ARG H 316 " pdb=" CD ARG H 316 " ideal model delta sigma weight residual 111.30 126.86 -15.56 2.30e+00 1.89e-01 4.58e+01 angle pdb=" N GLU H 402 " pdb=" CA GLU H 402 " pdb=" CB GLU H 402 " ideal model delta sigma weight residual 110.16 119.46 -9.30 1.48e+00 4.57e-01 3.95e+01 angle pdb=" N GLU F 116 " pdb=" CA GLU F 116 " pdb=" CB GLU F 116 " ideal model delta sigma weight residual 110.28 119.06 -8.78 1.55e+00 4.16e-01 3.21e+01 angle pdb=" CA GLU H 126 " pdb=" CB GLU H 126 " pdb=" CG GLU H 126 " ideal model delta sigma weight residual 114.10 125.27 -11.17 2.00e+00 2.50e-01 3.12e+01 angle pdb=" N GLU 7 91 " pdb=" CA GLU 7 91 " pdb=" CB GLU 7 91 " ideal model delta sigma weight residual 110.40 119.13 -8.73 1.63e+00 3.76e-01 2.87e+01 ... (remaining 93991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.76: 41905 32.76 - 65.52: 798 65.52 - 98.28: 82 98.28 - 131.04: 4 131.04 - 163.80: 4 Dihedral angle restraints: 42793 sinusoidal: 17665 harmonic: 25128 Sorted by residual: dihedral pdb=" CB CYS 7 474 " pdb=" SG CYS 7 474 " pdb=" SG CYS 7 522 " pdb=" CB CYS 7 522 " ideal model delta sinusoidal sigma weight residual -86.00 -146.09 60.09 1 1.00e+01 1.00e-02 4.81e+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 66.87 -126.87 1 2.00e+01 2.50e-03 3.84e+01 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 65.89 -125.89 1 2.00e+01 2.50e-03 3.81e+01 ... (remaining 42790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 9869 0.091 - 0.182: 917 0.182 - 0.274: 37 0.274 - 0.365: 8 0.365 - 0.456: 3 Chirality restraints: 10834 Sorted by residual: chirality pdb=" CG LEU I 268 " pdb=" CB LEU I 268 " pdb=" CD1 LEU I 268 " pdb=" CD2 LEU I 268 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.46 2.00e-01 2.50e+01 5.20e+00 chirality pdb=" CB ILE I 126 " pdb=" CA ILE I 126 " pdb=" CG1 ILE I 126 " pdb=" CG2 ILE I 126 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" CB ILE H 53 " pdb=" CA ILE H 53 " pdb=" CG1 ILE H 53 " pdb=" CG2 ILE H 53 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.80e+00 ... (remaining 10831 not shown) Planarity restraints: 12062 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS 6 390 " -0.092 5.00e-02 4.00e+02 1.38e-01 3.03e+01 pdb=" N PRO 6 391 " 0.238 5.00e-02 4.00e+02 pdb=" CA PRO 6 391 " -0.074 5.00e-02 4.00e+02 pdb=" CD PRO 6 391 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE H 398 " -0.024 2.00e-02 2.50e+03 4.80e-02 2.31e+01 pdb=" C PHE H 398 " 0.083 2.00e-02 2.50e+03 pdb=" O PHE H 398 " -0.031 2.00e-02 2.50e+03 pdb=" N LEU H 399 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA G 358 " 0.080 5.00e-02 4.00e+02 1.18e-01 2.23e+01 pdb=" N PRO G 359 " -0.204 5.00e-02 4.00e+02 pdb=" CA PRO G 359 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO G 359 " 0.062 5.00e-02 4.00e+02 ... (remaining 12059 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 724 2.61 - 3.19: 57579 3.19 - 3.76: 107451 3.76 - 4.33: 149880 4.33 - 4.90: 244606 Nonbonded interactions: 560240 Sorted by model distance: nonbonded pdb=" OG SER 7 467 " pdb="MG MG 72002 " model vdw 2.042 2.170 nonbonded pdb=" O3B AGS 52001 " pdb="MG MG 52002 " model vdw 2.044 2.170 nonbonded pdb=" OG SER B 550 " pdb="MG MG B2002 " model vdw 2.044 2.170 nonbonded pdb=" O3B AGS E2001 " pdb="MG MG E2002 " model vdw 2.044 2.170 nonbonded pdb=" OG SER G 467 " pdb="MG MG G2002 " model vdw 2.050 2.170 ... (remaining 560235 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 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: 3.890 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: 0.070 Extract box with map and model: 11.730 Check model and map are aligned: 0.750 Set scattering table: 0.490 Process input model: 152.130 Find NCS groups from input model: 5.500 Set up NCS constraints: 0.570 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 185.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 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 0.106 69476 Z= 0.276 Angle : 0.819 16.003 93996 Z= 0.437 Chirality : 0.052 0.456 10834 Planarity : 0.007 0.138 12062 Dihedral : 13.446 163.798 26483 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.64 % Favored : 97.31 % Rotamer: Outliers : 0.07 % Allowed : 0.38 % Favored : 99.55 % Cbeta Deviations : 0.02 % 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: -0.55 (0.08), residues: 8483 helix: -0.22 (0.08), residues: 3448 sheet: -0.14 (0.12), residues: 1589 loop : -0.41 (0.10), residues: 3446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.004 TRP H 436 HIS 0.016 0.001 HIS H 24 PHE 0.071 0.002 PHE H 169 TYR 0.033 0.002 TYR 4 519 ARG 0.020 0.001 ARG I 341 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1951 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1946 time to evaluate : 5.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 210 GLU cc_start: 0.5400 (mm-30) cc_final: 0.5136 (mm-30) REVERT: 2 232 ARG cc_start: 0.6378 (mmm-85) cc_final: 0.5721 (mtp180) REVERT: 2 258 LEU cc_start: 0.6859 (tt) cc_final: 0.6444 (mt) REVERT: 2 269 LYS cc_start: 0.6553 (ttmm) cc_final: 0.6303 (ttmt) REVERT: 2 651 ASN cc_start: 0.8164 (m-40) cc_final: 0.7704 (m-40) REVERT: 2 686 LEU cc_start: 0.4893 (pt) cc_final: 0.4210 (mt) REVERT: 2 798 ILE cc_start: 0.5147 (mt) cc_final: 0.4679 (pt) REVERT: 3 27 ARG cc_start: 0.7314 (tpt170) cc_final: 0.6979 (ttp80) REVERT: 3 97 ILE cc_start: 0.7400 (mm) cc_final: 0.7056 (mt) REVERT: 3 188 LYS cc_start: 0.7737 (mtmm) cc_final: 0.7292 (ttpt) REVERT: 3 261 MET cc_start: 0.7809 (mtp) cc_final: 0.7528 (mtt) REVERT: 3 274 ILE cc_start: 0.8757 (pt) cc_final: 0.8156 (tp) REVERT: 3 556 ILE cc_start: 0.6723 (tp) cc_final: 0.6509 (mm) REVERT: 3 682 ASN cc_start: 0.8107 (m110) cc_final: 0.7898 (m-40) REVERT: 4 178 ARG cc_start: 0.7188 (mmm160) cc_final: 0.6948 (mmm-85) REVERT: 4 266 GLN cc_start: 0.7670 (tp40) cc_final: 0.7440 (tp-100) REVERT: 4 375 ASP cc_start: 0.6733 (m-30) cc_final: 0.6448 (m-30) REVERT: 4 404 ASP cc_start: 0.6688 (m-30) cc_final: 0.6434 (m-30) REVERT: 4 583 LYS cc_start: 0.7868 (mmpt) cc_final: 0.7568 (mtmm) REVERT: 4 666 ASN cc_start: 0.7934 (m-40) cc_final: 0.7700 (m110) REVERT: 4 715 LYS cc_start: 0.6891 (pttp) cc_final: 0.6250 (tptm) REVERT: 4 811 MET cc_start: 0.8496 (ttp) cc_final: 0.8245 (ttm) REVERT: 5 25 THR cc_start: 0.7159 (m) cc_final: 0.6927 (p) REVERT: 5 249 LYS cc_start: 0.7848 (mmmm) cc_final: 0.7562 (mttp) REVERT: 5 279 ASP cc_start: 0.6707 (p0) cc_final: 0.6418 (p0) REVERT: 5 358 LEU cc_start: 0.5114 (mt) cc_final: 0.4898 (tm) REVERT: 5 379 PHE cc_start: 0.7439 (t80) cc_final: 0.7050 (t80) REVERT: 5 556 VAL cc_start: 0.6463 (t) cc_final: 0.6210 (p) REVERT: 5 581 ASN cc_start: 0.5674 (t0) cc_final: 0.4623 (m-40) REVERT: 5 625 ASN cc_start: 0.6223 (m110) cc_final: 0.5301 (t0) REVERT: 5 671 ILE cc_start: 0.7111 (mm) cc_final: 0.6754 (mp) REVERT: 6 105 ASP cc_start: 0.7283 (m-30) cc_final: 0.6785 (t0) REVERT: 6 116 GLU cc_start: 0.6774 (pt0) cc_final: 0.6559 (mt-10) REVERT: 6 156 GLN cc_start: 0.6841 (mm-40) cc_final: 0.6457 (mt0) REVERT: 6 174 TYR cc_start: 0.7836 (t80) cc_final: 0.7438 (t80) REVERT: 6 299 GLU cc_start: 0.6890 (pm20) cc_final: 0.6494 (pt0) REVERT: 6 328 THR cc_start: 0.6302 (p) cc_final: 0.5819 (t) REVERT: 6 347 ASN cc_start: 0.6590 (t0) cc_final: 0.5719 (m-40) REVERT: 6 367 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7538 (mt-10) REVERT: 6 724 ASP cc_start: 0.6317 (m-30) cc_final: 0.6106 (m-30) REVERT: 6 764 ILE cc_start: 0.7120 (mt) cc_final: 0.6669 (pp) REVERT: 6 776 LYS cc_start: 0.7270 (mmtt) cc_final: 0.7017 (mmtp) REVERT: 6 794 ARG cc_start: 0.5272 (mtp-110) cc_final: 0.4604 (mtm110) REVERT: 6 798 ARG cc_start: 0.6894 (mtt90) cc_final: 0.6648 (ttp-170) REVERT: 6 829 ASP cc_start: 0.6740 (t0) cc_final: 0.6271 (t70) REVERT: 7 64 MET cc_start: 0.8712 (mmt) cc_final: 0.8262 (mmt) REVERT: 7 69 LYS cc_start: 0.8035 (mtmm) cc_final: 0.7734 (mtpt) REVERT: 7 76 ASN cc_start: 0.7276 (t0) cc_final: 0.7020 (m110) REVERT: 7 81 ASP cc_start: 0.7603 (m-30) cc_final: 0.7174 (t0) REVERT: 7 159 ASN cc_start: 0.7365 (m-40) cc_final: 0.6965 (m110) REVERT: 7 162 ARG cc_start: 0.7133 (ttm-80) cc_final: 0.6699 (ttt90) REVERT: 7 247 ARG cc_start: 0.7867 (tpp80) cc_final: 0.7574 (tmm160) REVERT: 7 268 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7910 (mt-10) REVERT: 7 396 ASP cc_start: 0.5880 (p0) cc_final: 0.5665 (m-30) REVERT: 7 484 THR cc_start: 0.7352 (m) cc_final: 0.7062 (m) REVERT: 7 498 MET cc_start: 0.5830 (ptt) cc_final: 0.5562 (ppp) REVERT: 7 515 LEU cc_start: 0.8336 (mt) cc_final: 0.8107 (mm) REVERT: 7 537 ILE cc_start: 0.7766 (mt) cc_final: 0.7500 (mm) REVERT: 7 556 THR cc_start: 0.8563 (t) cc_final: 0.8322 (m) REVERT: 7 598 PHE cc_start: 0.8244 (m-80) cc_final: 0.7932 (m-80) REVERT: 7 621 MET cc_start: 0.7767 (ttp) cc_final: 0.7533 (ttm) REVERT: 7 688 THR cc_start: 0.8425 (m) cc_final: 0.8115 (p) REVERT: 7 714 GLU cc_start: 0.6809 (mm-30) cc_final: 0.6454 (tm-30) REVERT: B 227 TYR cc_start: 0.6252 (m-80) cc_final: 0.5676 (m-80) REVERT: B 269 LYS cc_start: 0.6520 (ttmm) cc_final: 0.5299 (mppt) REVERT: B 272 ASP cc_start: 0.5871 (t0) cc_final: 0.5649 (m-30) REVERT: B 823 MET cc_start: 0.7932 (mtt) cc_final: 0.7572 (mtt) REVERT: B 834 LEU cc_start: 0.6823 (mm) cc_final: 0.6067 (tp) REVERT: C 39 ARG cc_start: 0.6703 (ttm110) cc_final: 0.6262 (ttp-110) REVERT: C 48 TYR cc_start: 0.7356 (t80) cc_final: 0.7089 (t80) REVERT: C 188 LYS cc_start: 0.7797 (mtmt) cc_final: 0.7067 (mptt) REVERT: C 215 THR cc_start: 0.8340 (p) cc_final: 0.7959 (t) REVERT: C 234 GLU cc_start: 0.6483 (mt-10) cc_final: 0.5964 (mp0) REVERT: C 235 ASP cc_start: 0.6344 (p0) cc_final: 0.5978 (p0) REVERT: C 237 GLU cc_start: 0.6988 (mp0) cc_final: 0.6634 (mt-10) REVERT: C 318 LYS cc_start: 0.7556 (ptpt) cc_final: 0.7194 (pttm) REVERT: C 322 LEU cc_start: 0.8030 (mm) cc_final: 0.7816 (mm) REVERT: C 348 ARG cc_start: 0.6643 (mtm110) cc_final: 0.6242 (mtt90) REVERT: C 361 ASP cc_start: 0.7494 (m-30) cc_final: 0.7254 (m-30) REVERT: C 362 ILE cc_start: 0.7969 (mt) cc_final: 0.7644 (mm) REVERT: C 407 MET cc_start: 0.8218 (mtp) cc_final: 0.8015 (mtm) REVERT: C 477 LYS cc_start: 0.7346 (mttm) cc_final: 0.7072 (mttm) REVERT: C 505 THR cc_start: 0.8292 (t) cc_final: 0.7812 (m) REVERT: C 556 ILE cc_start: 0.7415 (pt) cc_final: 0.7096 (tp) REVERT: C 664 LYS cc_start: 0.7645 (mtpp) cc_final: 0.7271 (mtpt) REVERT: C 665 GLU cc_start: 0.6872 (mt-10) cc_final: 0.6512 (mp0) REVERT: D 204 LYS cc_start: 0.7437 (pttp) cc_final: 0.7222 (pttm) REVERT: D 408 ASP cc_start: 0.7188 (m-30) cc_final: 0.6902 (m-30) REVERT: D 483 GLN cc_start: 0.6386 (tp40) cc_final: 0.6067 (mt0) REVERT: D 580 TYR cc_start: 0.7467 (t80) cc_final: 0.7256 (t80) REVERT: D 609 VAL cc_start: 0.7302 (m) cc_final: 0.7060 (t) REVERT: D 649 MET cc_start: 0.7580 (mmt) cc_final: 0.6866 (mmt) REVERT: D 686 LEU cc_start: 0.7412 (mt) cc_final: 0.7146 (mp) REVERT: E 5 ARG cc_start: 0.7376 (ttp80) cc_final: 0.7000 (ttp-110) REVERT: E 33 ASN cc_start: 0.7307 (m-40) cc_final: 0.7000 (m110) REVERT: E 182 MET cc_start: 0.8289 (ttm) cc_final: 0.8045 (ttp) REVERT: E 209 ARG cc_start: 0.7129 (mmm-85) cc_final: 0.6905 (mmt-90) REVERT: E 249 LYS cc_start: 0.7826 (mmtp) cc_final: 0.7472 (mppt) REVERT: E 300 ILE cc_start: 0.8175 (mm) cc_final: 0.7885 (mm) REVERT: E 356 GLU cc_start: 0.5173 (mp0) cc_final: 0.4915 (mm-30) REVERT: E 369 ILE cc_start: 0.6890 (pt) cc_final: 0.6656 (mt) REVERT: E 404 MET cc_start: 0.6942 (ttm) cc_final: 0.6266 (tpt) REVERT: E 485 MET cc_start: 0.8380 (ttm) cc_final: 0.8101 (ttp) REVERT: E 497 MET cc_start: 0.8261 (mtt) cc_final: 0.8054 (mtm) REVERT: E 592 SER cc_start: 0.6593 (m) cc_final: 0.5691 (p) REVERT: E 597 GLU cc_start: 0.6101 (pm20) cc_final: 0.5882 (mm-30) REVERT: E 614 LEU cc_start: 0.7858 (mt) cc_final: 0.7651 (mt) REVERT: E 661 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6698 (mt-10) REVERT: F 147 ASP cc_start: 0.6027 (t0) cc_final: 0.5763 (t0) REVERT: F 348 VAL cc_start: 0.6827 (m) cc_final: 0.6555 (t) REVERT: F 362 GLN cc_start: 0.8225 (tt0) cc_final: 0.7869 (tt0) REVERT: F 608 LEU cc_start: 0.8214 (mt) cc_final: 0.7981 (mt) REVERT: F 764 ILE cc_start: 0.7034 (mp) cc_final: 0.6593 (pp) REVERT: G 15 ASN cc_start: 0.7027 (m-40) cc_final: 0.5910 (t0) REVERT: G 133 ASP cc_start: 0.6119 (p0) cc_final: 0.5857 (t70) REVERT: G 282 SER cc_start: 0.8223 (p) cc_final: 0.8002 (m) REVERT: G 291 GLN cc_start: 0.7971 (mt0) cc_final: 0.7606 (mt0) REVERT: G 317 GLU cc_start: 0.6698 (tt0) cc_final: 0.6432 (tt0) REVERT: G 402 MET cc_start: 0.3603 (mpp) cc_final: 0.3386 (tpt) REVERT: G 412 ASN cc_start: 0.7504 (t0) cc_final: 0.7057 (m-40) REVERT: G 449 LYS cc_start: 0.7185 (mtmm) cc_final: 0.6734 (mmmm) REVERT: G 459 MET cc_start: 0.7681 (ttp) cc_final: 0.7294 (ttm) REVERT: G 618 TYR cc_start: 0.7520 (t80) cc_final: 0.7198 (t80) REVERT: G 640 GLU cc_start: 0.7510 (pt0) cc_final: 0.6841 (pt0) REVERT: G 690 LEU cc_start: 0.8568 (mt) cc_final: 0.8350 (mt) REVERT: H 34 LYS cc_start: 0.3929 (tttt) cc_final: 0.3697 (tptp) REVERT: H 92 ASN cc_start: 0.5095 (t0) cc_final: 0.4760 (t0) REVERT: H 138 LYS cc_start: 0.3443 (mmmt) cc_final: 0.2405 (tptm) REVERT: H 288 GLU cc_start: 0.5147 (pm20) cc_final: 0.4772 (mm-30) REVERT: H 300 ILE cc_start: 0.5733 (mp) cc_final: 0.5420 (mp) REVERT: H 310 LEU cc_start: 0.5495 (tt) cc_final: 0.5174 (pp) REVERT: H 324 ASP cc_start: 0.6655 (p0) cc_final: 0.6381 (p0) REVERT: H 332 LEU cc_start: 0.6044 (mt) cc_final: 0.5723 (tp) REVERT: H 339 LYS cc_start: 0.6180 (mmpt) cc_final: 0.5688 (mttt) REVERT: H 358 ILE cc_start: 0.3342 (pt) cc_final: 0.3135 (mt) REVERT: H 398 PHE cc_start: 0.3084 (t80) cc_final: 0.2822 (t80) REVERT: H 402 GLU cc_start: 0.1981 (mp0) cc_final: 0.1461 (mt-10) REVERT: H 452 MET cc_start: 0.5993 (mmp) cc_final: 0.5595 (mmt) REVERT: H 465 LYS cc_start: 0.4018 (mppt) cc_final: 0.3655 (mmmt) REVERT: I 152 LYS cc_start: 0.4068 (mttt) cc_final: 0.3861 (tppt) REVERT: I 158 LEU cc_start: 0.2630 (tt) cc_final: 0.2375 (mt) REVERT: I 233 THR cc_start: 0.4841 (p) cc_final: 0.4345 (p) REVERT: I 325 LYS cc_start: 0.3803 (mppt) cc_final: 0.3492 (ttpp) REVERT: I 382 MET cc_start: 0.2503 (mmp) cc_final: 0.1094 (tpt) REVERT: I 524 MET cc_start: 0.8730 (mmp) cc_final: 0.8413 (mmm) REVERT: I 662 GLU cc_start: 0.6373 (tt0) cc_final: 0.6121 (tp30) REVERT: I 672 GLU cc_start: 0.5562 (pm20) cc_final: 0.5329 (pm20) REVERT: I 697 ILE cc_start: 0.2752 (mm) cc_final: 0.2421 (pt) outliers start: 5 outliers final: 6 residues processed: 1951 average time/residue: 1.5946 time to fit residues: 3984.3015 Evaluate side-chains 1035 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1029 time to evaluate : 5.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 339 THR Chi-restraints excluded: chain B residue 673 ILE Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 671 ILE Chi-restraints excluded: chain G residue 350 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 717 optimal weight: 5.9990 chunk 644 optimal weight: 7.9990 chunk 357 optimal weight: 4.9990 chunk 220 optimal weight: 0.0980 chunk 434 optimal weight: 5.9990 chunk 344 optimal weight: 0.8980 chunk 666 optimal weight: 0.6980 chunk 257 optimal weight: 8.9990 chunk 405 optimal weight: 6.9990 chunk 495 optimal weight: 0.8980 chunk 771 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 454 ASN ** 2 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 856 GLN 3 52 ASN 3 307 ASN 3 340 GLN ** 3 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 493 GLN 3 587 ASN ** 3 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 327 ASN 4 377 ASN 4 380 ASN ** 4 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 726 ASN 5 195 ASN 5 334 GLN ** 5 499 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 539 ASN 5 585 ASN 5 587 GLN 6 264 GLN 6 274 HIS ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 700 ASN 6 786 GLN 7 87 GLN ** 7 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 108 GLN 7 297 GLN 7 320 GLN ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 662 GLN B 433 ASN B 615 GLN B 658 ASN B 666 ASN C 29 GLN ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN C 374 HIS C 395 ASN C 487 HIS C 691 ASN C 722 ASN D 229 GLN D 253 GLN D 320 ASN D 327 ASN D 685 ASN D 716 ASN D 726 ASN E 108 GLN E 235 ASN E 454 GLN E 499 GLN E 571 HIS E 625 ASN E 685 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 GLN F 264 GLN F 347 ASN F 583 GLN F 633 ASN F 698 ASN G 123 ASN G 178 ASN G 274 ASN H 378 ASN H 439 HIS ** H 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 470 ASN ** I 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 69476 Z= 0.166 Angle : 0.536 11.088 93996 Z= 0.276 Chirality : 0.042 0.236 10834 Planarity : 0.005 0.080 12062 Dihedral : 7.789 171.381 9640 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.13 % Favored : 97.82 % Rotamer: Outliers : 2.69 % Allowed : 12.71 % Favored : 84.61 % 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: 0.11 (0.09), residues: 8483 helix: 0.57 (0.09), residues: 3469 sheet: -0.10 (0.13), residues: 1553 loop : -0.18 (0.10), residues: 3461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 303 HIS 0.011 0.001 HIS 6 653 PHE 0.020 0.001 PHE H 169 TYR 0.020 0.001 TYR 4 519 ARG 0.009 0.000 ARG B 795 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1270 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1066 time to evaluate : 5.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 196 GLU cc_start: 0.5732 (OUTLIER) cc_final: 0.5522 (mt-10) REVERT: 2 232 ARG cc_start: 0.6507 (mmm-85) cc_final: 0.5920 (ttp-170) REVERT: 2 258 LEU cc_start: 0.6875 (tt) cc_final: 0.6492 (mt) REVERT: 2 269 LYS cc_start: 0.6506 (ttmm) cc_final: 0.6234 (ttmt) REVERT: 2 374 ARG cc_start: 0.6241 (OUTLIER) cc_final: 0.5502 (ttm110) REVERT: 2 425 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6172 (tm-30) REVERT: 2 457 LYS cc_start: 0.6068 (mmmt) cc_final: 0.5707 (mttt) REVERT: 2 651 ASN cc_start: 0.8127 (m-40) cc_final: 0.7657 (m-40) REVERT: 2 667 VAL cc_start: 0.7376 (OUTLIER) cc_final: 0.7000 (p) REVERT: 2 684 ARG cc_start: 0.3778 (OUTLIER) cc_final: 0.3112 (ptp90) REVERT: 2 686 LEU cc_start: 0.4713 (pt) cc_final: 0.4264 (mt) REVERT: 3 27 ARG cc_start: 0.7564 (tpt170) cc_final: 0.6989 (ttp80) REVERT: 3 52 ASN cc_start: 0.5288 (m-40) cc_final: 0.5014 (m110) REVERT: 3 97 ILE cc_start: 0.7744 (mm) cc_final: 0.7451 (mt) REVERT: 3 188 LYS cc_start: 0.7839 (mtmm) cc_final: 0.7311 (ttpt) REVERT: 3 189 THR cc_start: 0.7987 (m) cc_final: 0.7521 (t) REVERT: 3 234 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.6006 (tm-30) REVERT: 3 261 MET cc_start: 0.7889 (mtp) cc_final: 0.7457 (mtt) REVERT: 3 274 ILE cc_start: 0.8630 (pt) cc_final: 0.8224 (tp) REVERT: 3 353 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8431 (mm) REVERT: 3 365 GLN cc_start: 0.7122 (mm-40) cc_final: 0.6588 (mm110) REVERT: 3 504 THR cc_start: 0.8509 (OUTLIER) cc_final: 0.8077 (t) REVERT: 3 556 ILE cc_start: 0.6749 (tp) cc_final: 0.6452 (mm) REVERT: 3 682 ASN cc_start: 0.8289 (m110) cc_final: 0.8068 (m-40) REVERT: 4 266 GLN cc_start: 0.7776 (tp40) cc_final: 0.7541 (tp-100) REVERT: 4 275 THR cc_start: 0.8721 (t) cc_final: 0.8434 (m) REVERT: 4 327 ASN cc_start: 0.7949 (OUTLIER) cc_final: 0.7498 (m110) REVERT: 4 375 ASP cc_start: 0.6652 (m-30) cc_final: 0.6361 (m-30) REVERT: 4 404 ASP cc_start: 0.6829 (m-30) cc_final: 0.6544 (m-30) REVERT: 4 583 LYS cc_start: 0.7911 (mmpt) cc_final: 0.7544 (mtmm) REVERT: 4 715 LYS cc_start: 0.6801 (pttp) cc_final: 0.6271 (tptm) REVERT: 5 25 THR cc_start: 0.7140 (m) cc_final: 0.6914 (p) REVERT: 5 139 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8331 (pp) REVERT: 5 184 ARG cc_start: 0.6491 (OUTLIER) cc_final: 0.6129 (mtm-85) REVERT: 5 239 ASP cc_start: 0.7074 (m-30) cc_final: 0.6858 (m-30) REVERT: 5 302 ASN cc_start: 0.5386 (t0) cc_final: 0.5138 (t0) REVERT: 5 383 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7011 (p0) REVERT: 5 495 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7410 (tt0) REVERT: 5 556 VAL cc_start: 0.6315 (t) cc_final: 0.6067 (p) REVERT: 5 574 ASN cc_start: 0.7363 (m-40) cc_final: 0.7158 (m-40) REVERT: 5 581 ASN cc_start: 0.5515 (t0) cc_final: 0.5279 (m110) REVERT: 5 625 ASN cc_start: 0.6628 (m110) cc_final: 0.5566 (t0) REVERT: 5 654 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7178 (mt-10) REVERT: 5 671 ILE cc_start: 0.7075 (mm) cc_final: 0.6753 (mp) REVERT: 5 675 ARG cc_start: 0.7197 (ttp80) cc_final: 0.6818 (ptt90) REVERT: 6 105 ASP cc_start: 0.7454 (m-30) cc_final: 0.6858 (t0) REVERT: 6 156 GLN cc_start: 0.6950 (mm-40) cc_final: 0.6621 (mt0) REVERT: 6 172 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6780 (mm-30) REVERT: 6 174 TYR cc_start: 0.7910 (t80) cc_final: 0.7427 (t80) REVERT: 6 299 GLU cc_start: 0.7094 (pm20) cc_final: 0.6336 (mt-10) REVERT: 6 328 THR cc_start: 0.6358 (p) cc_final: 0.6123 (p) REVERT: 6 347 ASN cc_start: 0.6494 (t0) cc_final: 0.5714 (m-40) REVERT: 6 367 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7593 (mt-10) REVERT: 6 624 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6232 (tt0) REVERT: 6 696 ARG cc_start: 0.7082 (tpm170) cc_final: 0.6119 (tmt-80) REVERT: 6 764 ILE cc_start: 0.7159 (mt) cc_final: 0.6675 (pp) REVERT: 6 794 ARG cc_start: 0.5296 (mtp-110) cc_final: 0.4633 (mtm110) REVERT: 7 64 MET cc_start: 0.8788 (mmt) cc_final: 0.8547 (mmt) REVERT: 7 69 LYS cc_start: 0.8002 (mtmm) cc_final: 0.7760 (mtpt) REVERT: 7 76 ASN cc_start: 0.7508 (t0) cc_final: 0.7147 (m110) REVERT: 7 81 ASP cc_start: 0.7648 (m-30) cc_final: 0.7256 (t0) REVERT: 7 159 ASN cc_start: 0.7336 (m-40) cc_final: 0.6935 (m110) REVERT: 7 162 ARG cc_start: 0.7085 (ttm-80) cc_final: 0.6766 (ttm170) REVERT: 7 188 GLU cc_start: 0.5732 (tt0) cc_final: 0.5407 (tt0) REVERT: 7 320 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7701 (mp-120) REVERT: 7 396 ASP cc_start: 0.6059 (p0) cc_final: 0.5698 (m-30) REVERT: 7 498 MET cc_start: 0.5963 (ptt) cc_final: 0.5620 (mtm) REVERT: 7 515 LEU cc_start: 0.8355 (mt) cc_final: 0.8096 (mm) REVERT: 7 537 ILE cc_start: 0.7832 (mt) cc_final: 0.7537 (mm) REVERT: 7 598 PHE cc_start: 0.8312 (m-80) cc_final: 0.7906 (m-80) REVERT: 7 652 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.6729 (mtp) REVERT: 7 688 THR cc_start: 0.8454 (m) cc_final: 0.8013 (p) REVERT: 7 714 GLU cc_start: 0.6908 (mm-30) cc_final: 0.6459 (tm-30) REVERT: B 227 TYR cc_start: 0.6267 (m-80) cc_final: 0.5667 (m-80) REVERT: B 267 MET cc_start: 0.6908 (mmm) cc_final: 0.6694 (mmm) REVERT: B 269 LYS cc_start: 0.6615 (ttmm) cc_final: 0.5427 (mppt) REVERT: B 290 HIS cc_start: 0.6088 (m-70) cc_final: 0.5778 (m170) REVERT: B 374 ARG cc_start: 0.5426 (ttt-90) cc_final: 0.5027 (ttt180) REVERT: B 413 ASP cc_start: 0.6852 (OUTLIER) cc_final: 0.6618 (m-30) REVERT: B 496 LYS cc_start: 0.6931 (OUTLIER) cc_final: 0.6634 (ttmm) REVERT: B 501 MET cc_start: 0.7771 (mmm) cc_final: 0.7298 (mmt) REVERT: B 506 TYR cc_start: 0.6117 (t80) cc_final: 0.5830 (t80) REVERT: B 694 ARG cc_start: 0.6406 (mtm110) cc_final: 0.6179 (mtm110) REVERT: B 705 ARG cc_start: 0.6306 (OUTLIER) cc_final: 0.5754 (mtp180) REVERT: B 834 LEU cc_start: 0.6926 (mm) cc_final: 0.6202 (tp) REVERT: C 39 ARG cc_start: 0.6849 (ttm110) cc_final: 0.6333 (ttp-110) REVERT: C 43 ARG cc_start: 0.6081 (mmm160) cc_final: 0.5787 (tpp-160) REVERT: C 48 TYR cc_start: 0.7450 (t80) cc_final: 0.7188 (t80) REVERT: C 188 LYS cc_start: 0.7846 (mtmt) cc_final: 0.7463 (mttp) REVERT: C 234 GLU cc_start: 0.6663 (mt-10) cc_final: 0.5896 (mp0) REVERT: C 235 ASP cc_start: 0.6355 (p0) cc_final: 0.5967 (p0) REVERT: C 237 GLU cc_start: 0.7091 (mp0) cc_final: 0.6749 (mt-10) REVERT: C 348 ARG cc_start: 0.6674 (mtm110) cc_final: 0.6278 (mtt90) REVERT: C 407 MET cc_start: 0.8257 (mtp) cc_final: 0.7999 (mtm) REVERT: C 458 GLU cc_start: 0.6123 (tp30) cc_final: 0.5729 (tp30) REVERT: C 464 LEU cc_start: 0.7879 (mt) cc_final: 0.7431 (mt) REVERT: C 477 LYS cc_start: 0.7341 (mttm) cc_final: 0.6947 (mttp) REVERT: C 505 THR cc_start: 0.8364 (t) cc_final: 0.7869 (m) REVERT: C 556 ILE cc_start: 0.7265 (pt) cc_final: 0.6875 (mm) REVERT: C 664 LYS cc_start: 0.7621 (mtpp) cc_final: 0.7187 (mtpt) REVERT: C 723 LYS cc_start: 0.7067 (pttt) cc_final: 0.6810 (tttt) REVERT: D 221 ASP cc_start: 0.7218 (m-30) cc_final: 0.6988 (m-30) REVERT: D 235 GLU cc_start: 0.6248 (mt-10) cc_final: 0.5611 (tp30) REVERT: D 408 ASP cc_start: 0.7243 (m-30) cc_final: 0.6906 (m-30) REVERT: D 483 GLN cc_start: 0.6528 (tp40) cc_final: 0.6175 (mt0) REVERT: E 5 ARG cc_start: 0.7498 (ttp80) cc_final: 0.7015 (ttp-110) REVERT: E 33 ASN cc_start: 0.7392 (m-40) cc_final: 0.7116 (m110) REVERT: E 144 ASN cc_start: 0.6821 (t0) cc_final: 0.6369 (t0) REVERT: E 182 MET cc_start: 0.8403 (ttm) cc_final: 0.8068 (ttp) REVERT: E 209 ARG cc_start: 0.7118 (mmm-85) cc_final: 0.6882 (mmt-90) REVERT: E 249 LYS cc_start: 0.7930 (mmtp) cc_final: 0.7598 (mppt) REVERT: E 280 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7507 (mtp85) REVERT: E 354 GLU cc_start: 0.6441 (OUTLIER) cc_final: 0.6064 (mm-30) REVERT: E 404 MET cc_start: 0.7059 (ttm) cc_final: 0.6366 (tpt) REVERT: E 430 GLU cc_start: 0.7222 (tm-30) cc_final: 0.6879 (tm-30) REVERT: E 458 MET cc_start: 0.5218 (mtp) cc_final: 0.4850 (mtm) REVERT: E 469 MET cc_start: 0.7947 (mmm) cc_final: 0.7294 (mmm) REVERT: E 513 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7730 (pp) REVERT: E 561 ASN cc_start: 0.5625 (t0) cc_final: 0.5398 (t0) REVERT: E 597 GLU cc_start: 0.6189 (pm20) cc_final: 0.5876 (mm-30) REVERT: E 661 GLU cc_start: 0.6872 (mt-10) cc_final: 0.6669 (mt-10) REVERT: F 313 MET cc_start: 0.3883 (mpt) cc_final: 0.2380 (ptt) REVERT: F 352 ARG cc_start: 0.6943 (mtp85) cc_final: 0.6697 (mmm160) REVERT: F 362 GLN cc_start: 0.8212 (tt0) cc_final: 0.7874 (tt0) REVERT: F 521 LYS cc_start: 0.4695 (mmpt) cc_final: 0.4325 (mmtp) REVERT: F 737 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.7080 (mttt) REVERT: F 764 ILE cc_start: 0.7086 (mp) cc_final: 0.6546 (pp) REVERT: G 15 ASN cc_start: 0.7047 (m-40) cc_final: 0.5892 (t0) REVERT: G 247 ARG cc_start: 0.8107 (ttt90) cc_final: 0.7671 (ttp80) REVERT: G 291 GLN cc_start: 0.7979 (mt0) cc_final: 0.7617 (mt0) REVERT: G 412 ASN cc_start: 0.7509 (t0) cc_final: 0.7003 (m-40) REVERT: G 427 ASP cc_start: 0.7770 (m-30) cc_final: 0.7466 (m-30) REVERT: G 449 LYS cc_start: 0.7229 (mtmm) cc_final: 0.6769 (mmmm) REVERT: G 508 LEU cc_start: 0.6852 (tp) cc_final: 0.6545 (mt) REVERT: G 529 MET cc_start: 0.6865 (mtm) cc_final: 0.6195 (mtt) REVERT: G 541 MET cc_start: 0.8085 (mtt) cc_final: 0.7245 (mtm) REVERT: G 554 ASN cc_start: 0.8522 (OUTLIER) cc_final: 0.8179 (t0) REVERT: G 556 THR cc_start: 0.8005 (t) cc_final: 0.7582 (m) REVERT: G 607 ASP cc_start: 0.7125 (OUTLIER) cc_final: 0.6506 (m-30) REVERT: G 618 TYR cc_start: 0.7523 (t80) cc_final: 0.7127 (t80) REVERT: G 640 GLU cc_start: 0.7459 (pt0) cc_final: 0.6666 (tt0) REVERT: G 659 TYR cc_start: 0.7841 (t80) cc_final: 0.7615 (t80) REVERT: G 690 LEU cc_start: 0.8550 (mt) cc_final: 0.8295 (mt) REVERT: G 714 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6542 (tp30) REVERT: H 34 LYS cc_start: 0.3987 (tttt) cc_final: 0.3464 (tptp) REVERT: H 51 LYS cc_start: 0.3258 (tttt) cc_final: 0.2915 (ttpm) REVERT: H 143 TYR cc_start: 0.2868 (t80) cc_final: 0.2576 (t80) REVERT: H 288 GLU cc_start: 0.5301 (pm20) cc_final: 0.4958 (mm-30) REVERT: H 332 LEU cc_start: 0.6309 (mt) cc_final: 0.5888 (tp) REVERT: H 358 ILE cc_start: 0.3990 (pt) cc_final: 0.3561 (mt) REVERT: H 402 GLU cc_start: 0.2585 (mp0) cc_final: 0.2266 (mm-30) REVERT: H 426 TYR cc_start: 0.2747 (t80) cc_final: 0.1559 (p90) REVERT: H 452 MET cc_start: 0.6072 (mmp) cc_final: 0.5650 (mmt) REVERT: H 465 LYS cc_start: 0.4097 (mppt) cc_final: 0.3651 (mmmt) REVERT: I 120 MET cc_start: 0.1798 (pp-130) cc_final: 0.0536 (mpt) REVERT: I 125 ARG cc_start: 0.3287 (mmm-85) cc_final: 0.3007 (mmm-85) REVERT: I 127 TYR cc_start: 0.3654 (t80) cc_final: 0.3147 (t80) REVERT: I 144 MET cc_start: 0.3817 (mmt) cc_final: 0.3587 (mmm) REVERT: I 152 LYS cc_start: 0.4189 (mttt) cc_final: 0.3910 (tppt) REVERT: I 158 LEU cc_start: 0.2988 (tt) cc_final: 0.2448 (mp) REVERT: I 325 LYS cc_start: 0.3674 (mppt) cc_final: 0.3302 (ttpp) REVERT: I 382 MET cc_start: 0.2280 (mmp) cc_final: 0.1008 (tpt) REVERT: I 662 GLU cc_start: 0.6434 (tt0) cc_final: 0.5799 (tp30) outliers start: 204 outliers final: 78 residues processed: 1210 average time/residue: 1.5366 time to fit residues: 2403.3055 Evaluate side-chains 1010 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 906 time to evaluate : 5.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 196 GLU Chi-restraints excluded: chain 2 residue 374 ARG Chi-restraints excluded: chain 2 residue 425 GLU Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 504 SER Chi-restraints excluded: chain 2 residue 590 THR Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 684 ARG Chi-restraints excluded: chain 2 residue 697 THR Chi-restraints excluded: chain 2 residue 786 VAL Chi-restraints excluded: chain 2 residue 851 VAL Chi-restraints excluded: chain 3 residue 234 GLU Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 353 LEU Chi-restraints excluded: chain 3 residue 440 VAL Chi-restraints excluded: chain 3 residue 486 ILE Chi-restraints excluded: chain 3 residue 504 THR Chi-restraints excluded: chain 3 residue 656 LEU Chi-restraints excluded: chain 4 residue 284 ILE Chi-restraints excluded: chain 4 residue 296 ILE Chi-restraints excluded: chain 4 residue 327 ASN Chi-restraints excluded: chain 4 residue 328 LEU Chi-restraints excluded: chain 4 residue 609 VAL Chi-restraints excluded: chain 4 residue 661 ILE Chi-restraints excluded: chain 4 residue 674 SER Chi-restraints excluded: chain 4 residue 749 MET Chi-restraints excluded: chain 4 residue 761 ILE Chi-restraints excluded: chain 4 residue 797 GLN Chi-restraints excluded: chain 5 residue 139 LEU Chi-restraints excluded: chain 5 residue 184 ARG Chi-restraints excluded: chain 5 residue 383 ASP Chi-restraints excluded: chain 5 residue 452 SER Chi-restraints excluded: chain 5 residue 495 GLU Chi-restraints excluded: chain 5 residue 583 MET Chi-restraints excluded: chain 5 residue 592 SER Chi-restraints excluded: chain 5 residue 624 SER Chi-restraints excluded: chain 5 residue 633 LEU Chi-restraints excluded: chain 5 residue 654 GLU Chi-restraints excluded: chain 5 residue 661 GLU Chi-restraints excluded: chain 6 residue 313 MET Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 446 ARG Chi-restraints excluded: chain 6 residue 462 ILE Chi-restraints excluded: chain 6 residue 771 SER Chi-restraints excluded: chain 6 residue 831 LEU Chi-restraints excluded: chain 7 residue 139 LEU Chi-restraints excluded: chain 7 residue 141 VAL Chi-restraints excluded: chain 7 residue 283 GLU Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 320 GLN Chi-restraints excluded: chain 7 residue 329 ARG Chi-restraints excluded: chain 7 residue 410 VAL Chi-restraints excluded: chain 7 residue 570 LEU Chi-restraints excluded: chain 7 residue 592 SER Chi-restraints excluded: chain 7 residue 652 MET Chi-restraints excluded: chain 7 residue 670 ASP Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 324 ASN Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 486 ILE Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 639 ASP Chi-restraints excluded: chain D residue 661 ILE Chi-restraints excluded: chain D residue 800 SER Chi-restraints excluded: chain D residue 833 ILE Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 280 ARG Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain E residue 517 THR Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 462 ILE Chi-restraints excluded: chain F residue 501 GLN Chi-restraints excluded: chain F residue 519 MET Chi-restraints excluded: chain F residue 727 LEU Chi-restraints excluded: chain F residue 737 LYS Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 554 ASN Chi-restraints excluded: chain G residue 607 ASP Chi-restraints excluded: chain G residue 656 VAL Chi-restraints excluded: chain G residue 714 GLU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 440 TYR Chi-restraints excluded: chain I residue 239 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 428 optimal weight: 3.9990 chunk 239 optimal weight: 1.9990 chunk 642 optimal weight: 0.3980 chunk 525 optimal weight: 10.0000 chunk 212 optimal weight: 9.9990 chunk 773 optimal weight: 0.7980 chunk 835 optimal weight: 4.9990 chunk 688 optimal weight: 9.9990 chunk 766 optimal weight: 5.9990 chunk 263 optimal weight: 9.9990 chunk 620 optimal weight: 0.9980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 561 HIS 3 259 GLN 3 269 GLN 3 307 ASN 3 324 ASN 3 340 GLN 3 503 HIS 3 564 HIS 3 587 ASN ** 3 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 327 ASN ** 4 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 613 GLN 4 666 ASN 4 726 ASN 5 20 ASN 5 253 GLN 5 334 GLN 5 499 GLN 5 579 ASN 5 587 GLN 6 264 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 297 GLN ** 7 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 657 ASN 7 662 GLN B 433 ASN ** B 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 ASN C 307 ASN C 395 ASN C 722 ASN D 229 GLN D 253 GLN D 413 HIS D 685 ASN D 726 ASN E 334 GLN E 454 GLN E 625 ASN E 636 ASN E 685 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 264 GLN F 347 ASN F 583 GLN F 698 ASN G 19 ASN ** G 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 ASN G 543 GLN G 558 ASN G 623 ASN I 657 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 69476 Z= 0.252 Angle : 0.578 10.452 93996 Z= 0.297 Chirality : 0.044 0.239 10834 Planarity : 0.005 0.064 12062 Dihedral : 7.601 179.218 9630 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.44 % Favored : 97.52 % Rotamer: Outliers : 3.96 % Allowed : 14.21 % Favored : 81.83 % 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: 0.23 (0.09), residues: 8483 helix: 0.75 (0.09), residues: 3470 sheet: -0.12 (0.12), residues: 1589 loop : -0.17 (0.10), residues: 3424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 338 HIS 0.008 0.001 HIS 6 653 PHE 0.023 0.002 PHE I 702 TYR 0.021 0.002 TYR 6 136 ARG 0.009 0.001 ARG G 162 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1304 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 1003 time to evaluate : 5.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 196 GLU cc_start: 0.6002 (OUTLIER) cc_final: 0.5736 (mt-10) REVERT: 2 232 ARG cc_start: 0.6559 (mmm-85) cc_final: 0.5963 (mtp180) REVERT: 2 258 LEU cc_start: 0.7103 (tt) cc_final: 0.6639 (mt) REVERT: 2 269 LYS cc_start: 0.6546 (ttmm) cc_final: 0.6291 (ttmt) REVERT: 2 326 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.6746 (pmt170) REVERT: 2 374 ARG cc_start: 0.6203 (OUTLIER) cc_final: 0.5434 (ttm110) REVERT: 2 651 ASN cc_start: 0.8233 (m-40) cc_final: 0.7667 (m-40) REVERT: 2 667 VAL cc_start: 0.7539 (OUTLIER) cc_final: 0.7164 (p) REVERT: 2 684 ARG cc_start: 0.3968 (OUTLIER) cc_final: 0.3254 (ptp90) REVERT: 2 687 VAL cc_start: 0.6206 (t) cc_final: 0.5865 (p) REVERT: 3 23 ASP cc_start: 0.7144 (m-30) cc_final: 0.6827 (m-30) REVERT: 3 27 ARG cc_start: 0.7878 (tpt170) cc_final: 0.7146 (ttp80) REVERT: 3 52 ASN cc_start: 0.5203 (m-40) cc_final: 0.4920 (m110) REVERT: 3 188 LYS cc_start: 0.7956 (mtmm) cc_final: 0.7279 (ttpt) REVERT: 3 208 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7345 (mtp180) REVERT: 3 234 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.6049 (tm-30) REVERT: 3 261 MET cc_start: 0.7945 (mtp) cc_final: 0.7436 (mtt) REVERT: 3 274 ILE cc_start: 0.8745 (pt) cc_final: 0.8238 (tp) REVERT: 3 353 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8611 (mm) REVERT: 3 357 LYS cc_start: 0.7083 (pmtt) cc_final: 0.6136 (pmtt) REVERT: 3 497 ILE cc_start: 0.7522 (pt) cc_final: 0.7223 (mt) REVERT: 3 504 THR cc_start: 0.8542 (OUTLIER) cc_final: 0.8127 (t) REVERT: 3 556 ILE cc_start: 0.6836 (tp) cc_final: 0.6615 (mm) REVERT: 4 266 GLN cc_start: 0.7799 (tp40) cc_final: 0.7466 (tp-100) REVERT: 4 375 ASP cc_start: 0.6674 (m-30) cc_final: 0.6407 (m-30) REVERT: 4 404 ASP cc_start: 0.6797 (m-30) cc_final: 0.6468 (m-30) REVERT: 4 477 ASP cc_start: 0.7324 (t0) cc_final: 0.6759 (t0) REVERT: 4 579 GLN cc_start: 0.7893 (mm-40) cc_final: 0.7440 (mm-40) REVERT: 4 583 LYS cc_start: 0.7849 (mmpt) cc_final: 0.7470 (mtmm) REVERT: 4 686 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.7119 (tp) REVERT: 4 713 ASP cc_start: 0.6293 (t0) cc_final: 0.6038 (t70) REVERT: 4 715 LYS cc_start: 0.7043 (pttp) cc_final: 0.6604 (tppp) REVERT: 4 756 GLU cc_start: 0.7709 (tt0) cc_final: 0.7464 (tp30) REVERT: 5 5 ARG cc_start: 0.6952 (OUTLIER) cc_final: 0.6403 (mmm-85) REVERT: 5 82 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7379 (pt0) REVERT: 5 139 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8343 (pp) REVERT: 5 210 SER cc_start: 0.8070 (m) cc_final: 0.7717 (t) REVERT: 5 362 ARG cc_start: 0.6048 (mpp80) cc_final: 0.5624 (mpt90) REVERT: 5 383 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.6974 (p0) REVERT: 5 388 ILE cc_start: 0.8260 (mt) cc_final: 0.7981 (mm) REVERT: 5 404 MET cc_start: 0.7089 (ptp) cc_final: 0.5836 (mmp) REVERT: 5 469 MET cc_start: 0.7501 (mmm) cc_final: 0.7207 (mmm) REVERT: 5 556 VAL cc_start: 0.6512 (t) cc_final: 0.6226 (p) REVERT: 5 581 ASN cc_start: 0.5511 (t0) cc_final: 0.5308 (m110) REVERT: 5 625 ASN cc_start: 0.6757 (m110) cc_final: 0.5658 (t0) REVERT: 5 654 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7087 (mt-10) REVERT: 5 689 MET cc_start: 0.7148 (mmm) cc_final: 0.6875 (mmm) REVERT: 6 105 ASP cc_start: 0.7150 (m-30) cc_final: 0.6888 (t0) REVERT: 6 174 TYR cc_start: 0.7947 (t80) cc_final: 0.7377 (t80) REVERT: 6 282 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7050 (pm20) REVERT: 6 299 GLU cc_start: 0.7170 (pm20) cc_final: 0.6730 (tp30) REVERT: 6 328 THR cc_start: 0.6459 (p) cc_final: 0.6245 (p) REVERT: 6 347 ASN cc_start: 0.6611 (t0) cc_final: 0.5843 (m-40) REVERT: 6 367 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7758 (mt-10) REVERT: 6 594 ARG cc_start: 0.8062 (mmm160) cc_final: 0.7788 (mmm160) REVERT: 6 675 ARG cc_start: 0.8054 (mtm180) cc_final: 0.7393 (mpp-170) REVERT: 6 764 ILE cc_start: 0.7311 (mt) cc_final: 0.6745 (pp) REVERT: 6 794 ARG cc_start: 0.5476 (mtp-110) cc_final: 0.4599 (mtm110) REVERT: 7 69 LYS cc_start: 0.8017 (mtmm) cc_final: 0.7704 (mtpt) REVERT: 7 76 ASN cc_start: 0.7795 (t0) cc_final: 0.7412 (m110) REVERT: 7 81 ASP cc_start: 0.7832 (m-30) cc_final: 0.7422 (t0) REVERT: 7 159 ASN cc_start: 0.7392 (m-40) cc_final: 0.6984 (m110) REVERT: 7 162 ARG cc_start: 0.7172 (ttm-80) cc_final: 0.6716 (ttt90) REVERT: 7 188 GLU cc_start: 0.6069 (tt0) cc_final: 0.5630 (tt0) REVERT: 7 247 ARG cc_start: 0.8135 (ttm170) cc_final: 0.7417 (ttp-110) REVERT: 7 396 ASP cc_start: 0.6325 (p0) cc_final: 0.5293 (m-30) REVERT: 7 498 MET cc_start: 0.6062 (ptt) cc_final: 0.5750 (mtm) REVERT: 7 537 ILE cc_start: 0.7816 (mt) cc_final: 0.7578 (tt) REVERT: 7 598 PHE cc_start: 0.8382 (m-80) cc_final: 0.8001 (m-80) REVERT: 7 714 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6655 (tm-30) REVERT: B 198 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7549 (mp) REVERT: B 269 LYS cc_start: 0.6478 (ttmm) cc_final: 0.5175 (mppt) REVERT: B 273 LEU cc_start: 0.6954 (OUTLIER) cc_final: 0.6749 (mt) REVERT: B 290 HIS cc_start: 0.5996 (m-70) cc_final: 0.5681 (m170) REVERT: B 293 ILE cc_start: 0.6881 (mt) cc_final: 0.6644 (mm) REVERT: B 413 ASP cc_start: 0.7044 (OUTLIER) cc_final: 0.6759 (m-30) REVERT: B 501 MET cc_start: 0.7745 (mmm) cc_final: 0.7279 (mmt) REVERT: B 633 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7012 (mptt) REVERT: B 705 ARG cc_start: 0.6315 (OUTLIER) cc_final: 0.5766 (mtp180) REVERT: B 781 MET cc_start: 0.4926 (OUTLIER) cc_final: 0.4684 (mpm) REVERT: B 834 LEU cc_start: 0.6918 (mm) cc_final: 0.6212 (tp) REVERT: C 39 ARG cc_start: 0.7204 (ttm110) cc_final: 0.6653 (ttp-110) REVERT: C 48 TYR cc_start: 0.7451 (t80) cc_final: 0.7182 (t80) REVERT: C 188 LYS cc_start: 0.8000 (mtmt) cc_final: 0.7567 (mttp) REVERT: C 222 THR cc_start: 0.8514 (OUTLIER) cc_final: 0.8044 (p) REVERT: C 234 GLU cc_start: 0.6894 (mt-10) cc_final: 0.6080 (mp0) REVERT: C 235 ASP cc_start: 0.6538 (p0) cc_final: 0.6089 (p0) REVERT: C 237 GLU cc_start: 0.7166 (mp0) cc_final: 0.6536 (mt-10) REVERT: C 348 ARG cc_start: 0.6922 (mtm110) cc_final: 0.6415 (mtt90) REVERT: C 407 MET cc_start: 0.8252 (mtp) cc_final: 0.7961 (mtm) REVERT: C 464 LEU cc_start: 0.7879 (mt) cc_final: 0.7473 (mt) REVERT: C 477 LYS cc_start: 0.7396 (mttm) cc_final: 0.6861 (mttp) REVERT: C 505 THR cc_start: 0.8410 (t) cc_final: 0.7947 (m) REVERT: C 556 ILE cc_start: 0.7296 (pt) cc_final: 0.6978 (mm) REVERT: C 656 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7539 (tp) REVERT: C 664 LYS cc_start: 0.7713 (mtpp) cc_final: 0.7278 (mtpt) REVERT: C 681 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7578 (tmmm) REVERT: C 723 LYS cc_start: 0.7319 (pttt) cc_final: 0.6867 (tttt) REVERT: D 235 GLU cc_start: 0.6373 (mt-10) cc_final: 0.5741 (tp30) REVERT: D 302 LYS cc_start: 0.7553 (mmtp) cc_final: 0.7079 (mtpp) REVERT: D 408 ASP cc_start: 0.7495 (m-30) cc_final: 0.7162 (m-30) REVERT: D 445 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.7082 (mtt90) REVERT: D 483 GLN cc_start: 0.6701 (tp40) cc_final: 0.6116 (mt0) REVERT: D 503 ASP cc_start: 0.6235 (m-30) cc_final: 0.5856 (m-30) REVERT: D 690 GLU cc_start: 0.6691 (tt0) cc_final: 0.6147 (tp30) REVERT: D 693 ASP cc_start: 0.6580 (t0) cc_final: 0.5863 (p0) REVERT: D 715 LYS cc_start: 0.6785 (OUTLIER) cc_final: 0.6170 (ptmm) REVERT: D 730 GLU cc_start: 0.6073 (OUTLIER) cc_final: 0.5470 (mt-10) REVERT: D 779 LYS cc_start: 0.7224 (OUTLIER) cc_final: 0.6974 (ptmt) REVERT: E 5 ARG cc_start: 0.7544 (ttp80) cc_final: 0.6953 (ttp-110) REVERT: E 29 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7738 (mtpt) REVERT: E 33 ASN cc_start: 0.7388 (m-40) cc_final: 0.7123 (m110) REVERT: E 209 ARG cc_start: 0.7124 (mmm-85) cc_final: 0.6766 (mmt-90) REVERT: E 249 LYS cc_start: 0.7878 (mmtp) cc_final: 0.7483 (mppt) REVERT: E 354 GLU cc_start: 0.6542 (OUTLIER) cc_final: 0.6203 (mm-30) REVERT: E 368 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.6206 (tm-30) REVERT: E 404 MET cc_start: 0.7128 (ttm) cc_final: 0.6028 (mmp) REVERT: E 430 GLU cc_start: 0.7305 (tm-30) cc_final: 0.6813 (tm-30) REVERT: E 458 MET cc_start: 0.5776 (mtp) cc_final: 0.5434 (mtm) REVERT: E 469 MET cc_start: 0.7944 (mmm) cc_final: 0.7397 (mmm) REVERT: E 513 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8097 (pt) REVERT: E 546 ILE cc_start: 0.7281 (OUTLIER) cc_final: 0.6888 (mm) REVERT: E 592 SER cc_start: 0.6551 (m) cc_final: 0.6145 (p) REVERT: E 593 GLU cc_start: 0.6851 (mt-10) cc_final: 0.6467 (mt-10) REVERT: E 597 GLU cc_start: 0.6271 (pm20) cc_final: 0.5782 (mm-30) REVERT: E 601 ARG cc_start: 0.7458 (mmp-170) cc_final: 0.7254 (mtp180) REVERT: E 661 GLU cc_start: 0.6936 (mt-10) cc_final: 0.6725 (mt-10) REVERT: F 313 MET cc_start: 0.4131 (mpt) cc_final: 0.2512 (ptt) REVERT: F 362 GLN cc_start: 0.8370 (tt0) cc_final: 0.7955 (tt0) REVERT: F 421 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6305 (mm) REVERT: F 737 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.7285 (mttm) REVERT: G 15 ASN cc_start: 0.7308 (m-40) cc_final: 0.6059 (t0) REVERT: G 187 ASP cc_start: 0.6768 (t0) cc_final: 0.6089 (m-30) REVERT: G 223 LYS cc_start: 0.7016 (OUTLIER) cc_final: 0.6351 (mmmt) REVERT: G 247 ARG cc_start: 0.8090 (ttt90) cc_final: 0.7608 (ttp80) REVERT: G 291 GLN cc_start: 0.7950 (mt0) cc_final: 0.7609 (mt0) REVERT: G 297 GLN cc_start: 0.7890 (OUTLIER) cc_final: 0.7348 (tt0) REVERT: G 402 MET cc_start: 0.4549 (mmm) cc_final: 0.3917 (tmm) REVERT: G 412 ASN cc_start: 0.7567 (t0) cc_final: 0.7070 (m-40) REVERT: G 449 LYS cc_start: 0.7575 (mtmm) cc_final: 0.6966 (mmmm) REVERT: G 502 VAL cc_start: 0.5711 (OUTLIER) cc_final: 0.5480 (t) REVERT: G 537 ILE cc_start: 0.8050 (mt) cc_final: 0.7743 (mm) REVERT: G 556 THR cc_start: 0.8077 (t) cc_final: 0.7673 (m) REVERT: G 607 ASP cc_start: 0.7243 (OUTLIER) cc_final: 0.6741 (m-30) REVERT: G 618 TYR cc_start: 0.7540 (t80) cc_final: 0.7116 (t80) REVERT: G 640 GLU cc_start: 0.7293 (pt0) cc_final: 0.6582 (tt0) REVERT: G 659 TYR cc_start: 0.7901 (t80) cc_final: 0.7622 (t80) REVERT: G 690 LEU cc_start: 0.8576 (mt) cc_final: 0.8308 (mt) REVERT: G 714 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6668 (tp30) REVERT: H 31 ASN cc_start: 0.3961 (p0) cc_final: 0.3749 (m-40) REVERT: H 34 LYS cc_start: 0.4005 (tttt) cc_final: 0.3464 (tptp) REVERT: H 51 LYS cc_start: 0.3168 (tttt) cc_final: 0.2866 (ttpm) REVERT: H 172 ASN cc_start: 0.3685 (p0) cc_final: 0.3406 (p0) REVERT: H 173 LEU cc_start: 0.1845 (mt) cc_final: 0.1559 (pp) REVERT: H 278 ARG cc_start: 0.4260 (ppp80) cc_final: 0.3905 (tmm-80) REVERT: H 284 PHE cc_start: 0.5245 (m-80) cc_final: 0.4823 (m-80) REVERT: H 288 GLU cc_start: 0.5396 (pm20) cc_final: 0.4985 (mm-30) REVERT: H 300 ILE cc_start: 0.5337 (mp) cc_final: 0.5013 (mt) REVERT: H 310 LEU cc_start: 0.5080 (OUTLIER) cc_final: 0.4757 (pp) REVERT: H 332 LEU cc_start: 0.6018 (mt) cc_final: 0.5617 (tp) REVERT: H 342 ARG cc_start: 0.5029 (mtm180) cc_final: 0.4567 (ttm-80) REVERT: H 402 GLU cc_start: 0.2744 (OUTLIER) cc_final: 0.2494 (mm-30) REVERT: H 426 TYR cc_start: 0.2914 (t80) cc_final: 0.1525 (p90) REVERT: H 452 MET cc_start: 0.6077 (mmp) cc_final: 0.5783 (mmt) REVERT: H 465 LYS cc_start: 0.4128 (mppt) cc_final: 0.3640 (mmmt) REVERT: I 127 TYR cc_start: 0.3814 (t80) cc_final: 0.3502 (t80) REVERT: I 152 LYS cc_start: 0.4021 (mttt) cc_final: 0.3676 (ttpt) REVERT: I 155 PHE cc_start: 0.2878 (OUTLIER) cc_final: 0.2458 (m-80) REVERT: I 158 LEU cc_start: 0.3304 (tt) cc_final: 0.2935 (mp) REVERT: I 325 LYS cc_start: 0.3624 (mppt) cc_final: 0.3297 (ttpp) REVERT: I 382 MET cc_start: 0.2340 (mmp) cc_final: 0.1045 (tpt) REVERT: I 524 MET cc_start: 0.8578 (mmm) cc_final: 0.8320 (mmp) REVERT: I 662 GLU cc_start: 0.6536 (tt0) cc_final: 0.6191 (tp30) REVERT: I 697 ILE cc_start: 0.2801 (mm) cc_final: 0.2574 (mm) outliers start: 301 outliers final: 129 residues processed: 1205 average time/residue: 1.5209 time to fit residues: 2379.5383 Evaluate side-chains 1073 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 900 time to evaluate : 5.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 196 GLU Chi-restraints excluded: chain 2 residue 326 ARG Chi-restraints excluded: chain 2 residue 374 ARG Chi-restraints excluded: chain 2 residue 396 THR Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 590 THR Chi-restraints excluded: chain 2 residue 656 ARG Chi-restraints excluded: chain 2 residue 661 LEU Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 670 THR Chi-restraints excluded: chain 2 residue 684 ARG Chi-restraints excluded: chain 2 residue 697 THR Chi-restraints excluded: chain 2 residue 786 VAL Chi-restraints excluded: chain 2 residue 851 VAL Chi-restraints excluded: chain 3 residue 117 GLU Chi-restraints excluded: chain 3 residue 208 ARG Chi-restraints excluded: chain 3 residue 234 GLU Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 324 ASN Chi-restraints excluded: chain 3 residue 353 LEU Chi-restraints excluded: chain 3 residue 440 VAL Chi-restraints excluded: chain 3 residue 486 ILE Chi-restraints excluded: chain 3 residue 504 THR Chi-restraints excluded: chain 3 residue 537 ASP Chi-restraints excluded: chain 4 residue 284 ILE Chi-restraints excluded: chain 4 residue 296 ILE Chi-restraints excluded: chain 4 residue 328 LEU Chi-restraints excluded: chain 4 residue 358 VAL Chi-restraints excluded: chain 4 residue 436 THR Chi-restraints excluded: chain 4 residue 592 SER Chi-restraints excluded: chain 4 residue 661 ILE Chi-restraints excluded: chain 4 residue 674 SER Chi-restraints excluded: chain 4 residue 686 LEU Chi-restraints excluded: chain 4 residue 720 LEU Chi-restraints excluded: chain 4 residue 749 MET Chi-restraints excluded: chain 4 residue 797 GLN Chi-restraints excluded: chain 5 residue 5 ARG Chi-restraints excluded: chain 5 residue 82 GLU Chi-restraints excluded: chain 5 residue 139 LEU Chi-restraints excluded: chain 5 residue 205 VAL Chi-restraints excluded: chain 5 residue 221 MET Chi-restraints excluded: chain 5 residue 383 ASP Chi-restraints excluded: chain 5 residue 583 MET Chi-restraints excluded: chain 5 residue 592 SER Chi-restraints excluded: chain 5 residue 624 SER Chi-restraints excluded: chain 5 residue 631 LYS Chi-restraints excluded: chain 5 residue 654 GLU Chi-restraints excluded: chain 5 residue 661 GLU Chi-restraints excluded: chain 6 residue 282 GLU Chi-restraints excluded: chain 6 residue 313 MET Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 446 ARG Chi-restraints excluded: chain 6 residue 460 ILE Chi-restraints excluded: chain 6 residue 598 THR Chi-restraints excluded: chain 6 residue 647 SER Chi-restraints excluded: chain 6 residue 660 THR Chi-restraints excluded: chain 6 residue 829 ASP Chi-restraints excluded: chain 6 residue 831 LEU Chi-restraints excluded: chain 7 residue 141 VAL Chi-restraints excluded: chain 7 residue 207 LEU Chi-restraints excluded: chain 7 residue 283 GLU Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 294 THR Chi-restraints excluded: chain 7 residue 329 ARG Chi-restraints excluded: chain 7 residue 410 VAL Chi-restraints excluded: chain 7 residue 483 THR Chi-restraints excluded: chain 7 residue 484 THR Chi-restraints excluded: chain 7 residue 556 THR Chi-restraints excluded: chain 7 residue 570 LEU Chi-restraints excluded: chain 7 residue 592 SER Chi-restraints excluded: chain 7 residue 670 ASP Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain B residue 781 MET Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 681 LYS Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain D residue 445 ARG Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 639 ASP Chi-restraints excluded: chain D residue 661 ILE Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain D residue 730 GLU Chi-restraints excluded: chain D residue 768 THR Chi-restraints excluded: chain D residue 779 LYS Chi-restraints excluded: chain D residue 800 SER Chi-restraints excluded: chain D residue 833 ILE Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 29 LYS Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 368 GLU Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain E residue 497 MET Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain E residue 517 THR Chi-restraints excluded: chain E residue 546 ILE Chi-restraints excluded: chain E residue 599 MET Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 462 ILE Chi-restraints excluded: chain F residue 501 GLN Chi-restraints excluded: chain F residue 519 MET Chi-restraints excluded: chain F residue 639 ASP Chi-restraints excluded: chain F residue 706 MET Chi-restraints excluded: chain F residue 727 LEU Chi-restraints excluded: chain F residue 737 LYS Chi-restraints excluded: chain F residue 796 THR Chi-restraints excluded: chain G residue 223 LYS Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 282 SER Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 297 GLN Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 350 ASP Chi-restraints excluded: chain G residue 382 ARG Chi-restraints excluded: chain G residue 426 LEU Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 554 ASN Chi-restraints excluded: chain G residue 561 THR Chi-restraints excluded: chain G residue 601 LEU Chi-restraints excluded: chain G residue 607 ASP Chi-restraints excluded: chain G residue 656 VAL Chi-restraints excluded: chain G residue 706 ASP Chi-restraints excluded: chain G residue 714 GLU Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 281 THR Chi-restraints excluded: chain H residue 310 LEU Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 402 GLU Chi-restraints excluded: chain H residue 472 LEU Chi-restraints excluded: chain I residue 155 PHE Chi-restraints excluded: chain I residue 192 SER Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 280 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 764 optimal weight: 0.4980 chunk 581 optimal weight: 0.0030 chunk 401 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 369 optimal weight: 1.9990 chunk 519 optimal weight: 9.9990 chunk 776 optimal weight: 2.9990 chunk 821 optimal weight: 0.7980 chunk 405 optimal weight: 0.0980 chunk 735 optimal weight: 0.0370 chunk 221 optimal weight: 2.9990 overall best weight: 0.2868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 666 ASN 2 856 GLN 3 29 GLN 3 340 GLN 3 503 HIS 3 587 ASN ** 3 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 613 GLN 4 726 ASN 5 334 GLN 5 560 HIS 5 579 ASN 5 585 ASN 5 587 GLN 6 264 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 16 ASN 7 178 ASN 7 271 GLN 7 297 GLN 7 320 GLN 7 384 HIS 7 662 GLN 7 683 GLN B 433 ASN ** B 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 ASN ** C 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 722 ASN D 229 GLN D 253 GLN D 685 ASN E 108 GLN E 636 ASN E 685 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 ASN ** G 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 HIS G 274 ASN G 623 ASN H 378 ASN ** I 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 69476 Z= 0.127 Angle : 0.483 10.294 93996 Z= 0.248 Chirality : 0.041 0.226 10834 Planarity : 0.004 0.056 12062 Dihedral : 7.234 177.720 9630 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.98 % Favored : 97.98 % Rotamer: Outliers : 2.70 % Allowed : 17.06 % Favored : 80.24 % 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: 0.54 (0.09), residues: 8483 helix: 1.12 (0.09), residues: 3473 sheet: -0.04 (0.13), residues: 1541 loop : -0.09 (0.10), residues: 3469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 3 111 HIS 0.009 0.001 HIS 6 653 PHE 0.025 0.001 PHE C 345 TYR 0.022 0.001 TYR H 143 ARG 0.007 0.000 ARG G 162 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1154 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 949 time to evaluate : 5.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 232 ARG cc_start: 0.6553 (mmm-85) cc_final: 0.5942 (mtp180) REVERT: 2 258 LEU cc_start: 0.7042 (tt) cc_final: 0.6631 (mt) REVERT: 2 276 MET cc_start: 0.6953 (tpt) cc_final: 0.6621 (tpt) REVERT: 2 326 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.6553 (pmt170) REVERT: 2 374 ARG cc_start: 0.6128 (OUTLIER) cc_final: 0.5350 (ttm110) REVERT: 2 457 LYS cc_start: 0.6087 (mmmt) cc_final: 0.5882 (tttp) REVERT: 2 651 ASN cc_start: 0.8223 (m-40) cc_final: 0.7618 (m-40) REVERT: 2 684 ARG cc_start: 0.3888 (OUTLIER) cc_final: 0.3189 (ptp90) REVERT: 2 686 LEU cc_start: 0.4672 (pt) cc_final: 0.4336 (mt) REVERT: 2 687 VAL cc_start: 0.5996 (t) cc_final: 0.5711 (p) REVERT: 2 690 GLU cc_start: 0.5762 (pm20) cc_final: 0.5278 (pm20) REVERT: 3 23 ASP cc_start: 0.7105 (m-30) cc_final: 0.6785 (m-30) REVERT: 3 27 ARG cc_start: 0.7810 (tpt170) cc_final: 0.7102 (ttp80) REVERT: 3 52 ASN cc_start: 0.5042 (m-40) cc_final: 0.4751 (m110) REVERT: 3 188 LYS cc_start: 0.7972 (mtmm) cc_final: 0.7358 (ttpt) REVERT: 3 234 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.6152 (tm-30) REVERT: 3 274 ILE cc_start: 0.8681 (pt) cc_final: 0.8236 (tp) REVERT: 3 318 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7076 (tmtt) REVERT: 3 353 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8642 (mm) REVERT: 3 357 LYS cc_start: 0.6938 (pmtt) cc_final: 0.6101 (pmtt) REVERT: 3 365 GLN cc_start: 0.7106 (mm-40) cc_final: 0.6788 (mm110) REVERT: 3 386 MET cc_start: 0.8387 (mmp) cc_final: 0.8118 (mmm) REVERT: 3 397 SER cc_start: 0.8391 (p) cc_final: 0.8133 (t) REVERT: 3 455 ARG cc_start: 0.5833 (mmm160) cc_final: 0.5444 (mtt180) REVERT: 3 497 ILE cc_start: 0.7407 (pt) cc_final: 0.7076 (mt) REVERT: 3 556 ILE cc_start: 0.6789 (tp) cc_final: 0.6544 (mm) REVERT: 4 266 GLN cc_start: 0.7679 (tp40) cc_final: 0.7361 (tp-100) REVERT: 4 341 ASP cc_start: 0.8142 (p0) cc_final: 0.7856 (p0) REVERT: 4 404 ASP cc_start: 0.6789 (m-30) cc_final: 0.6445 (m-30) REVERT: 4 477 ASP cc_start: 0.7299 (t0) cc_final: 0.6702 (t0) REVERT: 4 579 GLN cc_start: 0.7809 (mm-40) cc_final: 0.7395 (mm-40) REVERT: 4 583 LYS cc_start: 0.7882 (mmpt) cc_final: 0.7473 (mtmm) REVERT: 4 713 ASP cc_start: 0.6190 (t0) cc_final: 0.5937 (t70) REVERT: 4 715 LYS cc_start: 0.6985 (pttp) cc_final: 0.6577 (tptm) REVERT: 4 722 LYS cc_start: 0.7876 (mttt) cc_final: 0.7661 (mtmm) REVERT: 4 726 ASN cc_start: 0.7501 (m-40) cc_final: 0.7005 (t0) REVERT: 4 756 GLU cc_start: 0.7684 (tt0) cc_final: 0.7410 (tp30) REVERT: 4 811 MET cc_start: 0.9087 (ttm) cc_final: 0.8883 (ttp) REVERT: 5 139 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8306 (pp) REVERT: 5 210 SER cc_start: 0.8110 (m) cc_final: 0.7756 (t) REVERT: 5 362 ARG cc_start: 0.6234 (mpp80) cc_final: 0.5965 (mmt180) REVERT: 5 369 ILE cc_start: 0.7522 (pt) cc_final: 0.7297 (tt) REVERT: 5 388 ILE cc_start: 0.8231 (mt) cc_final: 0.7977 (mm) REVERT: 5 469 MET cc_start: 0.7348 (mmm) cc_final: 0.7042 (mmm) REVERT: 5 556 VAL cc_start: 0.6463 (t) cc_final: 0.6186 (p) REVERT: 5 625 ASN cc_start: 0.6404 (m110) cc_final: 0.5671 (t0) REVERT: 5 689 MET cc_start: 0.6957 (mmm) cc_final: 0.6653 (mmm) REVERT: 6 172 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6830 (mm-30) REVERT: 6 174 TYR cc_start: 0.7925 (t80) cc_final: 0.7372 (t80) REVERT: 6 299 GLU cc_start: 0.7168 (pm20) cc_final: 0.6623 (tp30) REVERT: 6 347 ASN cc_start: 0.6473 (t0) cc_final: 0.5724 (m-40) REVERT: 6 367 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7615 (mt-10) REVERT: 6 561 GLU cc_start: 0.5990 (pt0) cc_final: 0.5713 (mt-10) REVERT: 6 594 ARG cc_start: 0.8041 (mmm160) cc_final: 0.7784 (mmm160) REVERT: 6 675 ARG cc_start: 0.8027 (mtm180) cc_final: 0.7282 (mpp-170) REVERT: 6 696 ARG cc_start: 0.6936 (tpm170) cc_final: 0.6074 (tmt-80) REVERT: 6 723 ILE cc_start: 0.7187 (pp) cc_final: 0.6954 (mt) REVERT: 6 764 ILE cc_start: 0.7271 (mt) cc_final: 0.6722 (pp) REVERT: 6 794 ARG cc_start: 0.5434 (mtp-110) cc_final: 0.4602 (mtm110) REVERT: 7 69 LYS cc_start: 0.7882 (mtmm) cc_final: 0.7601 (mtpt) REVERT: 7 76 ASN cc_start: 0.7628 (t0) cc_final: 0.7225 (m110) REVERT: 7 81 ASP cc_start: 0.7780 (m-30) cc_final: 0.7362 (t0) REVERT: 7 159 ASN cc_start: 0.7354 (m-40) cc_final: 0.6960 (m110) REVERT: 7 162 ARG cc_start: 0.7002 (ttm-80) cc_final: 0.6757 (ttt90) REVERT: 7 188 GLU cc_start: 0.6032 (tt0) cc_final: 0.5535 (tt0) REVERT: 7 244 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8415 (tp) REVERT: 7 247 ARG cc_start: 0.8107 (ttm170) cc_final: 0.7490 (ttp-110) REVERT: 7 396 ASP cc_start: 0.6224 (p0) cc_final: 0.5494 (m-30) REVERT: 7 498 MET cc_start: 0.5916 (ptt) cc_final: 0.5622 (ppp) REVERT: 7 502 VAL cc_start: 0.4915 (OUTLIER) cc_final: 0.4462 (t) REVERT: 7 538 HIS cc_start: 0.6462 (t70) cc_final: 0.6258 (t70) REVERT: 7 598 PHE cc_start: 0.8283 (m-80) cc_final: 0.8002 (m-80) REVERT: 7 621 MET cc_start: 0.7960 (ttp) cc_final: 0.7673 (ttm) REVERT: B 198 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7568 (mp) REVERT: B 269 LYS cc_start: 0.6716 (ttmm) cc_final: 0.5364 (mppt) REVERT: B 290 HIS cc_start: 0.5957 (m-70) cc_final: 0.5271 (m170) REVERT: B 293 ILE cc_start: 0.6821 (mt) cc_final: 0.6472 (tt) REVERT: B 413 ASP cc_start: 0.7015 (OUTLIER) cc_final: 0.6639 (m-30) REVERT: B 501 MET cc_start: 0.7675 (mmm) cc_final: 0.7138 (mmt) REVERT: B 534 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7586 (ttm170) REVERT: B 626 GLN cc_start: 0.7364 (mt0) cc_final: 0.7081 (mm110) REVERT: B 633 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.6941 (mptt) REVERT: B 705 ARG cc_start: 0.6257 (OUTLIER) cc_final: 0.5770 (mtp180) REVERT: B 834 LEU cc_start: 0.6963 (mm) cc_final: 0.6243 (tp) REVERT: C 39 ARG cc_start: 0.7204 (ttm110) cc_final: 0.6651 (ttp-110) REVERT: C 188 LYS cc_start: 0.7867 (mtmt) cc_final: 0.7377 (mttp) REVERT: C 222 THR cc_start: 0.8477 (m) cc_final: 0.8024 (p) REVERT: C 234 GLU cc_start: 0.6696 (mt-10) cc_final: 0.6064 (mp0) REVERT: C 237 GLU cc_start: 0.7174 (mp0) cc_final: 0.6914 (mt-10) REVERT: C 348 ARG cc_start: 0.6897 (mtm110) cc_final: 0.6409 (mtt90) REVERT: C 464 LEU cc_start: 0.7886 (mt) cc_final: 0.7500 (mt) REVERT: C 477 LYS cc_start: 0.7397 (mttm) cc_final: 0.6942 (mttm) REVERT: C 490 MET cc_start: 0.8628 (mtm) cc_final: 0.8406 (mtm) REVERT: C 505 THR cc_start: 0.8380 (t) cc_final: 0.7935 (m) REVERT: C 556 ILE cc_start: 0.7256 (pt) cc_final: 0.6933 (mm) REVERT: C 664 LYS cc_start: 0.7725 (mtpp) cc_final: 0.7302 (mtpt) REVERT: C 681 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7513 (tmmm) REVERT: C 723 LYS cc_start: 0.7251 (pttt) cc_final: 0.6806 (tttp) REVERT: D 235 GLU cc_start: 0.6442 (mt-10) cc_final: 0.5761 (tp30) REVERT: D 302 LYS cc_start: 0.7424 (mmtp) cc_final: 0.7042 (mtpp) REVERT: D 327 ASN cc_start: 0.8270 (OUTLIER) cc_final: 0.7477 (m110) REVERT: D 394 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8490 (tmtp) REVERT: D 408 ASP cc_start: 0.7432 (m-30) cc_final: 0.7076 (m-30) REVERT: D 434 GLU cc_start: 0.7544 (tp30) cc_final: 0.7277 (tm-30) REVERT: D 483 GLN cc_start: 0.6607 (tp40) cc_final: 0.6118 (mt0) REVERT: D 503 ASP cc_start: 0.6216 (m-30) cc_final: 0.5843 (m-30) REVERT: D 690 GLU cc_start: 0.6681 (tt0) cc_final: 0.6136 (tp30) REVERT: D 693 ASP cc_start: 0.6542 (t0) cc_final: 0.5857 (p0) REVERT: D 819 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7155 (mm) REVERT: E 3 PHE cc_start: 0.7015 (m-80) cc_final: 0.6807 (m-10) REVERT: E 5 ARG cc_start: 0.7656 (ttp80) cc_final: 0.7015 (ttp-110) REVERT: E 33 ASN cc_start: 0.7414 (m-40) cc_final: 0.7193 (m110) REVERT: E 209 ARG cc_start: 0.7052 (mmm-85) cc_final: 0.6738 (mmt-90) REVERT: E 221 MET cc_start: 0.3343 (OUTLIER) cc_final: 0.3140 (pmm) REVERT: E 249 LYS cc_start: 0.7860 (mmtp) cc_final: 0.7513 (mppt) REVERT: E 354 GLU cc_start: 0.6517 (OUTLIER) cc_final: 0.6128 (mm-30) REVERT: E 404 MET cc_start: 0.7060 (ttm) cc_final: 0.5985 (mmp) REVERT: E 458 MET cc_start: 0.5678 (mtp) cc_final: 0.5297 (mtm) REVERT: E 469 MET cc_start: 0.7898 (mmm) cc_final: 0.7181 (mmm) REVERT: E 497 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8066 (mtm) REVERT: E 513 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7857 (pp) REVERT: E 593 GLU cc_start: 0.6722 (mt-10) cc_final: 0.6339 (mt-10) REVERT: E 661 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6639 (mt-10) REVERT: F 161 ARG cc_start: 0.5496 (tpp-160) cc_final: 0.5292 (tpp80) REVERT: F 313 MET cc_start: 0.4325 (mpt) cc_final: 0.3012 (ptm) REVERT: F 446 ARG cc_start: 0.7090 (ptt90) cc_final: 0.6845 (ptt90) REVERT: F 654 GLU cc_start: 0.6878 (tm-30) cc_final: 0.6202 (tp30) REVERT: F 715 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7180 (mt) REVERT: F 719 CYS cc_start: 0.4702 (m) cc_final: 0.4396 (t) REVERT: G 15 ASN cc_start: 0.7142 (m-40) cc_final: 0.5937 (t0) REVERT: G 247 ARG cc_start: 0.8004 (ttt90) cc_final: 0.7524 (ttp80) REVERT: G 291 GLN cc_start: 0.7943 (mt0) cc_final: 0.7590 (mt0) REVERT: G 398 GLU cc_start: 0.4937 (tt0) cc_final: 0.4727 (tt0) REVERT: G 402 MET cc_start: 0.4617 (mmm) cc_final: 0.3846 (tpt) REVERT: G 412 ASN cc_start: 0.7560 (t0) cc_final: 0.7037 (m-40) REVERT: G 427 ASP cc_start: 0.7722 (m-30) cc_final: 0.7452 (m-30) REVERT: G 449 LYS cc_start: 0.7502 (mtmm) cc_final: 0.6856 (mmtt) REVERT: G 508 LEU cc_start: 0.6628 (tp) cc_final: 0.6335 (mt) REVERT: G 529 MET cc_start: 0.6839 (mtm) cc_final: 0.6542 (OUTLIER) REVERT: G 541 MET cc_start: 0.8093 (mtt) cc_final: 0.7109 (mtm) REVERT: G 554 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.8020 (t0) REVERT: G 556 THR cc_start: 0.8007 (t) cc_final: 0.7532 (m) REVERT: G 618 TYR cc_start: 0.7474 (t80) cc_final: 0.7033 (t80) REVERT: G 659 TYR cc_start: 0.7900 (t80) cc_final: 0.7676 (t80) REVERT: G 690 LEU cc_start: 0.8442 (mt) cc_final: 0.8158 (mt) REVERT: H 31 ASN cc_start: 0.3930 (OUTLIER) cc_final: 0.3629 (m-40) REVERT: H 34 LYS cc_start: 0.4012 (tttt) cc_final: 0.3489 (tptp) REVERT: H 72 TYR cc_start: 0.4391 (m-10) cc_final: 0.4111 (m-10) REVERT: H 152 LYS cc_start: 0.4960 (pttp) cc_final: 0.4691 (pptt) REVERT: H 172 ASN cc_start: 0.3504 (p0) cc_final: 0.3231 (p0) REVERT: H 173 LEU cc_start: 0.1830 (mt) cc_final: 0.1450 (pp) REVERT: H 278 ARG cc_start: 0.4326 (ppp80) cc_final: 0.3911 (tmm-80) REVERT: H 284 PHE cc_start: 0.5128 (m-80) cc_final: 0.4737 (m-80) REVERT: H 288 GLU cc_start: 0.5316 (pm20) cc_final: 0.4970 (mm-30) REVERT: H 300 ILE cc_start: 0.5335 (mp) cc_final: 0.5011 (mt) REVERT: H 319 MET cc_start: 0.4003 (OUTLIER) cc_final: 0.3532 (tpp) REVERT: H 332 LEU cc_start: 0.6077 (mt) cc_final: 0.5683 (tp) REVERT: H 342 ARG cc_start: 0.5035 (mtm180) cc_final: 0.4722 (ttp-110) REVERT: H 426 TYR cc_start: 0.2944 (t80) cc_final: 0.1675 (p90) REVERT: H 452 MET cc_start: 0.6368 (mmp) cc_final: 0.6041 (mmt) REVERT: H 465 LYS cc_start: 0.4001 (mppt) cc_final: 0.3509 (mmmt) REVERT: I 120 MET cc_start: 0.2172 (pp-130) cc_final: 0.0709 (mpt) REVERT: I 125 ARG cc_start: 0.3391 (OUTLIER) cc_final: 0.2989 (mmm-85) REVERT: I 127 TYR cc_start: 0.3749 (t80) cc_final: 0.3462 (t80) REVERT: I 152 LYS cc_start: 0.4002 (mttt) cc_final: 0.3668 (ttpt) REVERT: I 155 PHE cc_start: 0.2858 (OUTLIER) cc_final: 0.2612 (m-80) REVERT: I 158 LEU cc_start: 0.3342 (tt) cc_final: 0.2763 (mp) REVERT: I 341 ARG cc_start: 0.4084 (mtt90) cc_final: 0.3432 (mmm160) REVERT: I 382 MET cc_start: 0.2090 (mmp) cc_final: 0.0827 (tpt) REVERT: I 662 GLU cc_start: 0.6539 (tt0) cc_final: 0.6184 (tp30) REVERT: I 672 GLU cc_start: 0.5606 (pm20) cc_final: 0.5400 (pm20) outliers start: 205 outliers final: 80 residues processed: 1093 average time/residue: 1.5312 time to fit residues: 2169.7631 Evaluate side-chains 979 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 872 time to evaluate : 5.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 326 ARG Chi-restraints excluded: chain 2 residue 374 ARG Chi-restraints excluded: chain 2 residue 396 THR Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 590 THR Chi-restraints excluded: chain 2 residue 684 ARG Chi-restraints excluded: chain 3 residue 234 GLU Chi-restraints excluded: chain 3 residue 318 LYS Chi-restraints excluded: chain 3 residue 325 THR Chi-restraints excluded: chain 3 residue 353 LEU Chi-restraints excluded: chain 3 residue 440 VAL Chi-restraints excluded: chain 3 residue 486 ILE Chi-restraints excluded: chain 3 residue 641 ASN Chi-restraints excluded: chain 3 residue 656 LEU Chi-restraints excluded: chain 4 residue 284 ILE Chi-restraints excluded: chain 4 residue 661 ILE Chi-restraints excluded: chain 4 residue 674 SER Chi-restraints excluded: chain 4 residue 699 LEU Chi-restraints excluded: chain 4 residue 712 VAL Chi-restraints excluded: chain 4 residue 720 LEU Chi-restraints excluded: chain 4 residue 749 MET Chi-restraints excluded: chain 4 residue 761 ILE Chi-restraints excluded: chain 4 residue 797 GLN Chi-restraints excluded: chain 5 residue 139 LEU Chi-restraints excluded: chain 5 residue 544 THR Chi-restraints excluded: chain 5 residue 592 SER Chi-restraints excluded: chain 5 residue 624 SER Chi-restraints excluded: chain 5 residue 633 LEU Chi-restraints excluded: chain 5 residue 661 GLU Chi-restraints excluded: chain 6 residue 313 MET Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 6 residue 462 ILE Chi-restraints excluded: chain 6 residue 598 THR Chi-restraints excluded: chain 6 residue 659 GLN Chi-restraints excluded: chain 6 residue 660 THR Chi-restraints excluded: chain 6 residue 829 ASP Chi-restraints excluded: chain 6 residue 831 LEU Chi-restraints excluded: chain 7 residue 244 ILE Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 297 GLN Chi-restraints excluded: chain 7 residue 410 VAL Chi-restraints excluded: chain 7 residue 502 VAL Chi-restraints excluded: chain 7 residue 556 THR Chi-restraints excluded: chain 7 residue 570 LEU Chi-restraints excluded: chain 7 residue 592 SER Chi-restraints excluded: chain 7 residue 670 ASP Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 534 ARG Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 681 LYS Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 639 ASP Chi-restraints excluded: chain D residue 661 ILE Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 819 LEU Chi-restraints excluded: chain D residue 833 ILE Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain E residue 497 MET Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain E residue 517 THR Chi-restraints excluded: chain E residue 599 MET Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 501 GLN Chi-restraints excluded: chain F residue 639 ASP Chi-restraints excluded: chain F residue 715 ILE Chi-restraints excluded: chain F residue 727 LEU Chi-restraints excluded: chain F residue 796 THR Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 382 ARG Chi-restraints excluded: chain G residue 426 LEU Chi-restraints excluded: chain G residue 554 ASN Chi-restraints excluded: chain G residue 656 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 281 THR Chi-restraints excluded: chain H residue 319 MET Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 472 LEU Chi-restraints excluded: chain I residue 125 ARG Chi-restraints excluded: chain I residue 155 PHE Chi-restraints excluded: chain I residue 280 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 684 optimal weight: 3.9990 chunk 466 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 611 optimal weight: 0.7980 chunk 339 optimal weight: 0.0770 chunk 701 optimal weight: 0.6980 chunk 567 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 419 optimal weight: 0.0980 chunk 737 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 666 ASN ** 2 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 856 GLN 3 29 GLN 3 340 GLN 3 365 GLN 3 587 ASN ** 3 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 613 GLN 5 334 GLN 5 585 ASN 5 587 GLN 6 264 GLN 6 362 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 297 GLN B 433 ASN ** B 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 722 ASN D 229 GLN D 253 GLN D 685 ASN D 726 ASN E 685 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 ASN H 367 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 69476 Z= 0.137 Angle : 0.481 10.716 93996 Z= 0.245 Chirality : 0.041 0.282 10834 Planarity : 0.004 0.055 12062 Dihedral : 7.072 179.797 9630 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.26 % Favored : 97.70 % Rotamer: Outliers : 3.00 % Allowed : 17.30 % Favored : 79.70 % 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: 0.70 (0.09), residues: 8483 helix: 1.28 (0.09), residues: 3472 sheet: -0.00 (0.12), residues: 1557 loop : -0.01 (0.10), residues: 3454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 338 HIS 0.011 0.001 HIS 6 653 PHE 0.029 0.001 PHE C 345 TYR 0.015 0.001 TYR 6 136 ARG 0.010 0.000 ARG G 162 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1146 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 918 time to evaluate : 5.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 196 GLU cc_start: 0.5931 (OUTLIER) cc_final: 0.5683 (mt-10) REVERT: 2 232 ARG cc_start: 0.6619 (mmm-85) cc_final: 0.5994 (mtp180) REVERT: 2 258 LEU cc_start: 0.7076 (tt) cc_final: 0.6625 (mt) REVERT: 2 276 MET cc_start: 0.7021 (tpt) cc_final: 0.6754 (tpt) REVERT: 2 326 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.6606 (pmt170) REVERT: 2 374 ARG cc_start: 0.6120 (OUTLIER) cc_final: 0.5327 (ttm110) REVERT: 2 651 ASN cc_start: 0.8324 (m-40) cc_final: 0.7684 (m-40) REVERT: 2 667 VAL cc_start: 0.7467 (OUTLIER) cc_final: 0.7047 (p) REVERT: 2 684 ARG cc_start: 0.4001 (OUTLIER) cc_final: 0.3326 (ptp90) REVERT: 2 687 VAL cc_start: 0.6039 (t) cc_final: 0.5702 (p) REVERT: 2 690 GLU cc_start: 0.5729 (pm20) cc_final: 0.5402 (pm20) REVERT: 3 23 ASP cc_start: 0.7115 (m-30) cc_final: 0.6791 (m-30) REVERT: 3 27 ARG cc_start: 0.7840 (tpt170) cc_final: 0.7102 (ttp80) REVERT: 3 52 ASN cc_start: 0.5025 (m-40) cc_final: 0.4767 (m110) REVERT: 3 188 LYS cc_start: 0.7988 (mtmm) cc_final: 0.7316 (ttpt) REVERT: 3 208 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7334 (mtp180) REVERT: 3 234 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.6110 (tm-30) REVERT: 3 274 ILE cc_start: 0.8662 (pt) cc_final: 0.8234 (tp) REVERT: 3 353 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8639 (mm) REVERT: 3 365 GLN cc_start: 0.7139 (mm110) cc_final: 0.6645 (mm110) REVERT: 3 386 MET cc_start: 0.8349 (mmp) cc_final: 0.8126 (mmm) REVERT: 3 455 ARG cc_start: 0.5814 (mmm160) cc_final: 0.5468 (mtt180) REVERT: 3 556 ILE cc_start: 0.6799 (tp) cc_final: 0.6525 (mm) REVERT: 4 266 GLN cc_start: 0.7763 (tp40) cc_final: 0.7439 (tp-100) REVERT: 4 341 ASP cc_start: 0.8132 (p0) cc_final: 0.7859 (p0) REVERT: 4 404 ASP cc_start: 0.6744 (m-30) cc_final: 0.6407 (m-30) REVERT: 4 477 ASP cc_start: 0.7271 (t0) cc_final: 0.6733 (t0) REVERT: 4 579 GLN cc_start: 0.7764 (mm-40) cc_final: 0.7366 (mm-40) REVERT: 4 583 LYS cc_start: 0.7929 (mmpt) cc_final: 0.7466 (mtmm) REVERT: 4 713 ASP cc_start: 0.6192 (t0) cc_final: 0.5984 (t70) REVERT: 4 715 LYS cc_start: 0.7004 (pttp) cc_final: 0.6598 (tptm) REVERT: 4 726 ASN cc_start: 0.7477 (m-40) cc_final: 0.6994 (t0) REVERT: 4 772 ARG cc_start: 0.7185 (mtp-110) cc_final: 0.6979 (ptm160) REVERT: 5 139 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8285 (pp) REVERT: 5 210 SER cc_start: 0.8156 (m) cc_final: 0.7811 (t) REVERT: 5 362 ARG cc_start: 0.6275 (mpp80) cc_final: 0.6000 (mmt180) REVERT: 5 369 ILE cc_start: 0.7798 (pt) cc_final: 0.7347 (tt) REVERT: 5 388 ILE cc_start: 0.8232 (mt) cc_final: 0.7988 (mm) REVERT: 5 404 MET cc_start: 0.6981 (ptp) cc_final: 0.5747 (mmm) REVERT: 5 469 MET cc_start: 0.7389 (mmm) cc_final: 0.6982 (mmm) REVERT: 5 495 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7322 (tt0) REVERT: 5 556 VAL cc_start: 0.6493 (t) cc_final: 0.6205 (p) REVERT: 5 625 ASN cc_start: 0.6384 (m110) cc_final: 0.5677 (t0) REVERT: 5 654 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7466 (mp0) REVERT: 5 661 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: 6 174 TYR cc_start: 0.7930 (t80) cc_final: 0.7363 (t80) REVERT: 6 299 GLU cc_start: 0.7207 (pm20) cc_final: 0.6252 (mt-10) REVERT: 6 347 ASN cc_start: 0.6448 (t0) cc_final: 0.5726 (m-40) REVERT: 6 367 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7661 (mt-10) REVERT: 6 594 ARG cc_start: 0.8085 (mmm160) cc_final: 0.7833 (mmm160) REVERT: 6 653 HIS cc_start: 0.7019 (OUTLIER) cc_final: 0.6447 (p-80) REVERT: 6 654 GLU cc_start: 0.7032 (tm-30) cc_final: 0.6571 (tp30) REVERT: 6 696 ARG cc_start: 0.6928 (tpm170) cc_final: 0.6047 (tmt-80) REVERT: 6 764 ILE cc_start: 0.7271 (mt) cc_final: 0.6725 (pp) REVERT: 6 783 ASP cc_start: 0.6208 (t0) cc_final: 0.5875 (t0) REVERT: 6 794 ARG cc_start: 0.5489 (mtp-110) cc_final: 0.4551 (mtm110) REVERT: 7 69 LYS cc_start: 0.7920 (mtmm) cc_final: 0.7659 (mtpt) REVERT: 7 76 ASN cc_start: 0.7605 (t0) cc_final: 0.7200 (m110) REVERT: 7 81 ASP cc_start: 0.7770 (m-30) cc_final: 0.7379 (t0) REVERT: 7 159 ASN cc_start: 0.7341 (m-40) cc_final: 0.6963 (m110) REVERT: 7 162 ARG cc_start: 0.7117 (ttm-80) cc_final: 0.6870 (ttt90) REVERT: 7 188 GLU cc_start: 0.5980 (tt0) cc_final: 0.5559 (tt0) REVERT: 7 244 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8375 (tp) REVERT: 7 247 ARG cc_start: 0.8105 (ttm170) cc_final: 0.7495 (ttp-110) REVERT: 7 288 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6930 (tt0) REVERT: 7 396 ASP cc_start: 0.6406 (p0) cc_final: 0.5478 (m-30) REVERT: 7 449 LYS cc_start: 0.7214 (mtmt) cc_final: 0.6717 (tmtp) REVERT: 7 498 MET cc_start: 0.5646 (ptt) cc_final: 0.5440 (ppp) REVERT: 7 502 VAL cc_start: 0.4906 (OUTLIER) cc_final: 0.4458 (t) REVERT: 7 598 PHE cc_start: 0.8278 (m-80) cc_final: 0.8038 (m-80) REVERT: B 269 LYS cc_start: 0.6595 (ttmm) cc_final: 0.5235 (mppt) REVERT: B 290 HIS cc_start: 0.5953 (m-70) cc_final: 0.5280 (m170) REVERT: B 293 ILE cc_start: 0.6847 (mt) cc_final: 0.6514 (tt) REVERT: B 413 ASP cc_start: 0.7077 (OUTLIER) cc_final: 0.6758 (m-30) REVERT: B 501 MET cc_start: 0.7614 (mmm) cc_final: 0.7079 (mmt) REVERT: B 506 TYR cc_start: 0.6128 (t80) cc_final: 0.5849 (t80) REVERT: B 534 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7604 (ttm170) REVERT: B 633 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.6972 (mptt) REVERT: B 694 ARG cc_start: 0.6544 (mtm110) cc_final: 0.5887 (mpp80) REVERT: B 705 ARG cc_start: 0.6240 (OUTLIER) cc_final: 0.5746 (mtp180) REVERT: B 800 THR cc_start: 0.6738 (m) cc_final: 0.6190 (p) REVERT: B 834 LEU cc_start: 0.6937 (mm) cc_final: 0.6222 (tp) REVERT: C 39 ARG cc_start: 0.7156 (ttm110) cc_final: 0.6600 (ttp-110) REVERT: C 188 LYS cc_start: 0.7914 (mtmt) cc_final: 0.7410 (mttp) REVERT: C 222 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.7986 (p) REVERT: C 234 GLU cc_start: 0.6735 (mt-10) cc_final: 0.6069 (mp0) REVERT: C 237 GLU cc_start: 0.7189 (mp0) cc_final: 0.6914 (mt-10) REVERT: C 348 ARG cc_start: 0.6916 (mtm110) cc_final: 0.6445 (mtt90) REVERT: C 464 LEU cc_start: 0.7894 (mt) cc_final: 0.7520 (mt) REVERT: C 477 LYS cc_start: 0.7375 (mttm) cc_final: 0.6901 (mttm) REVERT: C 505 THR cc_start: 0.8406 (t) cc_final: 0.7939 (m) REVERT: C 556 ILE cc_start: 0.7200 (pt) cc_final: 0.6873 (mm) REVERT: C 664 LYS cc_start: 0.7735 (mtpp) cc_final: 0.7308 (mtpt) REVERT: C 681 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7428 (tmmm) REVERT: C 723 LYS cc_start: 0.7408 (pttt) cc_final: 0.6939 (tttp) REVERT: D 235 GLU cc_start: 0.6442 (mt-10) cc_final: 0.5758 (tp30) REVERT: D 302 LYS cc_start: 0.7432 (mmtp) cc_final: 0.7043 (mtpp) REVERT: D 327 ASN cc_start: 0.8266 (OUTLIER) cc_final: 0.7412 (m110) REVERT: D 394 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8495 (tmtp) REVERT: D 408 ASP cc_start: 0.7452 (m-30) cc_final: 0.7110 (m-30) REVERT: D 434 GLU cc_start: 0.7570 (tp30) cc_final: 0.7288 (tm-30) REVERT: D 445 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6879 (mtt180) REVERT: D 483 GLN cc_start: 0.6699 (tp40) cc_final: 0.6148 (mt0) REVERT: D 503 ASP cc_start: 0.6218 (m-30) cc_final: 0.5852 (m-30) REVERT: D 661 ILE cc_start: 0.6812 (OUTLIER) cc_final: 0.6417 (mt) REVERT: D 690 GLU cc_start: 0.6674 (tt0) cc_final: 0.6121 (tp30) REVERT: D 693 ASP cc_start: 0.6527 (t0) cc_final: 0.5885 (p0) REVERT: D 779 LYS cc_start: 0.7198 (OUTLIER) cc_final: 0.6988 (ptmt) REVERT: D 819 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7199 (mm) REVERT: D 847 MET cc_start: 0.5535 (OUTLIER) cc_final: 0.5054 (mmm) REVERT: E 3 PHE cc_start: 0.7050 (m-80) cc_final: 0.6680 (m-10) REVERT: E 5 ARG cc_start: 0.7684 (ttp80) cc_final: 0.7061 (ttp-110) REVERT: E 33 ASN cc_start: 0.7413 (m-40) cc_final: 0.7167 (m110) REVERT: E 77 LYS cc_start: 0.7964 (mttm) cc_final: 0.7625 (mtpp) REVERT: E 209 ARG cc_start: 0.7069 (mmm-85) cc_final: 0.6748 (mmt180) REVERT: E 221 MET cc_start: 0.3460 (OUTLIER) cc_final: 0.3246 (pmm) REVERT: E 249 LYS cc_start: 0.7855 (mmtp) cc_final: 0.7510 (mppt) REVERT: E 354 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6212 (mt-10) REVERT: E 368 GLU cc_start: 0.6395 (OUTLIER) cc_final: 0.6132 (tm-30) REVERT: E 458 MET cc_start: 0.5818 (mtp) cc_final: 0.5435 (mtm) REVERT: E 469 MET cc_start: 0.7893 (mmm) cc_final: 0.7200 (mmm) REVERT: E 513 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7874 (pp) REVERT: E 546 ILE cc_start: 0.7297 (OUTLIER) cc_final: 0.6917 (mm) REVERT: E 593 GLU cc_start: 0.6724 (mt-10) cc_final: 0.6338 (mt-10) REVERT: E 661 GLU cc_start: 0.6717 (mt-10) cc_final: 0.6417 (mt-10) REVERT: F 161 ARG cc_start: 0.5566 (tpp-160) cc_final: 0.5363 (tpp80) REVERT: F 288 LEU cc_start: 0.8005 (tt) cc_final: 0.7787 (tm) REVERT: F 313 MET cc_start: 0.4377 (mpt) cc_final: 0.2955 (ptm) REVERT: F 421 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6336 (mm) REVERT: F 521 LYS cc_start: 0.4828 (mmpt) cc_final: 0.4452 (mmtt) REVERT: F 715 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7188 (mt) REVERT: F 719 CYS cc_start: 0.4670 (m) cc_final: 0.4304 (t) REVERT: G 15 ASN cc_start: 0.7032 (m-40) cc_final: 0.5895 (t0) REVERT: G 247 ARG cc_start: 0.7987 (ttt90) cc_final: 0.7501 (ttp80) REVERT: G 291 GLN cc_start: 0.7925 (mt0) cc_final: 0.7542 (mt0) REVERT: G 398 GLU cc_start: 0.4832 (tt0) cc_final: 0.4607 (tt0) REVERT: G 402 MET cc_start: 0.4602 (mmm) cc_final: 0.3914 (tpt) REVERT: G 412 ASN cc_start: 0.7553 (t0) cc_final: 0.7040 (m-40) REVERT: G 427 ASP cc_start: 0.7692 (m-30) cc_final: 0.7433 (m-30) REVERT: G 449 LYS cc_start: 0.7536 (mtmm) cc_final: 0.6830 (mmmt) REVERT: G 484 THR cc_start: 0.6960 (m) cc_final: 0.6451 (p) REVERT: G 498 MET cc_start: 0.6190 (mpp) cc_final: 0.5985 (mtt) REVERT: G 502 VAL cc_start: 0.5612 (OUTLIER) cc_final: 0.5342 (t) REVERT: G 529 MET cc_start: 0.6889 (mtm) cc_final: 0.6594 (OUTLIER) REVERT: G 541 MET cc_start: 0.8087 (mtt) cc_final: 0.7240 (mtm) REVERT: G 554 ASN cc_start: 0.8421 (OUTLIER) cc_final: 0.8034 (t0) REVERT: G 556 THR cc_start: 0.7986 (t) cc_final: 0.7527 (m) REVERT: G 618 TYR cc_start: 0.7478 (t80) cc_final: 0.7044 (t80) REVERT: G 659 TYR cc_start: 0.7906 (t80) cc_final: 0.7689 (t80) REVERT: G 690 LEU cc_start: 0.8438 (mt) cc_final: 0.8159 (mt) REVERT: H 31 ASN cc_start: 0.4042 (OUTLIER) cc_final: 0.3719 (m-40) REVERT: H 34 LYS cc_start: 0.3887 (tttt) cc_final: 0.3437 (tptp) REVERT: H 77 LYS cc_start: 0.5463 (OUTLIER) cc_final: 0.5214 (tttm) REVERT: H 126 GLU cc_start: 0.3750 (pp20) cc_final: 0.3307 (tm-30) REVERT: H 135 LEU cc_start: 0.2451 (OUTLIER) cc_final: 0.2085 (tp) REVERT: H 152 LYS cc_start: 0.4974 (pttp) cc_final: 0.4710 (pptt) REVERT: H 173 LEU cc_start: 0.1985 (mt) cc_final: 0.1628 (pp) REVERT: H 278 ARG cc_start: 0.4188 (OUTLIER) cc_final: 0.3832 (tmm-80) REVERT: H 284 PHE cc_start: 0.5161 (m-80) cc_final: 0.4733 (m-80) REVERT: H 288 GLU cc_start: 0.5442 (pm20) cc_final: 0.5103 (mm-30) REVERT: H 300 ILE cc_start: 0.5428 (mp) cc_final: 0.5150 (mt) REVERT: H 319 MET cc_start: 0.3906 (OUTLIER) cc_final: 0.3493 (tpp) REVERT: H 331 GLU cc_start: 0.5496 (mt-10) cc_final: 0.5266 (mt-10) REVERT: H 332 LEU cc_start: 0.6032 (mt) cc_final: 0.5605 (tp) REVERT: H 342 ARG cc_start: 0.4981 (mtm180) cc_final: 0.4711 (ttm-80) REVERT: H 371 GLU cc_start: 0.3915 (OUTLIER) cc_final: 0.3531 (pm20) REVERT: H 389 TYR cc_start: 0.1182 (m-80) cc_final: 0.0693 (m-80) REVERT: H 426 TYR cc_start: 0.2899 (t80) cc_final: 0.1670 (p90) REVERT: H 452 MET cc_start: 0.6339 (mmp) cc_final: 0.6050 (mmt) REVERT: H 465 LYS cc_start: 0.4001 (mppt) cc_final: 0.3468 (mmmt) REVERT: I 125 ARG cc_start: 0.3374 (OUTLIER) cc_final: 0.2986 (mmm-85) REVERT: I 127 TYR cc_start: 0.3762 (t80) cc_final: 0.3506 (t80) REVERT: I 152 LYS cc_start: 0.4043 (mttt) cc_final: 0.3689 (ttpt) REVERT: I 155 PHE cc_start: 0.2760 (OUTLIER) cc_final: 0.2448 (m-80) REVERT: I 158 LEU cc_start: 0.3081 (tt) cc_final: 0.2327 (mm) REVERT: I 341 ARG cc_start: 0.3953 (mtt90) cc_final: 0.3374 (mmm160) REVERT: I 382 MET cc_start: 0.2249 (mmp) cc_final: 0.1011 (tpp) REVERT: I 662 GLU cc_start: 0.6488 (tt0) cc_final: 0.6197 (tp30) REVERT: I 672 GLU cc_start: 0.5756 (pm20) cc_final: 0.5555 (pm20) outliers start: 228 outliers final: 103 residues processed: 1075 average time/residue: 1.5312 time to fit residues: 2134.8476 Evaluate side-chains 1009 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 861 time to evaluate : 5.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 196 GLU Chi-restraints excluded: chain 2 residue 326 ARG Chi-restraints excluded: chain 2 residue 374 ARG Chi-restraints excluded: chain 2 residue 396 THR Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 590 THR Chi-restraints excluded: chain 2 residue 656 ARG Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 684 ARG Chi-restraints excluded: chain 2 residue 786 VAL Chi-restraints excluded: chain 2 residue 851 VAL Chi-restraints excluded: chain 3 residue 208 ARG Chi-restraints excluded: chain 3 residue 234 GLU Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 324 ASN Chi-restraints excluded: chain 3 residue 353 LEU Chi-restraints excluded: chain 3 residue 440 VAL Chi-restraints excluded: chain 3 residue 486 ILE Chi-restraints excluded: chain 3 residue 656 LEU Chi-restraints excluded: chain 3 residue 701 THR Chi-restraints excluded: chain 4 residue 284 ILE Chi-restraints excluded: chain 4 residue 661 ILE Chi-restraints excluded: chain 4 residue 674 SER Chi-restraints excluded: chain 4 residue 699 LEU Chi-restraints excluded: chain 4 residue 749 MET Chi-restraints excluded: chain 4 residue 797 GLN Chi-restraints excluded: chain 5 residue 102 SER Chi-restraints excluded: chain 5 residue 139 LEU Chi-restraints excluded: chain 5 residue 177 THR Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 495 GLU Chi-restraints excluded: chain 5 residue 544 THR Chi-restraints excluded: chain 5 residue 624 SER Chi-restraints excluded: chain 5 residue 633 LEU Chi-restraints excluded: chain 5 residue 654 GLU Chi-restraints excluded: chain 5 residue 661 GLU Chi-restraints excluded: chain 6 residue 313 MET Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 6 residue 446 ARG Chi-restraints excluded: chain 6 residue 462 ILE Chi-restraints excluded: chain 6 residue 501 GLN Chi-restraints excluded: chain 6 residue 598 THR Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 6 residue 659 GLN Chi-restraints excluded: chain 6 residue 660 THR Chi-restraints excluded: chain 6 residue 829 ASP Chi-restraints excluded: chain 6 residue 831 LEU Chi-restraints excluded: chain 6 residue 833 GLN Chi-restraints excluded: chain 7 residue 141 VAL Chi-restraints excluded: chain 7 residue 207 LEU Chi-restraints excluded: chain 7 residue 244 ILE Chi-restraints excluded: chain 7 residue 283 GLU Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 288 GLU Chi-restraints excluded: chain 7 residue 329 ARG Chi-restraints excluded: chain 7 residue 410 VAL Chi-restraints excluded: chain 7 residue 502 VAL Chi-restraints excluded: chain 7 residue 556 THR Chi-restraints excluded: chain 7 residue 570 LEU Chi-restraints excluded: chain 7 residue 592 SER Chi-restraints excluded: chain 7 residue 670 ASP Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 378 GLU Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 534 ARG Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 581 ARG Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 681 LYS Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain D residue 445 ARG Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 661 ILE Chi-restraints excluded: chain D residue 674 SER Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 779 LYS Chi-restraints excluded: chain D residue 819 LEU Chi-restraints excluded: chain D residue 833 ILE Chi-restraints excluded: chain D residue 847 MET Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 368 GLU Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain E residue 517 THR Chi-restraints excluded: chain E residue 546 ILE Chi-restraints excluded: chain E residue 599 MET Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 501 GLN Chi-restraints excluded: chain F residue 519 MET Chi-restraints excluded: chain F residue 639 ASP Chi-restraints excluded: chain F residue 706 MET Chi-restraints excluded: chain F residue 715 ILE Chi-restraints excluded: chain F residue 727 LEU Chi-restraints excluded: chain F residue 796 THR Chi-restraints excluded: chain G residue 282 SER Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 350 ASP Chi-restraints excluded: chain G residue 382 ARG Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 554 ASN Chi-restraints excluded: chain G residue 656 VAL Chi-restraints excluded: chain G residue 706 ASP Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 77 LYS Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 277 ASN Chi-restraints excluded: chain H residue 278 ARG Chi-restraints excluded: chain H residue 281 THR Chi-restraints excluded: chain H residue 319 MET Chi-restraints excluded: chain H residue 322 SER Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 371 GLU Chi-restraints excluded: chain I residue 125 ARG Chi-restraints excluded: chain I residue 155 PHE Chi-restraints excluded: chain I residue 239 HIS Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 280 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 276 optimal weight: 0.9990 chunk 739 optimal weight: 0.8980 chunk 162 optimal weight: 5.9990 chunk 482 optimal weight: 7.9990 chunk 202 optimal weight: 5.9990 chunk 822 optimal weight: 6.9990 chunk 682 optimal weight: 7.9990 chunk 380 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 272 optimal weight: 0.7980 chunk 431 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 856 GLN 3 340 GLN 3 587 ASN 3 682 ASN ** 3 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 613 GLN 5 585 ASN 5 587 GLN 6 264 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 ASN ** B 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 722 ASN D 229 GLN D 253 GLN E 685 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 ASN G 274 ASN ** H 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 367 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 69476 Z= 0.170 Angle : 0.502 10.976 93996 Z= 0.256 Chirality : 0.042 0.249 10834 Planarity : 0.004 0.056 12062 Dihedral : 7.024 178.545 9630 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.25 % Favored : 97.71 % Rotamer: Outliers : 3.45 % Allowed : 17.67 % Favored : 78.88 % 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: 0.69 (0.09), residues: 8483 helix: 1.31 (0.09), residues: 3470 sheet: -0.08 (0.12), residues: 1580 loop : -0.01 (0.10), residues: 3433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 338 HIS 0.011 0.001 HIS 6 653 PHE 0.021 0.001 PHE I 702 TYR 0.022 0.001 TYR B 769 ARG 0.010 0.000 ARG G 162 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1163 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 901 time to evaluate : 6.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 196 GLU cc_start: 0.5823 (OUTLIER) cc_final: 0.5568 (mt-10) REVERT: 2 232 ARG cc_start: 0.6568 (mmm-85) cc_final: 0.5956 (mtp180) REVERT: 2 258 LEU cc_start: 0.7029 (tt) cc_final: 0.6571 (mt) REVERT: 2 326 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.6718 (pmt170) REVERT: 2 374 ARG cc_start: 0.5950 (OUTLIER) cc_final: 0.5243 (ttm110) REVERT: 2 422 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6790 (pp20) REVERT: 2 554 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.6896 (mptt) REVERT: 2 651 ASN cc_start: 0.8320 (m-40) cc_final: 0.7715 (m-40) REVERT: 2 667 VAL cc_start: 0.7476 (OUTLIER) cc_final: 0.7060 (p) REVERT: 2 684 ARG cc_start: 0.4045 (OUTLIER) cc_final: 0.3352 (ptp90) REVERT: 2 687 VAL cc_start: 0.6094 (t) cc_final: 0.5772 (p) REVERT: 2 690 GLU cc_start: 0.5627 (pm20) cc_final: 0.5292 (pm20) REVERT: 3 23 ASP cc_start: 0.7143 (m-30) cc_final: 0.6820 (m-30) REVERT: 3 27 ARG cc_start: 0.7904 (tpt170) cc_final: 0.7101 (ttp80) REVERT: 3 52 ASN cc_start: 0.5081 (m-40) cc_final: 0.4828 (m110) REVERT: 3 188 LYS cc_start: 0.7962 (mtmm) cc_final: 0.7308 (ttpt) REVERT: 3 208 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7296 (mtp180) REVERT: 3 234 GLU cc_start: 0.6654 (OUTLIER) cc_final: 0.6159 (tm-30) REVERT: 3 274 ILE cc_start: 0.8699 (pt) cc_final: 0.8252 (tp) REVERT: 3 353 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8628 (mm) REVERT: 3 365 GLN cc_start: 0.7274 (mm110) cc_final: 0.6965 (mm110) REVERT: 3 455 ARG cc_start: 0.5844 (mmm160) cc_final: 0.5521 (mtt180) REVERT: 3 486 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7855 (mt) REVERT: 3 556 ILE cc_start: 0.6942 (tp) cc_final: 0.6606 (mm) REVERT: 3 566 LEU cc_start: 0.8323 (mm) cc_final: 0.8021 (mm) REVERT: 4 178 ARG cc_start: 0.7257 (mmm160) cc_final: 0.6960 (mmm-85) REVERT: 4 266 GLN cc_start: 0.7702 (tp40) cc_final: 0.7410 (tp-100) REVERT: 4 404 ASP cc_start: 0.6867 (m-30) cc_final: 0.6559 (m-30) REVERT: 4 411 THR cc_start: 0.8369 (OUTLIER) cc_final: 0.7827 (p) REVERT: 4 477 ASP cc_start: 0.7233 (t0) cc_final: 0.6645 (t0) REVERT: 4 579 GLN cc_start: 0.7764 (mm-40) cc_final: 0.7363 (mm-40) REVERT: 4 583 LYS cc_start: 0.8098 (mmpt) cc_final: 0.7555 (mtmm) REVERT: 4 612 LYS cc_start: 0.7582 (mmpt) cc_final: 0.7065 (mmtp) REVERT: 4 649 MET cc_start: 0.8624 (mtp) cc_final: 0.8323 (mtt) REVERT: 4 715 LYS cc_start: 0.7076 (pttp) cc_final: 0.6461 (tptm) REVERT: 4 726 ASN cc_start: 0.7547 (m-40) cc_final: 0.7049 (t0) REVERT: 4 756 GLU cc_start: 0.7637 (tt0) cc_final: 0.7370 (tp30) REVERT: 5 5 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.6657 (tmm-80) REVERT: 5 139 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8302 (pp) REVERT: 5 362 ARG cc_start: 0.6381 (mpp80) cc_final: 0.6092 (mmt180) REVERT: 5 369 ILE cc_start: 0.7826 (pt) cc_final: 0.7385 (tt) REVERT: 5 388 ILE cc_start: 0.8158 (mt) cc_final: 0.7900 (mm) REVERT: 5 404 MET cc_start: 0.7069 (ptp) cc_final: 0.5729 (mmp) REVERT: 5 469 MET cc_start: 0.7429 (mmm) cc_final: 0.7050 (mmm) REVERT: 5 495 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7272 (tt0) REVERT: 5 556 VAL cc_start: 0.6538 (t) cc_final: 0.6219 (p) REVERT: 5 625 ASN cc_start: 0.6414 (m110) cc_final: 0.5654 (t0) REVERT: 5 646 ILE cc_start: 0.3759 (OUTLIER) cc_final: 0.3526 (pt) REVERT: 5 654 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7496 (mp0) REVERT: 5 689 MET cc_start: 0.6968 (mmm) cc_final: 0.6758 (mmm) REVERT: 6 174 TYR cc_start: 0.7942 (t80) cc_final: 0.7389 (t80) REVERT: 6 299 GLU cc_start: 0.7191 (pm20) cc_final: 0.6237 (mt-10) REVERT: 6 347 ASN cc_start: 0.6448 (t0) cc_final: 0.5729 (m-40) REVERT: 6 367 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7877 (mt-10) REVERT: 6 614 ARG cc_start: 0.6435 (ttp-170) cc_final: 0.6137 (ttm110) REVERT: 6 653 HIS cc_start: 0.7133 (OUTLIER) cc_final: 0.6522 (p-80) REVERT: 6 753 ARG cc_start: 0.6902 (mtm110) cc_final: 0.6690 (ttm-80) REVERT: 6 764 ILE cc_start: 0.7307 (mt) cc_final: 0.6729 (pp) REVERT: 6 783 ASP cc_start: 0.6228 (t0) cc_final: 0.5912 (t0) REVERT: 6 833 GLN cc_start: 0.7204 (OUTLIER) cc_final: 0.6504 (mp10) REVERT: 7 69 LYS cc_start: 0.7931 (mtmm) cc_final: 0.7674 (mtpt) REVERT: 7 76 ASN cc_start: 0.7748 (t0) cc_final: 0.7330 (m110) REVERT: 7 81 ASP cc_start: 0.7779 (m-30) cc_final: 0.7392 (t0) REVERT: 7 159 ASN cc_start: 0.7259 (m-40) cc_final: 0.6892 (m110) REVERT: 7 162 ARG cc_start: 0.7098 (ttm-80) cc_final: 0.6795 (ttt90) REVERT: 7 188 GLU cc_start: 0.6139 (tt0) cc_final: 0.5813 (tt0) REVERT: 7 244 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8412 (tp) REVERT: 7 247 ARG cc_start: 0.8106 (ttm170) cc_final: 0.7499 (ttp80) REVERT: 7 288 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.7018 (tt0) REVERT: 7 449 LYS cc_start: 0.7347 (mtmt) cc_final: 0.6824 (tmtp) REVERT: 7 502 VAL cc_start: 0.4810 (OUTLIER) cc_final: 0.4311 (t) REVERT: 7 598 PHE cc_start: 0.8397 (m-80) cc_final: 0.8104 (m-80) REVERT: B 269 LYS cc_start: 0.6558 (ttmm) cc_final: 0.5181 (mppt) REVERT: B 290 HIS cc_start: 0.5971 (m-70) cc_final: 0.5298 (m170) REVERT: B 413 ASP cc_start: 0.7044 (OUTLIER) cc_final: 0.6739 (m-30) REVERT: B 534 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7549 (ttm170) REVERT: B 633 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.6962 (mptt) REVERT: B 705 ARG cc_start: 0.6248 (OUTLIER) cc_final: 0.5758 (mtp180) REVERT: B 781 MET cc_start: 0.5141 (mpm) cc_final: 0.4788 (mmt) REVERT: B 834 LEU cc_start: 0.6873 (mm) cc_final: 0.6306 (tp) REVERT: C 39 ARG cc_start: 0.7125 (ttm110) cc_final: 0.6526 (ttp-110) REVERT: C 188 LYS cc_start: 0.7980 (mtmt) cc_final: 0.7533 (mttp) REVERT: C 222 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8069 (p) REVERT: C 234 GLU cc_start: 0.6818 (mt-10) cc_final: 0.5855 (mp0) REVERT: C 235 ASP cc_start: 0.6467 (p0) cc_final: 0.5940 (p0) REVERT: C 237 GLU cc_start: 0.7185 (mp0) cc_final: 0.6484 (mt-10) REVERT: C 348 ARG cc_start: 0.6947 (mtm110) cc_final: 0.6415 (mtt90) REVERT: C 390 GLU cc_start: 0.7700 (pt0) cc_final: 0.7465 (pt0) REVERT: C 464 LEU cc_start: 0.7915 (mt) cc_final: 0.7566 (mt) REVERT: C 477 LYS cc_start: 0.7401 (mttm) cc_final: 0.6992 (mttm) REVERT: C 505 THR cc_start: 0.8434 (t) cc_final: 0.7971 (m) REVERT: C 556 ILE cc_start: 0.7215 (pt) cc_final: 0.6865 (mm) REVERT: C 664 LYS cc_start: 0.7764 (mtpp) cc_final: 0.7319 (mtpt) REVERT: C 681 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7489 (tmmm) REVERT: C 723 LYS cc_start: 0.7388 (pttt) cc_final: 0.6949 (tttp) REVERT: D 235 GLU cc_start: 0.6386 (mt-10) cc_final: 0.5683 (tp30) REVERT: D 302 LYS cc_start: 0.7569 (mmtp) cc_final: 0.7078 (mtpp) REVERT: D 327 ASN cc_start: 0.8183 (OUTLIER) cc_final: 0.7373 (m-40) REVERT: D 394 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8530 (tmtp) REVERT: D 408 ASP cc_start: 0.7475 (m-30) cc_final: 0.7130 (m-30) REVERT: D 434 GLU cc_start: 0.7601 (tp30) cc_final: 0.7305 (tm-30) REVERT: D 445 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.7008 (mtt180) REVERT: D 483 GLN cc_start: 0.6824 (tp40) cc_final: 0.6207 (mt0) REVERT: D 503 ASP cc_start: 0.6218 (m-30) cc_final: 0.5852 (m-30) REVERT: D 661 ILE cc_start: 0.6796 (OUTLIER) cc_final: 0.6426 (mt) REVERT: D 690 GLU cc_start: 0.6664 (tt0) cc_final: 0.6075 (tp30) REVERT: D 693 ASP cc_start: 0.6553 (t0) cc_final: 0.5930 (p0) REVERT: D 779 LYS cc_start: 0.7215 (OUTLIER) cc_final: 0.7009 (ptmt) REVERT: D 819 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7194 (mm) REVERT: D 847 MET cc_start: 0.5501 (OUTLIER) cc_final: 0.4969 (mmm) REVERT: E 3 PHE cc_start: 0.7264 (m-80) cc_final: 0.7024 (m-10) REVERT: E 5 ARG cc_start: 0.7471 (ttp80) cc_final: 0.6995 (ttp-110) REVERT: E 77 LYS cc_start: 0.7971 (mttm) cc_final: 0.7649 (mtpp) REVERT: E 182 MET cc_start: 0.8465 (ttm) cc_final: 0.8164 (ttp) REVERT: E 209 ARG cc_start: 0.7113 (mmm-85) cc_final: 0.6773 (mmt180) REVERT: E 221 MET cc_start: 0.3458 (OUTLIER) cc_final: 0.3060 (pmm) REVERT: E 249 LYS cc_start: 0.7850 (mmtp) cc_final: 0.7484 (mppt) REVERT: E 301 TYR cc_start: 0.8003 (p90) cc_final: 0.7468 (p90) REVERT: E 354 GLU cc_start: 0.6663 (OUTLIER) cc_final: 0.6242 (mt-10) REVERT: E 368 GLU cc_start: 0.6401 (OUTLIER) cc_final: 0.6135 (tm-30) REVERT: E 458 MET cc_start: 0.5893 (mtp) cc_final: 0.5477 (mtm) REVERT: E 469 MET cc_start: 0.7884 (mmm) cc_final: 0.7238 (mmm) REVERT: E 497 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8120 (mtm) REVERT: E 513 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7870 (pp) REVERT: E 546 ILE cc_start: 0.7349 (OUTLIER) cc_final: 0.6952 (mm) REVERT: E 593 GLU cc_start: 0.6805 (mt-10) cc_final: 0.6436 (mt-10) REVERT: E 597 GLU cc_start: 0.6243 (pm20) cc_final: 0.5742 (mm-30) REVERT: E 661 GLU cc_start: 0.6711 (mt-10) cc_final: 0.6390 (mt-10) REVERT: F 168 MET cc_start: 0.6546 (mmt) cc_final: 0.5996 (mmm) REVERT: F 421 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6449 (mm) REVERT: F 446 ARG cc_start: 0.7168 (ptt90) cc_final: 0.6853 (ptt90) REVERT: F 654 GLU cc_start: 0.6891 (tm-30) cc_final: 0.6132 (tp30) REVERT: F 700 ASN cc_start: 0.6762 (OUTLIER) cc_final: 0.6509 (p0) REVERT: F 715 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7359 (mt) REVERT: G 15 ASN cc_start: 0.7184 (m-40) cc_final: 0.6002 (t0) REVERT: G 247 ARG cc_start: 0.7992 (ttt90) cc_final: 0.7506 (ttp80) REVERT: G 291 GLN cc_start: 0.7935 (mt0) cc_final: 0.7581 (mt0) REVERT: G 297 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7290 (tt0) REVERT: G 412 ASN cc_start: 0.7578 (t0) cc_final: 0.7090 (m-40) REVERT: G 427 ASP cc_start: 0.7675 (m-30) cc_final: 0.7406 (m-30) REVERT: G 449 LYS cc_start: 0.7460 (mtmm) cc_final: 0.6715 (mmmt) REVERT: G 475 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7343 (ttmp) REVERT: G 484 THR cc_start: 0.7002 (m) cc_final: 0.6517 (p) REVERT: G 502 VAL cc_start: 0.5689 (OUTLIER) cc_final: 0.5436 (t) REVERT: G 537 ILE cc_start: 0.8032 (mt) cc_final: 0.7686 (mm) REVERT: G 554 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.8000 (t0) REVERT: G 556 THR cc_start: 0.7978 (t) cc_final: 0.7542 (m) REVERT: G 618 TYR cc_start: 0.7393 (t80) cc_final: 0.7075 (t80) REVERT: G 659 TYR cc_start: 0.7912 (t80) cc_final: 0.7644 (t80) REVERT: G 690 LEU cc_start: 0.8456 (mt) cc_final: 0.8166 (mt) REVERT: H 31 ASN cc_start: 0.4062 (OUTLIER) cc_final: 0.3723 (m-40) REVERT: H 34 LYS cc_start: 0.3653 (tttt) cc_final: 0.3431 (tptp) REVERT: H 77 LYS cc_start: 0.5453 (OUTLIER) cc_final: 0.5191 (tttm) REVERT: H 79 TYR cc_start: 0.5573 (m-80) cc_final: 0.5229 (m-10) REVERT: H 135 LEU cc_start: 0.2521 (OUTLIER) cc_final: 0.2158 (tp) REVERT: H 138 LYS cc_start: 0.3126 (mmmt) cc_final: 0.2069 (tptm) REVERT: H 141 LYS cc_start: 0.3142 (mmmt) cc_final: 0.2904 (mmtm) REVERT: H 152 LYS cc_start: 0.4978 (pttp) cc_final: 0.4701 (pptt) REVERT: H 278 ARG cc_start: 0.4312 (OUTLIER) cc_final: 0.3980 (tmm-80) REVERT: H 284 PHE cc_start: 0.5295 (m-80) cc_final: 0.4798 (m-80) REVERT: H 288 GLU cc_start: 0.5474 (pm20) cc_final: 0.5124 (mm-30) REVERT: H 300 ILE cc_start: 0.5424 (mp) cc_final: 0.5142 (mt) REVERT: H 319 MET cc_start: 0.3956 (OUTLIER) cc_final: 0.3498 (tpp) REVERT: H 331 GLU cc_start: 0.5628 (mt-10) cc_final: 0.5313 (mt-10) REVERT: H 332 LEU cc_start: 0.6018 (mt) cc_final: 0.5572 (tp) REVERT: H 342 ARG cc_start: 0.4960 (mtm180) cc_final: 0.4732 (ttm-80) REVERT: H 371 GLU cc_start: 0.3966 (OUTLIER) cc_final: 0.3524 (pm20) REVERT: H 389 TYR cc_start: 0.0998 (m-80) cc_final: 0.0624 (m-80) REVERT: H 426 TYR cc_start: 0.2972 (t80) cc_final: 0.1728 (p90) REVERT: H 452 MET cc_start: 0.6240 (mmp) cc_final: 0.5958 (mmt) REVERT: I 125 ARG cc_start: 0.3399 (OUTLIER) cc_final: 0.3084 (mmm-85) REVERT: I 127 TYR cc_start: 0.3924 (t80) cc_final: 0.2984 (t80) REVERT: I 147 ARG cc_start: 0.3159 (ptm160) cc_final: 0.2918 (ptm-80) REVERT: I 152 LYS cc_start: 0.3832 (mttt) cc_final: 0.3489 (tppt) REVERT: I 155 PHE cc_start: 0.2811 (OUTLIER) cc_final: 0.2372 (m-80) REVERT: I 158 LEU cc_start: 0.2616 (tt) cc_final: 0.2212 (mm) REVERT: I 341 ARG cc_start: 0.3827 (mtt90) cc_final: 0.3229 (mmm160) REVERT: I 382 MET cc_start: 0.2530 (mmp) cc_final: 0.1354 (tpp) REVERT: I 662 GLU cc_start: 0.6586 (tt0) cc_final: 0.6212 (tp30) outliers start: 262 outliers final: 122 residues processed: 1080 average time/residue: 1.5404 time to fit residues: 2153.9655 Evaluate side-chains 1020 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 842 time to evaluate : 6.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 196 GLU Chi-restraints excluded: chain 2 residue 326 ARG Chi-restraints excluded: chain 2 residue 374 ARG Chi-restraints excluded: chain 2 residue 396 THR Chi-restraints excluded: chain 2 residue 422 GLU Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 554 LYS Chi-restraints excluded: chain 2 residue 590 THR Chi-restraints excluded: chain 2 residue 656 ARG Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 684 ARG Chi-restraints excluded: chain 2 residue 697 THR Chi-restraints excluded: chain 2 residue 786 VAL Chi-restraints excluded: chain 2 residue 851 VAL Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 117 GLU Chi-restraints excluded: chain 3 residue 189 THR Chi-restraints excluded: chain 3 residue 208 ARG Chi-restraints excluded: chain 3 residue 234 GLU Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 353 LEU Chi-restraints excluded: chain 3 residue 440 VAL Chi-restraints excluded: chain 3 residue 486 ILE Chi-restraints excluded: chain 3 residue 641 ASN Chi-restraints excluded: chain 3 residue 656 LEU Chi-restraints excluded: chain 3 residue 667 VAL Chi-restraints excluded: chain 3 residue 701 THR Chi-restraints excluded: chain 4 residue 284 ILE Chi-restraints excluded: chain 4 residue 411 THR Chi-restraints excluded: chain 4 residue 592 SER Chi-restraints excluded: chain 4 residue 661 ILE Chi-restraints excluded: chain 4 residue 674 SER Chi-restraints excluded: chain 4 residue 699 LEU Chi-restraints excluded: chain 4 residue 749 MET Chi-restraints excluded: chain 4 residue 797 GLN Chi-restraints excluded: chain 5 residue 5 ARG Chi-restraints excluded: chain 5 residue 139 LEU Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 366 LEU Chi-restraints excluded: chain 5 residue 484 LYS Chi-restraints excluded: chain 5 residue 495 GLU Chi-restraints excluded: chain 5 residue 544 THR Chi-restraints excluded: chain 5 residue 583 MET Chi-restraints excluded: chain 5 residue 592 SER Chi-restraints excluded: chain 5 residue 624 SER Chi-restraints excluded: chain 5 residue 646 ILE Chi-restraints excluded: chain 5 residue 654 GLU Chi-restraints excluded: chain 6 residue 313 MET Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 6 residue 446 ARG Chi-restraints excluded: chain 6 residue 462 ILE Chi-restraints excluded: chain 6 residue 501 GLN Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 6 residue 598 THR Chi-restraints excluded: chain 6 residue 647 SER Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 6 residue 659 GLN Chi-restraints excluded: chain 6 residue 660 THR Chi-restraints excluded: chain 6 residue 829 ASP Chi-restraints excluded: chain 6 residue 831 LEU Chi-restraints excluded: chain 6 residue 833 GLN Chi-restraints excluded: chain 7 residue 141 VAL Chi-restraints excluded: chain 7 residue 207 LEU Chi-restraints excluded: chain 7 residue 244 ILE Chi-restraints excluded: chain 7 residue 283 GLU Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 288 GLU Chi-restraints excluded: chain 7 residue 410 VAL Chi-restraints excluded: chain 7 residue 502 VAL Chi-restraints excluded: chain 7 residue 556 THR Chi-restraints excluded: chain 7 residue 557 LEU Chi-restraints excluded: chain 7 residue 570 LEU Chi-restraints excluded: chain 7 residue 592 SER Chi-restraints excluded: chain 7 residue 670 ASP Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 534 ARG Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 581 ARG Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain B residue 789 VAL Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 340 GLN Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 681 LYS Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain D residue 445 ARG Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 661 ILE Chi-restraints excluded: chain D residue 674 SER Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 779 LYS Chi-restraints excluded: chain D residue 819 LEU Chi-restraints excluded: chain D residue 847 MET Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 368 GLU Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain E residue 497 MET Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain E residue 546 ILE Chi-restraints excluded: chain E residue 599 MET Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 501 GLN Chi-restraints excluded: chain F residue 519 MET Chi-restraints excluded: chain F residue 639 ASP Chi-restraints excluded: chain F residue 700 ASN Chi-restraints excluded: chain F residue 706 MET Chi-restraints excluded: chain F residue 715 ILE Chi-restraints excluded: chain F residue 727 LEU Chi-restraints excluded: chain F residue 796 THR Chi-restraints excluded: chain G residue 282 SER Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 297 GLN Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 350 ASP Chi-restraints excluded: chain G residue 382 ARG Chi-restraints excluded: chain G residue 475 LYS Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 554 ASN Chi-restraints excluded: chain G residue 656 VAL Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 77 LYS Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 277 ASN Chi-restraints excluded: chain H residue 278 ARG Chi-restraints excluded: chain H residue 281 THR Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 319 MET Chi-restraints excluded: chain H residue 322 SER Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 371 GLU Chi-restraints excluded: chain I residue 125 ARG Chi-restraints excluded: chain I residue 155 PHE Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 280 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 792 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 468 optimal weight: 0.0060 chunk 600 optimal weight: 0.8980 chunk 465 optimal weight: 2.9990 chunk 692 optimal weight: 5.9990 chunk 459 optimal weight: 1.9990 chunk 819 optimal weight: 3.9990 chunk 512 optimal weight: 0.8980 chunk 499 optimal weight: 0.8980 chunk 378 optimal weight: 2.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 528 ASN ** 2 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 856 GLN 3 587 ASN 3 641 ASN ** 3 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 543 GLN 4 613 GLN 5 587 GLN 6 156 GLN 6 264 GLN 6 366 ASN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 750 GLN B 433 ASN ** B 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 688 ASN ** C 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 722 ASN D 229 GLN D 253 GLN E 685 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 ASN G 274 ASN H 367 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 69476 Z= 0.170 Angle : 0.505 11.185 93996 Z= 0.257 Chirality : 0.042 0.232 10834 Planarity : 0.004 0.055 12062 Dihedral : 6.968 177.942 9630 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.33 % Favored : 97.63 % Rotamer: Outliers : 3.48 % Allowed : 18.30 % Favored : 78.22 % 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: 0.70 (0.09), residues: 8483 helix: 1.32 (0.09), residues: 3476 sheet: -0.10 (0.12), residues: 1584 loop : 0.00 (0.10), residues: 3423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 112 HIS 0.011 0.001 HIS 6 653 PHE 0.027 0.001 PHE C 345 TYR 0.016 0.001 TYR 6 136 ARG 0.008 0.000 ARG G 162 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1154 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 890 time to evaluate : 5.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 196 GLU cc_start: 0.5883 (OUTLIER) cc_final: 0.5630 (mt-10) REVERT: 2 232 ARG cc_start: 0.6561 (mmm-85) cc_final: 0.5949 (mtp180) REVERT: 2 258 LEU cc_start: 0.7163 (tt) cc_final: 0.6708 (mt) REVERT: 2 326 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.6666 (pmt170) REVERT: 2 370 LYS cc_start: 0.4255 (OUTLIER) cc_final: 0.3450 (ttpt) REVERT: 2 374 ARG cc_start: 0.5952 (OUTLIER) cc_final: 0.5246 (ttm110) REVERT: 2 422 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6841 (pp20) REVERT: 2 554 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.6889 (mptt) REVERT: 2 651 ASN cc_start: 0.8302 (m-40) cc_final: 0.7706 (m-40) REVERT: 2 667 VAL cc_start: 0.7464 (OUTLIER) cc_final: 0.7051 (p) REVERT: 2 684 ARG cc_start: 0.3979 (OUTLIER) cc_final: 0.3339 (ptp90) REVERT: 2 687 VAL cc_start: 0.6040 (t) cc_final: 0.5829 (p) REVERT: 2 690 GLU cc_start: 0.5610 (pm20) cc_final: 0.5276 (pm20) REVERT: 2 781 MET cc_start: 0.5162 (ptm) cc_final: 0.4961 (ttt) REVERT: 3 23 ASP cc_start: 0.7191 (m-30) cc_final: 0.6874 (m-30) REVERT: 3 27 ARG cc_start: 0.7933 (tpt170) cc_final: 0.7104 (ttp80) REVERT: 3 52 ASN cc_start: 0.5073 (m-40) cc_final: 0.4819 (m110) REVERT: 3 188 LYS cc_start: 0.7984 (mtmm) cc_final: 0.7303 (ttpt) REVERT: 3 208 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7226 (mtp180) REVERT: 3 234 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.6139 (tm-30) REVERT: 3 274 ILE cc_start: 0.8699 (pt) cc_final: 0.8262 (tp) REVERT: 3 290 ASP cc_start: 0.7820 (m-30) cc_final: 0.7498 (m-30) REVERT: 3 353 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8642 (mm) REVERT: 3 455 ARG cc_start: 0.5828 (mmm160) cc_final: 0.5512 (mtt180) REVERT: 3 556 ILE cc_start: 0.6922 (tp) cc_final: 0.6584 (mm) REVERT: 4 178 ARG cc_start: 0.7263 (mmm160) cc_final: 0.6971 (mmm-85) REVERT: 4 266 GLN cc_start: 0.7686 (tp40) cc_final: 0.7392 (tp-100) REVERT: 4 404 ASP cc_start: 0.6888 (m-30) cc_final: 0.6584 (m-30) REVERT: 4 411 THR cc_start: 0.8379 (OUTLIER) cc_final: 0.7846 (p) REVERT: 4 477 ASP cc_start: 0.7253 (t0) cc_final: 0.6640 (t0) REVERT: 4 579 GLN cc_start: 0.7713 (mm-40) cc_final: 0.7332 (mm-40) REVERT: 4 583 LYS cc_start: 0.8181 (mmpt) cc_final: 0.7576 (mtmm) REVERT: 4 612 LYS cc_start: 0.7634 (mmpt) cc_final: 0.7189 (mmtp) REVERT: 4 715 LYS cc_start: 0.7067 (pttp) cc_final: 0.6516 (tptm) REVERT: 4 726 ASN cc_start: 0.7591 (m-40) cc_final: 0.7082 (t0) REVERT: 4 756 GLU cc_start: 0.7633 (tt0) cc_final: 0.7359 (tp30) REVERT: 5 5 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6663 (tmm-80) REVERT: 5 362 ARG cc_start: 0.6375 (mpp80) cc_final: 0.6123 (mmt180) REVERT: 5 369 ILE cc_start: 0.7824 (pt) cc_final: 0.7377 (tt) REVERT: 5 388 ILE cc_start: 0.8167 (mt) cc_final: 0.7923 (mm) REVERT: 5 404 MET cc_start: 0.7032 (ptp) cc_final: 0.5691 (mmp) REVERT: 5 495 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7299 (tt0) REVERT: 5 556 VAL cc_start: 0.6588 (t) cc_final: 0.6246 (p) REVERT: 5 625 ASN cc_start: 0.6393 (m110) cc_final: 0.5631 (t0) REVERT: 5 654 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7503 (mp0) REVERT: 5 689 MET cc_start: 0.6982 (mmm) cc_final: 0.6762 (mmm) REVERT: 6 174 TYR cc_start: 0.7950 (t80) cc_final: 0.7349 (t80) REVERT: 6 299 GLU cc_start: 0.7189 (pm20) cc_final: 0.6242 (mt-10) REVERT: 6 347 ASN cc_start: 0.6611 (t0) cc_final: 0.5898 (m-40) REVERT: 6 367 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7883 (mt-10) REVERT: 6 614 ARG cc_start: 0.6479 (ttp-170) cc_final: 0.6231 (ttm110) REVERT: 6 653 HIS cc_start: 0.7193 (OUTLIER) cc_final: 0.6613 (p-80) REVERT: 6 750 GLN cc_start: 0.6099 (OUTLIER) cc_final: 0.5796 (pm20) REVERT: 6 764 ILE cc_start: 0.7235 (mt) cc_final: 0.6661 (pp) REVERT: 6 783 ASP cc_start: 0.6129 (t0) cc_final: 0.5821 (t0) REVERT: 6 833 GLN cc_start: 0.7203 (OUTLIER) cc_final: 0.6482 (mp10) REVERT: 7 69 LYS cc_start: 0.7930 (mtmm) cc_final: 0.7671 (mtpt) REVERT: 7 76 ASN cc_start: 0.7756 (t0) cc_final: 0.7225 (m110) REVERT: 7 81 ASP cc_start: 0.7685 (m-30) cc_final: 0.7339 (t0) REVERT: 7 159 ASN cc_start: 0.7220 (m-40) cc_final: 0.6773 (m110) REVERT: 7 162 ARG cc_start: 0.7125 (ttm-80) cc_final: 0.6814 (ttt90) REVERT: 7 188 GLU cc_start: 0.6068 (tt0) cc_final: 0.5698 (tt0) REVERT: 7 244 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8420 (tp) REVERT: 7 247 ARG cc_start: 0.8103 (ttm170) cc_final: 0.7486 (ttp80) REVERT: 7 288 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.7029 (tt0) REVERT: 7 449 LYS cc_start: 0.7381 (mtmt) cc_final: 0.6837 (tmtp) REVERT: 7 502 VAL cc_start: 0.4928 (OUTLIER) cc_final: 0.4402 (t) REVERT: 7 598 PHE cc_start: 0.8387 (m-80) cc_final: 0.8129 (m-80) REVERT: B 198 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7630 (mp) REVERT: B 247 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.6639 (mtm180) REVERT: B 269 LYS cc_start: 0.6611 (ttmm) cc_final: 0.5261 (mppt) REVERT: B 290 HIS cc_start: 0.5972 (m-70) cc_final: 0.5298 (m170) REVERT: B 413 ASP cc_start: 0.7084 (OUTLIER) cc_final: 0.6783 (m-30) REVERT: B 506 TYR cc_start: 0.6249 (t80) cc_final: 0.5910 (t80) REVERT: B 633 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.6959 (mptt) REVERT: B 694 ARG cc_start: 0.6423 (OUTLIER) cc_final: 0.5809 (mpp80) REVERT: B 705 ARG cc_start: 0.6242 (OUTLIER) cc_final: 0.5719 (mtp180) REVERT: B 781 MET cc_start: 0.5064 (mpm) cc_final: 0.4721 (mmt) REVERT: B 834 LEU cc_start: 0.6872 (mm) cc_final: 0.6321 (tp) REVERT: C 36 THR cc_start: 0.7186 (p) cc_final: 0.6889 (m) REVERT: C 39 ARG cc_start: 0.7114 (ttm110) cc_final: 0.6533 (ttp-110) REVERT: C 43 ARG cc_start: 0.6693 (tpt90) cc_final: 0.6044 (ttm170) REVERT: C 188 LYS cc_start: 0.8004 (mtmt) cc_final: 0.7541 (mttp) REVERT: C 222 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8121 (p) REVERT: C 234 GLU cc_start: 0.6766 (mt-10) cc_final: 0.5969 (mp0) REVERT: C 237 GLU cc_start: 0.7187 (mp0) cc_final: 0.6914 (mt-10) REVERT: C 348 ARG cc_start: 0.6939 (mtm110) cc_final: 0.6377 (mtt90) REVERT: C 390 GLU cc_start: 0.7711 (pt0) cc_final: 0.7484 (pt0) REVERT: C 464 LEU cc_start: 0.7942 (mt) cc_final: 0.7604 (mt) REVERT: C 477 LYS cc_start: 0.7398 (mttm) cc_final: 0.6871 (mttp) REVERT: C 505 THR cc_start: 0.8461 (t) cc_final: 0.8004 (m) REVERT: C 556 ILE cc_start: 0.7225 (pt) cc_final: 0.6867 (mm) REVERT: C 557 ARG cc_start: 0.6099 (ttt-90) cc_final: 0.5762 (tpt-90) REVERT: C 572 LEU cc_start: 0.6539 (OUTLIER) cc_final: 0.5638 (mm) REVERT: C 664 LYS cc_start: 0.7725 (mtpp) cc_final: 0.7275 (mtpt) REVERT: C 681 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7495 (tmmm) REVERT: C 723 LYS cc_start: 0.7368 (pttt) cc_final: 0.6931 (tttp) REVERT: D 235 GLU cc_start: 0.6440 (mt-10) cc_final: 0.5715 (tp30) REVERT: D 302 LYS cc_start: 0.7548 (mmtp) cc_final: 0.7071 (mtpp) REVERT: D 327 ASN cc_start: 0.8180 (OUTLIER) cc_final: 0.7360 (m-40) REVERT: D 394 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8519 (tmtp) REVERT: D 408 ASP cc_start: 0.7486 (m-30) cc_final: 0.7160 (m-30) REVERT: D 434 GLU cc_start: 0.7617 (tp30) cc_final: 0.7355 (tm-30) REVERT: D 445 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.6974 (mtt180) REVERT: D 483 GLN cc_start: 0.6946 (tp40) cc_final: 0.6218 (mt0) REVERT: D 503 ASP cc_start: 0.6207 (m-30) cc_final: 0.5853 (m-30) REVERT: D 651 GLN cc_start: 0.8108 (mt0) cc_final: 0.7793 (pm20) REVERT: D 661 ILE cc_start: 0.6813 (OUTLIER) cc_final: 0.6429 (mt) REVERT: D 690 GLU cc_start: 0.6592 (tt0) cc_final: 0.6114 (tp30) REVERT: D 693 ASP cc_start: 0.6572 (t0) cc_final: 0.5916 (p0) REVERT: D 715 LYS cc_start: 0.6947 (OUTLIER) cc_final: 0.6083 (ptmm) REVERT: D 730 GLU cc_start: 0.6078 (OUTLIER) cc_final: 0.5421 (mt-10) REVERT: D 819 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7214 (mm) REVERT: D 847 MET cc_start: 0.5563 (OUTLIER) cc_final: 0.5049 (mmm) REVERT: E 3 PHE cc_start: 0.7408 (m-80) cc_final: 0.7139 (m-10) REVERT: E 5 ARG cc_start: 0.7463 (ttp80) cc_final: 0.6987 (ttp-110) REVERT: E 77 LYS cc_start: 0.7965 (mttm) cc_final: 0.7665 (mtpp) REVERT: E 144 ASN cc_start: 0.6995 (OUTLIER) cc_final: 0.6730 (t0) REVERT: E 182 MET cc_start: 0.8472 (ttm) cc_final: 0.8159 (ttp) REVERT: E 209 ARG cc_start: 0.7114 (mmm-85) cc_final: 0.6762 (mmt180) REVERT: E 249 LYS cc_start: 0.7815 (mmtp) cc_final: 0.7459 (mppt) REVERT: E 354 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.6186 (mt-10) REVERT: E 368 GLU cc_start: 0.6389 (OUTLIER) cc_final: 0.6140 (tm-30) REVERT: E 458 MET cc_start: 0.5767 (mtp) cc_final: 0.5464 (mtm) REVERT: E 469 MET cc_start: 0.7912 (mmm) cc_final: 0.7280 (mmm) REVERT: E 497 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8074 (mtm) REVERT: E 513 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7894 (pp) REVERT: E 546 ILE cc_start: 0.7292 (OUTLIER) cc_final: 0.6889 (mm) REVERT: E 593 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6454 (mt-10) REVERT: E 597 GLU cc_start: 0.6323 (pm20) cc_final: 0.5901 (mm-30) REVERT: E 661 GLU cc_start: 0.6628 (mt-10) cc_final: 0.6312 (mt-10) REVERT: E 666 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6851 (mt) REVERT: F 168 MET cc_start: 0.6536 (mmt) cc_final: 0.6014 (mmm) REVERT: F 421 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6358 (mm) REVERT: F 446 ARG cc_start: 0.7065 (ptt90) cc_final: 0.6722 (ptt90) REVERT: F 654 GLU cc_start: 0.6830 (tm-30) cc_final: 0.6199 (tp30) REVERT: F 715 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7490 (mt) REVERT: G 15 ASN cc_start: 0.7186 (m-40) cc_final: 0.6021 (t0) REVERT: G 16 ASN cc_start: 0.7521 (p0) cc_final: 0.7315 (OUTLIER) REVERT: G 247 ARG cc_start: 0.7987 (ttt90) cc_final: 0.7499 (ttp80) REVERT: G 291 GLN cc_start: 0.7936 (mt0) cc_final: 0.7576 (mt0) REVERT: G 297 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7306 (tt0) REVERT: G 396 ASP cc_start: 0.4633 (p0) cc_final: 0.4331 (t0) REVERT: G 402 MET cc_start: 0.4543 (mmm) cc_final: 0.3755 (tpt) REVERT: G 412 ASN cc_start: 0.7578 (t0) cc_final: 0.7078 (m-40) REVERT: G 427 ASP cc_start: 0.7672 (m-30) cc_final: 0.7420 (m-30) REVERT: G 484 THR cc_start: 0.7210 (m) cc_final: 0.6716 (p) REVERT: G 502 VAL cc_start: 0.5842 (OUTLIER) cc_final: 0.5585 (t) REVERT: G 529 MET cc_start: 0.6980 (mtm) cc_final: 0.6386 (mtt) REVERT: G 554 ASN cc_start: 0.8453 (OUTLIER) cc_final: 0.8005 (t0) REVERT: G 556 THR cc_start: 0.8030 (t) cc_final: 0.7595 (m) REVERT: G 618 TYR cc_start: 0.7377 (t80) cc_final: 0.7056 (t80) REVERT: G 659 TYR cc_start: 0.7876 (t80) cc_final: 0.7614 (t80) REVERT: G 690 LEU cc_start: 0.8451 (mt) cc_final: 0.8144 (mt) REVERT: H 31 ASN cc_start: 0.3833 (OUTLIER) cc_final: 0.3521 (m-40) REVERT: H 34 LYS cc_start: 0.3682 (tttt) cc_final: 0.3429 (tptp) REVERT: H 77 LYS cc_start: 0.5447 (OUTLIER) cc_final: 0.5192 (tttm) REVERT: H 135 LEU cc_start: 0.2533 (OUTLIER) cc_final: 0.2187 (tp) REVERT: H 152 LYS cc_start: 0.5011 (pttp) cc_final: 0.4718 (pptt) REVERT: H 172 ASN cc_start: 0.3668 (p0) cc_final: 0.3379 (p0) REVERT: H 183 PHE cc_start: 0.5446 (m-10) cc_final: 0.5127 (m-10) REVERT: H 278 ARG cc_start: 0.4369 (OUTLIER) cc_final: 0.4100 (tmm-80) REVERT: H 281 THR cc_start: 0.6548 (OUTLIER) cc_final: 0.6082 (m) REVERT: H 284 PHE cc_start: 0.5355 (m-80) cc_final: 0.4820 (m-80) REVERT: H 319 MET cc_start: 0.3974 (OUTLIER) cc_final: 0.3511 (tpp) REVERT: H 331 GLU cc_start: 0.5708 (mt-10) cc_final: 0.5385 (mt-10) REVERT: H 332 LEU cc_start: 0.5998 (mt) cc_final: 0.5542 (tp) REVERT: H 342 ARG cc_start: 0.5065 (mtm180) cc_final: 0.4865 (ttm-80) REVERT: H 371 GLU cc_start: 0.3639 (OUTLIER) cc_final: 0.2877 (pm20) REVERT: H 389 TYR cc_start: 0.0973 (m-80) cc_final: 0.0681 (m-80) REVERT: H 426 TYR cc_start: 0.3000 (t80) cc_final: 0.1710 (p90) REVERT: I 120 MET cc_start: 0.2233 (pp-130) cc_final: 0.0719 (mpt) REVERT: I 125 ARG cc_start: 0.3414 (OUTLIER) cc_final: 0.3020 (mmm-85) REVERT: I 127 TYR cc_start: 0.3627 (t80) cc_final: 0.3192 (t80) REVERT: I 147 ARG cc_start: 0.3239 (ptm160) cc_final: 0.3000 (ptm-80) REVERT: I 152 LYS cc_start: 0.3909 (mttt) cc_final: 0.3593 (ttpt) REVERT: I 158 LEU cc_start: 0.2963 (tt) cc_final: 0.2133 (mm) REVERT: I 199 MET cc_start: 0.5189 (mtt) cc_final: 0.4764 (mtm) REVERT: I 341 ARG cc_start: 0.3583 (mtt90) cc_final: 0.3002 (mmm160) REVERT: I 382 MET cc_start: 0.2458 (mmp) cc_final: 0.1321 (tpt) REVERT: I 662 GLU cc_start: 0.6510 (tt0) cc_final: 0.6092 (tp30) outliers start: 264 outliers final: 129 residues processed: 1072 average time/residue: 1.5544 time to fit residues: 2163.3325 Evaluate side-chains 1032 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 846 time to evaluate : 5.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 196 GLU Chi-restraints excluded: chain 2 residue 326 ARG Chi-restraints excluded: chain 2 residue 370 LYS Chi-restraints excluded: chain 2 residue 374 ARG Chi-restraints excluded: chain 2 residue 396 THR Chi-restraints excluded: chain 2 residue 422 GLU Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 554 LYS Chi-restraints excluded: chain 2 residue 590 THR Chi-restraints excluded: chain 2 residue 656 ARG Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 670 THR Chi-restraints excluded: chain 2 residue 684 ARG Chi-restraints excluded: chain 2 residue 697 THR Chi-restraints excluded: chain 2 residue 786 VAL Chi-restraints excluded: chain 2 residue 797 SER Chi-restraints excluded: chain 2 residue 851 VAL Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 189 THR Chi-restraints excluded: chain 3 residue 208 ARG Chi-restraints excluded: chain 3 residue 234 GLU Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 324 ASN Chi-restraints excluded: chain 3 residue 353 LEU Chi-restraints excluded: chain 3 residue 440 VAL Chi-restraints excluded: chain 3 residue 656 LEU Chi-restraints excluded: chain 3 residue 667 VAL Chi-restraints excluded: chain 3 residue 701 THR Chi-restraints excluded: chain 4 residue 284 ILE Chi-restraints excluded: chain 4 residue 411 THR Chi-restraints excluded: chain 4 residue 661 ILE Chi-restraints excluded: chain 4 residue 674 SER Chi-restraints excluded: chain 4 residue 699 LEU Chi-restraints excluded: chain 4 residue 749 MET Chi-restraints excluded: chain 4 residue 797 GLN Chi-restraints excluded: chain 5 residue 5 ARG Chi-restraints excluded: chain 5 residue 177 THR Chi-restraints excluded: chain 5 residue 366 LEU Chi-restraints excluded: chain 5 residue 484 LYS Chi-restraints excluded: chain 5 residue 495 GLU Chi-restraints excluded: chain 5 residue 544 THR Chi-restraints excluded: chain 5 residue 624 SER Chi-restraints excluded: chain 5 residue 633 LEU Chi-restraints excluded: chain 5 residue 654 GLU Chi-restraints excluded: chain 5 residue 661 GLU Chi-restraints excluded: chain 6 residue 313 MET Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 6 residue 446 ARG Chi-restraints excluded: chain 6 residue 462 ILE Chi-restraints excluded: chain 6 residue 501 GLN Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 6 residue 598 THR Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 6 residue 659 GLN Chi-restraints excluded: chain 6 residue 660 THR Chi-restraints excluded: chain 6 residue 750 GLN Chi-restraints excluded: chain 6 residue 829 ASP Chi-restraints excluded: chain 6 residue 831 LEU Chi-restraints excluded: chain 6 residue 833 GLN Chi-restraints excluded: chain 7 residue 141 VAL Chi-restraints excluded: chain 7 residue 207 LEU Chi-restraints excluded: chain 7 residue 244 ILE Chi-restraints excluded: chain 7 residue 283 GLU Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 288 GLU Chi-restraints excluded: chain 7 residue 410 VAL Chi-restraints excluded: chain 7 residue 502 VAL Chi-restraints excluded: chain 7 residue 556 THR Chi-restraints excluded: chain 7 residue 557 LEU Chi-restraints excluded: chain 7 residue 570 LEU Chi-restraints excluded: chain 7 residue 592 SER Chi-restraints excluded: chain 7 residue 670 ASP Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 363 PHE Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 581 ARG Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 694 ARG Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain B residue 789 VAL Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 681 LYS Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain D residue 445 ARG Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 661 ILE Chi-restraints excluded: chain D residue 674 SER Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 730 GLU Chi-restraints excluded: chain D residue 800 SER Chi-restraints excluded: chain D residue 819 LEU Chi-restraints excluded: chain D residue 847 MET Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 368 GLU Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain E residue 497 MET Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain E residue 546 ILE Chi-restraints excluded: chain E residue 599 MET Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 666 LEU Chi-restraints excluded: chain E residue 667 GLU Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 501 GLN Chi-restraints excluded: chain F residue 639 ASP Chi-restraints excluded: chain F residue 706 MET Chi-restraints excluded: chain F residue 715 ILE Chi-restraints excluded: chain F residue 727 LEU Chi-restraints excluded: chain F residue 796 THR Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 282 SER Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 297 GLN Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 350 ASP Chi-restraints excluded: chain G residue 382 ARG Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 554 ASN Chi-restraints excluded: chain G residue 561 THR Chi-restraints excluded: chain G residue 656 VAL Chi-restraints excluded: chain G residue 685 THR Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 77 LYS Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 277 ASN Chi-restraints excluded: chain H residue 278 ARG Chi-restraints excluded: chain H residue 281 THR Chi-restraints excluded: chain H residue 298 THR Chi-restraints excluded: chain H residue 302 ILE Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 319 MET Chi-restraints excluded: chain H residue 322 SER Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 371 GLU Chi-restraints excluded: chain I residue 125 ARG Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 280 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 506 optimal weight: 9.9990 chunk 327 optimal weight: 3.9990 chunk 489 optimal weight: 4.9990 chunk 246 optimal weight: 6.9990 chunk 160 optimal weight: 6.9990 chunk 158 optimal weight: 0.4980 chunk 520 optimal weight: 0.9980 chunk 558 optimal weight: 10.0000 chunk 405 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 643 optimal weight: 0.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 254 GLN 3 587 ASN 3 641 ASN ** 3 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 240 ASN 4 543 GLN 4 613 GLN 4 666 ASN 5 253 GLN ** 5 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 156 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 673 ASN ** 6 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 ASN ** B 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 GLN ** C 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN D 253 GLN E 560 HIS E 571 HIS E 685 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 ASN ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 ASN H 367 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 69476 Z= 0.228 Angle : 0.557 11.906 93996 Z= 0.284 Chirality : 0.043 0.247 10834 Planarity : 0.004 0.060 12062 Dihedral : 7.095 174.408 9630 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.52 % Favored : 97.44 % Rotamer: Outliers : 3.75 % Allowed : 18.54 % Favored : 77.71 % 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: 0.56 (0.09), residues: 8483 helix: 1.19 (0.09), residues: 3488 sheet: -0.17 (0.12), residues: 1608 loop : -0.07 (0.10), residues: 3387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 112 HIS 0.011 0.001 HIS F 653 PHE 0.024 0.002 PHE F 142 TYR 0.024 0.002 TYR B 769 ARG 0.011 0.001 ARG 6 752 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1198 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 913 time to evaluate : 5.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 196 GLU cc_start: 0.5932 (OUTLIER) cc_final: 0.5677 (mt-10) REVERT: 2 232 ARG cc_start: 0.6585 (mmm-85) cc_final: 0.5954 (mtp180) REVERT: 2 326 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.6747 (pmt170) REVERT: 2 374 ARG cc_start: 0.5989 (OUTLIER) cc_final: 0.5276 (ttm110) REVERT: 2 422 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6718 (pp20) REVERT: 2 651 ASN cc_start: 0.8154 (m-40) cc_final: 0.7602 (m-40) REVERT: 2 667 VAL cc_start: 0.7591 (OUTLIER) cc_final: 0.7162 (p) REVERT: 2 684 ARG cc_start: 0.3996 (OUTLIER) cc_final: 0.3296 (ptp90) REVERT: 2 690 GLU cc_start: 0.5474 (pm20) cc_final: 0.5159 (pm20) REVERT: 2 783 MET cc_start: 0.6747 (OUTLIER) cc_final: 0.6485 (ttp) REVERT: 3 23 ASP cc_start: 0.7206 (m-30) cc_final: 0.6916 (m-30) REVERT: 3 52 ASN cc_start: 0.5094 (m-40) cc_final: 0.4842 (m110) REVERT: 3 188 LYS cc_start: 0.7974 (mtmm) cc_final: 0.7262 (ttpt) REVERT: 3 208 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7170 (mtp180) REVERT: 3 234 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6051 (tm-30) REVERT: 3 274 ILE cc_start: 0.8705 (pt) cc_final: 0.8280 (tp) REVERT: 3 290 ASP cc_start: 0.7864 (m-30) cc_final: 0.7597 (m-30) REVERT: 3 353 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8609 (mm) REVERT: 3 455 ARG cc_start: 0.5860 (mmm160) cc_final: 0.5568 (mtt180) REVERT: 3 535 LEU cc_start: 0.7809 (tp) cc_final: 0.7367 (mt) REVERT: 3 587 ASN cc_start: 0.6568 (m-40) cc_final: 0.4701 (t0) REVERT: 4 178 ARG cc_start: 0.7250 (mmm160) cc_final: 0.6985 (mmm-85) REVERT: 4 232 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7665 (pt0) REVERT: 4 266 GLN cc_start: 0.7631 (tp40) cc_final: 0.7400 (tp-100) REVERT: 4 296 ILE cc_start: 0.7922 (OUTLIER) cc_final: 0.7679 (mm) REVERT: 4 341 ASP cc_start: 0.8236 (p0) cc_final: 0.7933 (p0) REVERT: 4 404 ASP cc_start: 0.6906 (m-30) cc_final: 0.6586 (m-30) REVERT: 4 411 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.7855 (p) REVERT: 4 477 ASP cc_start: 0.7360 (t0) cc_final: 0.6704 (t0) REVERT: 4 579 GLN cc_start: 0.7811 (mm-40) cc_final: 0.7433 (mm-40) REVERT: 4 583 LYS cc_start: 0.8245 (mmpt) cc_final: 0.7635 (mtmm) REVERT: 4 594 LYS cc_start: 0.6242 (ttpp) cc_final: 0.5784 (tptp) REVERT: 4 612 LYS cc_start: 0.7782 (mmpt) cc_final: 0.7137 (mmtp) REVERT: 4 715 LYS cc_start: 0.7060 (pttp) cc_final: 0.6498 (mmtp) REVERT: 4 726 ASN cc_start: 0.7669 (m-40) cc_final: 0.7181 (t0) REVERT: 4 756 GLU cc_start: 0.7618 (tt0) cc_final: 0.7378 (tp30) REVERT: 4 772 ARG cc_start: 0.7116 (mtp-110) cc_final: 0.6844 (ttm-80) REVERT: 5 5 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.6664 (tmm-80) REVERT: 5 29 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7321 (mtmp) REVERT: 5 362 ARG cc_start: 0.6273 (mpp80) cc_final: 0.6047 (mmt180) REVERT: 5 383 ASP cc_start: 0.7204 (OUTLIER) cc_final: 0.6642 (p0) REVERT: 5 388 ILE cc_start: 0.8180 (mt) cc_final: 0.7925 (mm) REVERT: 5 404 MET cc_start: 0.7066 (ptp) cc_final: 0.5716 (mmp) REVERT: 5 495 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7551 (tt0) REVERT: 5 556 VAL cc_start: 0.6642 (t) cc_final: 0.6325 (p) REVERT: 5 625 ASN cc_start: 0.6322 (m110) cc_final: 0.5540 (t0) REVERT: 5 689 MET cc_start: 0.7052 (mmm) cc_final: 0.6763 (mmm) REVERT: 6 174 TYR cc_start: 0.8003 (t80) cc_final: 0.7428 (t80) REVERT: 6 299 GLU cc_start: 0.7133 (pm20) cc_final: 0.6667 (tp30) REVERT: 6 347 ASN cc_start: 0.6596 (t0) cc_final: 0.5891 (m-40) REVERT: 6 614 ARG cc_start: 0.6579 (ttp-170) cc_final: 0.6156 (ttm110) REVERT: 6 653 HIS cc_start: 0.7236 (OUTLIER) cc_final: 0.6693 (p-80) REVERT: 6 764 ILE cc_start: 0.7204 (mt) cc_final: 0.6607 (pp) REVERT: 6 783 ASP cc_start: 0.6080 (t0) cc_final: 0.5760 (t0) REVERT: 6 794 ARG cc_start: 0.5803 (mtp-110) cc_final: 0.5492 (mtp-110) REVERT: 6 833 GLN cc_start: 0.7279 (OUTLIER) cc_final: 0.6546 (mp10) REVERT: 7 69 LYS cc_start: 0.7974 (mtmm) cc_final: 0.7705 (mtpt) REVERT: 7 76 ASN cc_start: 0.7859 (t0) cc_final: 0.7378 (m110) REVERT: 7 81 ASP cc_start: 0.7697 (m-30) cc_final: 0.7381 (t0) REVERT: 7 159 ASN cc_start: 0.7251 (m-40) cc_final: 0.6816 (m110) REVERT: 7 162 ARG cc_start: 0.7081 (ttm-80) cc_final: 0.6773 (ttt90) REVERT: 7 188 GLU cc_start: 0.6272 (tt0) cc_final: 0.5909 (tt0) REVERT: 7 244 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8479 (tp) REVERT: 7 247 ARG cc_start: 0.8168 (ttm170) cc_final: 0.7484 (ttp-110) REVERT: 7 288 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7111 (tt0) REVERT: 7 449 LYS cc_start: 0.7445 (mtmt) cc_final: 0.6887 (tmtp) REVERT: 7 499 LYS cc_start: 0.7041 (tptm) cc_final: 0.6452 (ttmt) REVERT: 7 598 PHE cc_start: 0.8504 (m-80) cc_final: 0.8269 (m-80) REVERT: B 198 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7672 (mp) REVERT: B 220 ASP cc_start: 0.4692 (p0) cc_final: 0.4406 (t70) REVERT: B 247 ARG cc_start: 0.6953 (OUTLIER) cc_final: 0.6664 (mtm180) REVERT: B 269 LYS cc_start: 0.6496 (ttmm) cc_final: 0.5095 (mppt) REVERT: B 290 HIS cc_start: 0.5965 (m-70) cc_final: 0.5253 (m170) REVERT: B 413 ASP cc_start: 0.7041 (OUTLIER) cc_final: 0.6748 (m-30) REVERT: B 506 TYR cc_start: 0.6332 (t80) cc_final: 0.6013 (t80) REVERT: B 509 ARG cc_start: 0.6886 (OUTLIER) cc_final: 0.6135 (ttt90) REVERT: B 633 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.6959 (mptt) REVERT: B 694 ARG cc_start: 0.6586 (OUTLIER) cc_final: 0.5960 (mpp80) REVERT: B 705 ARG cc_start: 0.6265 (OUTLIER) cc_final: 0.5709 (mtp180) REVERT: B 834 LEU cc_start: 0.6904 (mm) cc_final: 0.6329 (tp) REVERT: C 36 THR cc_start: 0.7259 (p) cc_final: 0.7006 (m) REVERT: C 43 ARG cc_start: 0.6718 (OUTLIER) cc_final: 0.6126 (ttt180) REVERT: C 188 LYS cc_start: 0.8083 (mtmt) cc_final: 0.7574 (mttt) REVERT: C 222 THR cc_start: 0.8619 (OUTLIER) cc_final: 0.8202 (p) REVERT: C 234 GLU cc_start: 0.6880 (mt-10) cc_final: 0.5949 (mp0) REVERT: C 235 ASP cc_start: 0.6648 (p0) cc_final: 0.6298 (p0) REVERT: C 237 GLU cc_start: 0.7115 (mp0) cc_final: 0.6727 (mt-10) REVERT: C 348 ARG cc_start: 0.6998 (mtm110) cc_final: 0.6407 (mtt90) REVERT: C 464 LEU cc_start: 0.7957 (mt) cc_final: 0.7627 (mt) REVERT: C 477 LYS cc_start: 0.7443 (mttm) cc_final: 0.6926 (mttp) REVERT: C 505 THR cc_start: 0.8535 (t) cc_final: 0.8068 (m) REVERT: C 556 ILE cc_start: 0.7219 (pt) cc_final: 0.6856 (mm) REVERT: C 572 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.5650 (mm) REVERT: C 664 LYS cc_start: 0.7701 (mtpp) cc_final: 0.7230 (mtpt) REVERT: C 681 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7551 (tmmm) REVERT: C 723 LYS cc_start: 0.7376 (pttt) cc_final: 0.6914 (ttmm) REVERT: D 235 GLU cc_start: 0.6473 (mt-10) cc_final: 0.5872 (tp30) REVERT: D 302 LYS cc_start: 0.7699 (mmtp) cc_final: 0.7090 (mtpp) REVERT: D 327 ASN cc_start: 0.8181 (OUTLIER) cc_final: 0.7289 (m-40) REVERT: D 394 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8562 (tmtp) REVERT: D 408 ASP cc_start: 0.7624 (m-30) cc_final: 0.7290 (m-30) REVERT: D 434 GLU cc_start: 0.7688 (tp30) cc_final: 0.7356 (tm-30) REVERT: D 445 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.7084 (mtt180) REVERT: D 483 GLN cc_start: 0.7006 (tp40) cc_final: 0.6153 (mt0) REVERT: D 503 ASP cc_start: 0.6310 (m-30) cc_final: 0.5980 (m-30) REVERT: D 649 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7731 (mtt) REVERT: D 661 ILE cc_start: 0.6885 (OUTLIER) cc_final: 0.6475 (mt) REVERT: D 690 GLU cc_start: 0.6577 (tt0) cc_final: 0.6101 (tp30) REVERT: D 715 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6076 (ptmm) REVERT: D 819 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7224 (mm) REVERT: D 847 MET cc_start: 0.5668 (OUTLIER) cc_final: 0.5161 (mmm) REVERT: E 3 PHE cc_start: 0.7582 (m-80) cc_final: 0.7289 (m-80) REVERT: E 5 ARG cc_start: 0.7368 (ttp80) cc_final: 0.6839 (ttp-110) REVERT: E 77 LYS cc_start: 0.8012 (mttm) cc_final: 0.7718 (mtpp) REVERT: E 146 ILE cc_start: 0.7564 (pt) cc_final: 0.7323 (pt) REVERT: E 179 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8190 (pp) REVERT: E 182 MET cc_start: 0.8496 (ttm) cc_final: 0.8188 (ttp) REVERT: E 209 ARG cc_start: 0.7002 (mmm-85) cc_final: 0.6626 (mmt180) REVERT: E 221 MET cc_start: 0.3368 (OUTLIER) cc_final: 0.2724 (pmm) REVERT: E 249 LYS cc_start: 0.7719 (mmtp) cc_final: 0.7324 (mppt) REVERT: E 354 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.6178 (mt-10) REVERT: E 368 GLU cc_start: 0.6424 (OUTLIER) cc_final: 0.6200 (tt0) REVERT: E 379 PHE cc_start: 0.7344 (t80) cc_final: 0.7106 (t80) REVERT: E 431 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.6921 (mtmp) REVERT: E 458 MET cc_start: 0.5897 (mtp) cc_final: 0.5584 (mtm) REVERT: E 469 MET cc_start: 0.7982 (mmm) cc_final: 0.7461 (mmm) REVERT: E 497 MET cc_start: 0.8424 (mtm) cc_final: 0.8075 (mtm) REVERT: E 513 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8067 (pt) REVERT: E 546 ILE cc_start: 0.7359 (OUTLIER) cc_final: 0.6951 (mm) REVERT: E 557 LYS cc_start: 0.5467 (mmmt) cc_final: 0.5109 (tmtm) REVERT: E 592 SER cc_start: 0.6303 (m) cc_final: 0.6071 (p) REVERT: E 597 GLU cc_start: 0.6347 (pm20) cc_final: 0.5967 (mm-30) REVERT: E 661 GLU cc_start: 0.6614 (mt-10) cc_final: 0.6301 (mt-10) REVERT: E 666 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.6962 (mt) REVERT: F 338 CYS cc_start: 0.2802 (OUTLIER) cc_final: 0.1723 (m) REVERT: F 421 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6553 (mm) REVERT: F 446 ARG cc_start: 0.7196 (ptt90) cc_final: 0.6833 (ptt90) REVERT: F 521 LYS cc_start: 0.4798 (mmpt) cc_final: 0.4450 (mmtt) REVERT: F 700 ASN cc_start: 0.6653 (OUTLIER) cc_final: 0.6191 (p0) REVERT: F 715 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7698 (mt) REVERT: F 719 CYS cc_start: 0.5353 (m) cc_final: 0.4996 (t) REVERT: F 837 ARG cc_start: 0.4239 (mtp85) cc_final: 0.3756 (ttp-170) REVERT: G 15 ASN cc_start: 0.7414 (m-40) cc_final: 0.6142 (t0) REVERT: G 130 LYS cc_start: 0.7032 (pttp) cc_final: 0.6828 (ptpt) REVERT: G 247 ARG cc_start: 0.8017 (ttt90) cc_final: 0.7529 (ttp80) REVERT: G 291 GLN cc_start: 0.7901 (mt0) cc_final: 0.7535 (mt0) REVERT: G 297 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7315 (tt0) REVERT: G 402 MET cc_start: 0.4680 (mmm) cc_final: 0.3995 (tmm) REVERT: G 412 ASN cc_start: 0.7614 (t0) cc_final: 0.7132 (m-40) REVERT: G 427 ASP cc_start: 0.7638 (m-30) cc_final: 0.7407 (m-30) REVERT: G 475 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7559 (ttmt) REVERT: G 502 VAL cc_start: 0.5809 (OUTLIER) cc_final: 0.5576 (t) REVERT: G 529 MET cc_start: 0.7006 (mtm) cc_final: 0.6720 (OUTLIER) REVERT: G 556 THR cc_start: 0.8159 (t) cc_final: 0.7731 (m) REVERT: G 621 MET cc_start: 0.7239 (ttp) cc_final: 0.7010 (ttp) REVERT: G 659 TYR cc_start: 0.7890 (t80) cc_final: 0.7621 (t80) REVERT: G 690 LEU cc_start: 0.8453 (mt) cc_final: 0.8114 (mt) REVERT: H 15 ILE cc_start: 0.3168 (OUTLIER) cc_final: 0.2092 (mp) REVERT: H 31 ASN cc_start: 0.3885 (OUTLIER) cc_final: 0.3584 (m-40) REVERT: H 34 LYS cc_start: 0.3774 (tttt) cc_final: 0.3518 (tptp) REVERT: H 135 LEU cc_start: 0.2464 (OUTLIER) cc_final: 0.2233 (tp) REVERT: H 152 LYS cc_start: 0.5033 (pttp) cc_final: 0.4728 (pptt) REVERT: H 172 ASN cc_start: 0.3390 (p0) cc_final: 0.3124 (p0) REVERT: H 281 THR cc_start: 0.6599 (OUTLIER) cc_final: 0.6119 (m) REVERT: H 284 PHE cc_start: 0.5446 (m-80) cc_final: 0.4724 (m-80) REVERT: H 319 MET cc_start: 0.4020 (OUTLIER) cc_final: 0.3620 (tpp) REVERT: H 329 LEU cc_start: 0.7453 (mm) cc_final: 0.7121 (mm) REVERT: H 331 GLU cc_start: 0.5675 (mt-10) cc_final: 0.5281 (mt-10) REVERT: H 332 LEU cc_start: 0.6031 (mt) cc_final: 0.5540 (tp) REVERT: H 342 ARG cc_start: 0.5137 (mtm180) cc_final: 0.4916 (ttm-80) REVERT: H 371 GLU cc_start: 0.3613 (OUTLIER) cc_final: 0.2868 (pm20) REVERT: H 389 TYR cc_start: 0.1073 (m-80) cc_final: 0.0782 (m-80) REVERT: I 120 MET cc_start: 0.2225 (pp-130) cc_final: 0.0592 (mpt) REVERT: I 125 ARG cc_start: 0.3614 (OUTLIER) cc_final: 0.3109 (mmm-85) REVERT: I 127 TYR cc_start: 0.3621 (t80) cc_final: 0.3376 (t80) REVERT: I 152 LYS cc_start: 0.3840 (mttt) cc_final: 0.3526 (tppt) REVERT: I 158 LEU cc_start: 0.2924 (tt) cc_final: 0.2152 (mm) REVERT: I 199 MET cc_start: 0.5228 (mtt) cc_final: 0.4792 (mtm) REVERT: I 341 ARG cc_start: 0.3137 (mtt90) cc_final: 0.2662 (mmm160) REVERT: I 382 MET cc_start: 0.2093 (mmp) cc_final: 0.1100 (tpt) REVERT: I 519 VAL cc_start: 0.7316 (m) cc_final: 0.6853 (t) REVERT: I 662 GLU cc_start: 0.6500 (tt0) cc_final: 0.6208 (tp30) outliers start: 285 outliers final: 153 residues processed: 1107 average time/residue: 1.5140 time to fit residues: 2182.3741 Evaluate side-chains 1079 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 865 time to evaluate : 5.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 196 GLU Chi-restraints excluded: chain 2 residue 312 SER Chi-restraints excluded: chain 2 residue 326 ARG Chi-restraints excluded: chain 2 residue 374 ARG Chi-restraints excluded: chain 2 residue 396 THR Chi-restraints excluded: chain 2 residue 418 SER Chi-restraints excluded: chain 2 residue 422 GLU Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 590 THR Chi-restraints excluded: chain 2 residue 656 ARG Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 670 THR Chi-restraints excluded: chain 2 residue 684 ARG Chi-restraints excluded: chain 2 residue 697 THR Chi-restraints excluded: chain 2 residue 783 MET Chi-restraints excluded: chain 2 residue 786 VAL Chi-restraints excluded: chain 2 residue 797 SER Chi-restraints excluded: chain 2 residue 851 VAL Chi-restraints excluded: chain 2 residue 857 LEU Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 189 THR Chi-restraints excluded: chain 3 residue 208 ARG Chi-restraints excluded: chain 3 residue 234 GLU Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 353 LEU Chi-restraints excluded: chain 3 residue 440 VAL Chi-restraints excluded: chain 3 residue 486 ILE Chi-restraints excluded: chain 3 residue 667 VAL Chi-restraints excluded: chain 3 residue 670 GLN Chi-restraints excluded: chain 3 residue 701 THR Chi-restraints excluded: chain 4 residue 232 GLU Chi-restraints excluded: chain 4 residue 284 ILE Chi-restraints excluded: chain 4 residue 296 ILE Chi-restraints excluded: chain 4 residue 411 THR Chi-restraints excluded: chain 4 residue 436 THR Chi-restraints excluded: chain 4 residue 592 SER Chi-restraints excluded: chain 4 residue 661 ILE Chi-restraints excluded: chain 4 residue 674 SER Chi-restraints excluded: chain 4 residue 686 LEU Chi-restraints excluded: chain 4 residue 699 LEU Chi-restraints excluded: chain 4 residue 749 MET Chi-restraints excluded: chain 4 residue 797 GLN Chi-restraints excluded: chain 5 residue 5 ARG Chi-restraints excluded: chain 5 residue 29 LYS Chi-restraints excluded: chain 5 residue 102 SER Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 184 ARG Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 205 VAL Chi-restraints excluded: chain 5 residue 221 MET Chi-restraints excluded: chain 5 residue 366 LEU Chi-restraints excluded: chain 5 residue 370 LEU Chi-restraints excluded: chain 5 residue 383 ASP Chi-restraints excluded: chain 5 residue 484 LYS Chi-restraints excluded: chain 5 residue 495 GLU Chi-restraints excluded: chain 5 residue 544 THR Chi-restraints excluded: chain 5 residue 624 SER Chi-restraints excluded: chain 5 residue 633 LEU Chi-restraints excluded: chain 5 residue 661 GLU Chi-restraints excluded: chain 6 residue 124 VAL Chi-restraints excluded: chain 6 residue 313 MET Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 446 ARG Chi-restraints excluded: chain 6 residue 460 ILE Chi-restraints excluded: chain 6 residue 462 ILE Chi-restraints excluded: chain 6 residue 501 GLN Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 6 residue 598 THR Chi-restraints excluded: chain 6 residue 647 SER Chi-restraints excluded: chain 6 residue 653 HIS Chi-restraints excluded: chain 6 residue 659 GLN Chi-restraints excluded: chain 6 residue 660 THR Chi-restraints excluded: chain 6 residue 829 ASP Chi-restraints excluded: chain 6 residue 831 LEU Chi-restraints excluded: chain 6 residue 833 GLN Chi-restraints excluded: chain 7 residue 141 VAL Chi-restraints excluded: chain 7 residue 207 LEU Chi-restraints excluded: chain 7 residue 244 ILE Chi-restraints excluded: chain 7 residue 283 GLU Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 288 GLU Chi-restraints excluded: chain 7 residue 410 VAL Chi-restraints excluded: chain 7 residue 483 THR Chi-restraints excluded: chain 7 residue 502 VAL Chi-restraints excluded: chain 7 residue 556 THR Chi-restraints excluded: chain 7 residue 557 LEU Chi-restraints excluded: chain 7 residue 570 LEU Chi-restraints excluded: chain 7 residue 592 SER Chi-restraints excluded: chain 7 residue 624 LYS Chi-restraints excluded: chain 7 residue 670 ASP Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 581 ARG Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 694 ARG Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain B residue 789 VAL Chi-restraints excluded: chain B residue 800 THR Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 340 GLN Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 681 LYS Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain D residue 445 ARG Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 649 MET Chi-restraints excluded: chain D residue 661 ILE Chi-restraints excluded: chain D residue 674 SER Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 800 SER Chi-restraints excluded: chain D residue 819 LEU Chi-restraints excluded: chain D residue 847 MET Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 368 GLU Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain E residue 546 ILE Chi-restraints excluded: chain E residue 599 MET Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 666 LEU Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 338 CYS Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 501 GLN Chi-restraints excluded: chain F residue 700 ASN Chi-restraints excluded: chain F residue 706 MET Chi-restraints excluded: chain F residue 715 ILE Chi-restraints excluded: chain F residue 727 LEU Chi-restraints excluded: chain F residue 796 THR Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 282 SER Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 297 GLN Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 382 ARG Chi-restraints excluded: chain G residue 473 ILE Chi-restraints excluded: chain G residue 475 LYS Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 554 ASN Chi-restraints excluded: chain G residue 561 THR Chi-restraints excluded: chain G residue 656 VAL Chi-restraints excluded: chain G residue 685 THR Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 277 ASN Chi-restraints excluded: chain H residue 281 THR Chi-restraints excluded: chain H residue 298 THR Chi-restraints excluded: chain H residue 302 ILE Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 319 MET Chi-restraints excluded: chain H residue 322 SER Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 347 LEU Chi-restraints excluded: chain H residue 371 GLU Chi-restraints excluded: chain I residue 125 ARG Chi-restraints excluded: chain I residue 151 LEU Chi-restraints excluded: chain I residue 174 ILE Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain I residue 675 ILE Chi-restraints excluded: chain I residue 696 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 745 optimal weight: 0.5980 chunk 784 optimal weight: 4.9990 chunk 716 optimal weight: 1.9990 chunk 763 optimal weight: 4.9990 chunk 459 optimal weight: 1.9990 chunk 332 optimal weight: 2.9990 chunk 599 optimal weight: 0.8980 chunk 234 optimal weight: 10.0000 chunk 689 optimal weight: 9.9990 chunk 722 optimal weight: 4.9990 chunk 760 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 417 GLN 3 641 ASN ** 3 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 613 GLN 5 253 GLN ** 5 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 587 GLN 6 156 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 750 GLN 7 9 GLN ** 7 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 ASN ** B 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN D 253 GLN E 560 HIS E 685 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 269 ASN F 347 ASN ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 ASN H 367 ASN I 273 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 69476 Z= 0.247 Angle : 0.574 15.292 93996 Z= 0.291 Chirality : 0.044 0.338 10834 Planarity : 0.004 0.058 12062 Dihedral : 7.151 172.929 9630 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.51 % Favored : 97.45 % Rotamer: Outliers : 3.45 % Allowed : 19.18 % Favored : 77.37 % 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: 0.46 (0.09), residues: 8483 helix: 1.10 (0.09), residues: 3491 sheet: -0.21 (0.12), residues: 1592 loop : -0.12 (0.10), residues: 3400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 112 HIS 0.016 0.001 HIS F 653 PHE 0.029 0.002 PHE C 345 TYR 0.022 0.002 TYR B 769 ARG 0.029 0.001 ARG C 339 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1144 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 882 time to evaluate : 6.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 196 GLU cc_start: 0.5985 (OUTLIER) cc_final: 0.5724 (mt-10) REVERT: 2 232 ARG cc_start: 0.6593 (mmm-85) cc_final: 0.5956 (mtp180) REVERT: 2 326 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.6735 (pmt170) REVERT: 2 374 ARG cc_start: 0.6149 (OUTLIER) cc_final: 0.5331 (ttm110) REVERT: 2 422 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6816 (pp20) REVERT: 2 651 ASN cc_start: 0.8125 (m-40) cc_final: 0.7621 (m-40) REVERT: 2 684 ARG cc_start: 0.4040 (OUTLIER) cc_final: 0.3327 (ptp90) REVERT: 2 690 GLU cc_start: 0.5458 (pm20) cc_final: 0.4964 (pm20) REVERT: 2 783 MET cc_start: 0.6725 (OUTLIER) cc_final: 0.6480 (ttp) REVERT: 3 23 ASP cc_start: 0.7247 (m-30) cc_final: 0.6965 (m-30) REVERT: 3 52 ASN cc_start: 0.5100 (m-40) cc_final: 0.4886 (m110) REVERT: 3 188 LYS cc_start: 0.7976 (mtmm) cc_final: 0.7263 (ttpt) REVERT: 3 208 ARG cc_start: 0.7744 (OUTLIER) cc_final: 0.7159 (mtp180) REVERT: 3 234 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.6084 (tm-30) REVERT: 3 274 ILE cc_start: 0.8722 (pt) cc_final: 0.8321 (tp) REVERT: 3 349 ASN cc_start: 0.8156 (m-40) cc_final: 0.7786 (m-40) REVERT: 3 353 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8596 (mm) REVERT: 3 455 ARG cc_start: 0.5904 (mmm160) cc_final: 0.5622 (mtt180) REVERT: 3 535 LEU cc_start: 0.7884 (tp) cc_final: 0.7591 (tp) REVERT: 3 587 ASN cc_start: 0.6671 (m-40) cc_final: 0.4775 (t0) REVERT: 4 178 ARG cc_start: 0.7270 (mmm160) cc_final: 0.6993 (mmm-85) REVERT: 4 232 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7666 (pt0) REVERT: 4 266 GLN cc_start: 0.7705 (tp40) cc_final: 0.7478 (tp-100) REVERT: 4 296 ILE cc_start: 0.7924 (OUTLIER) cc_final: 0.7686 (mm) REVERT: 4 341 ASP cc_start: 0.8226 (p0) cc_final: 0.7927 (p0) REVERT: 4 404 ASP cc_start: 0.6856 (m-30) cc_final: 0.6550 (m-30) REVERT: 4 411 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.7884 (p) REVERT: 4 477 ASP cc_start: 0.7419 (t0) cc_final: 0.7211 (t0) REVERT: 4 579 GLN cc_start: 0.7811 (mm-40) cc_final: 0.7434 (mm-40) REVERT: 4 583 LYS cc_start: 0.8251 (mmpt) cc_final: 0.7635 (mtmm) REVERT: 4 612 LYS cc_start: 0.7784 (mmpt) cc_final: 0.7152 (mmtp) REVERT: 4 636 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.7624 (mppt) REVERT: 4 715 LYS cc_start: 0.7108 (pttp) cc_final: 0.6681 (mmtp) REVERT: 4 726 ASN cc_start: 0.7690 (m-40) cc_final: 0.7227 (t0) REVERT: 4 756 GLU cc_start: 0.7656 (tt0) cc_final: 0.7397 (tp30) REVERT: 4 772 ARG cc_start: 0.7261 (mtp-110) cc_final: 0.6876 (ttm-80) REVERT: 5 5 ARG cc_start: 0.6992 (OUTLIER) cc_final: 0.6672 (tmm-80) REVERT: 5 362 ARG cc_start: 0.6300 (mpp80) cc_final: 0.6065 (mmt180) REVERT: 5 388 ILE cc_start: 0.8185 (mt) cc_final: 0.7924 (mm) REVERT: 5 404 MET cc_start: 0.7068 (ptp) cc_final: 0.5746 (mmp) REVERT: 5 495 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7584 (tt0) REVERT: 5 556 VAL cc_start: 0.6678 (t) cc_final: 0.6314 (p) REVERT: 5 625 ASN cc_start: 0.6295 (m110) cc_final: 0.5505 (t0) REVERT: 6 174 TYR cc_start: 0.7982 (t80) cc_final: 0.7440 (t80) REVERT: 6 299 GLU cc_start: 0.7135 (pm20) cc_final: 0.6665 (tp30) REVERT: 6 347 ASN cc_start: 0.6579 (t0) cc_final: 0.5877 (m-40) REVERT: 6 753 ARG cc_start: 0.6863 (mtm110) cc_final: 0.6632 (ttm-80) REVERT: 6 764 ILE cc_start: 0.7272 (mt) cc_final: 0.6641 (pp) REVERT: 6 783 ASP cc_start: 0.5982 (t0) cc_final: 0.5698 (t0) REVERT: 6 833 GLN cc_start: 0.7274 (OUTLIER) cc_final: 0.6512 (mp10) REVERT: 7 69 LYS cc_start: 0.7981 (mtmm) cc_final: 0.7711 (mtpt) REVERT: 7 76 ASN cc_start: 0.7887 (t0) cc_final: 0.7415 (m110) REVERT: 7 81 ASP cc_start: 0.7694 (m-30) cc_final: 0.7388 (t0) REVERT: 7 151 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6933 (mp0) REVERT: 7 159 ASN cc_start: 0.7289 (m-40) cc_final: 0.6928 (m110) REVERT: 7 162 ARG cc_start: 0.7319 (ttm-80) cc_final: 0.7032 (ttt90) REVERT: 7 182 ARG cc_start: 0.6083 (ttp80) cc_final: 0.5548 (ttm110) REVERT: 7 188 GLU cc_start: 0.6279 (tt0) cc_final: 0.5949 (tt0) REVERT: 7 207 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7486 (pt) REVERT: 7 244 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8486 (tp) REVERT: 7 247 ARG cc_start: 0.8176 (ttm170) cc_final: 0.7581 (ttp80) REVERT: 7 288 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7106 (tt0) REVERT: 7 449 LYS cc_start: 0.7417 (mtmt) cc_final: 0.6872 (tmtp) REVERT: 7 499 LYS cc_start: 0.7107 (tptm) cc_final: 0.6454 (ttmt) REVERT: 7 598 PHE cc_start: 0.8465 (m-80) cc_final: 0.8255 (m-80) REVERT: B 198 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7677 (mp) REVERT: B 220 ASP cc_start: 0.4878 (p0) cc_final: 0.4562 (t70) REVERT: B 247 ARG cc_start: 0.6969 (OUTLIER) cc_final: 0.6674 (mtm180) REVERT: B 269 LYS cc_start: 0.6513 (ttmm) cc_final: 0.5103 (mppt) REVERT: B 290 HIS cc_start: 0.6107 (m-70) cc_final: 0.5275 (m170) REVERT: B 413 ASP cc_start: 0.7063 (OUTLIER) cc_final: 0.6776 (m-30) REVERT: B 509 ARG cc_start: 0.6912 (OUTLIER) cc_final: 0.6202 (ttt90) REVERT: B 633 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.6967 (mptt) REVERT: B 705 ARG cc_start: 0.6288 (OUTLIER) cc_final: 0.5742 (mtp180) REVERT: B 834 LEU cc_start: 0.6894 (mm) cc_final: 0.6355 (tp) REVERT: C 36 THR cc_start: 0.7343 (p) cc_final: 0.7080 (m) REVERT: C 43 ARG cc_start: 0.6773 (OUTLIER) cc_final: 0.6192 (ttt180) REVERT: C 188 LYS cc_start: 0.8106 (mtmt) cc_final: 0.7585 (mttt) REVERT: C 222 THR cc_start: 0.8733 (OUTLIER) cc_final: 0.8246 (p) REVERT: C 234 GLU cc_start: 0.6889 (mt-10) cc_final: 0.5963 (mp0) REVERT: C 235 ASP cc_start: 0.6747 (p0) cc_final: 0.6392 (p0) REVERT: C 237 GLU cc_start: 0.7111 (mp0) cc_final: 0.6706 (mt-10) REVERT: C 348 ARG cc_start: 0.7003 (mtm110) cc_final: 0.6411 (mtt90) REVERT: C 464 LEU cc_start: 0.7973 (mt) cc_final: 0.7642 (mt) REVERT: C 477 LYS cc_start: 0.7424 (mttm) cc_final: 0.6904 (mttp) REVERT: C 505 THR cc_start: 0.8543 (t) cc_final: 0.8073 (m) REVERT: C 556 ILE cc_start: 0.7228 (pt) cc_final: 0.6832 (mm) REVERT: C 572 LEU cc_start: 0.6602 (OUTLIER) cc_final: 0.5664 (mm) REVERT: C 656 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7429 (tp) REVERT: C 664 LYS cc_start: 0.7583 (mtpp) cc_final: 0.7127 (mtpt) REVERT: C 681 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7550 (tmmm) REVERT: C 723 LYS cc_start: 0.7313 (pttt) cc_final: 0.6830 (ttmm) REVERT: D 235 GLU cc_start: 0.6469 (mt-10) cc_final: 0.5881 (tp30) REVERT: D 302 LYS cc_start: 0.7713 (mmtp) cc_final: 0.7087 (mtpp) REVERT: D 327 ASN cc_start: 0.8161 (OUTLIER) cc_final: 0.7264 (m-40) REVERT: D 394 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8560 (tmtp) REVERT: D 408 ASP cc_start: 0.7536 (m-30) cc_final: 0.7228 (m-30) REVERT: D 434 GLU cc_start: 0.7734 (tp30) cc_final: 0.7404 (tm-30) REVERT: D 445 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.7082 (mtt180) REVERT: D 483 GLN cc_start: 0.6789 (tp40) cc_final: 0.5942 (mt0) REVERT: D 503 ASP cc_start: 0.6312 (m-30) cc_final: 0.5982 (m-30) REVERT: D 649 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7740 (mtt) REVERT: D 690 GLU cc_start: 0.6564 (tt0) cc_final: 0.6072 (tp30) REVERT: D 715 LYS cc_start: 0.6968 (OUTLIER) cc_final: 0.6080 (ptmm) REVERT: D 726 ASN cc_start: 0.7659 (OUTLIER) cc_final: 0.7116 (t0) REVERT: D 819 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7221 (mm) REVERT: D 847 MET cc_start: 0.5583 (OUTLIER) cc_final: 0.5097 (mmm) REVERT: E 3 PHE cc_start: 0.7595 (m-80) cc_final: 0.7350 (m-80) REVERT: E 5 ARG cc_start: 0.7361 (ttp80) cc_final: 0.6825 (ttp-110) REVERT: E 77 LYS cc_start: 0.8062 (mttm) cc_final: 0.7800 (mtpp) REVERT: E 146 ILE cc_start: 0.7617 (pt) cc_final: 0.7375 (pt) REVERT: E 182 MET cc_start: 0.8528 (ttm) cc_final: 0.8183 (ttp) REVERT: E 209 ARG cc_start: 0.7017 (mmm-85) cc_final: 0.6633 (mmt180) REVERT: E 221 MET cc_start: 0.3646 (OUTLIER) cc_final: 0.2963 (pmm) REVERT: E 249 LYS cc_start: 0.7710 (mmtp) cc_final: 0.7282 (mppt) REVERT: E 280 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7575 (mtp85) REVERT: E 354 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.6158 (mt-10) REVERT: E 368 GLU cc_start: 0.6468 (OUTLIER) cc_final: 0.6251 (tt0) REVERT: E 379 PHE cc_start: 0.7411 (t80) cc_final: 0.7159 (t80) REVERT: E 431 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.6878 (mtmp) REVERT: E 458 MET cc_start: 0.6122 (mtp) cc_final: 0.5742 (mtm) REVERT: E 469 MET cc_start: 0.7999 (mmm) cc_final: 0.7516 (mmm) REVERT: E 497 MET cc_start: 0.8399 (mtm) cc_final: 0.8133 (mtm) REVERT: E 513 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8078 (pt) REVERT: E 546 ILE cc_start: 0.7369 (OUTLIER) cc_final: 0.6913 (mm) REVERT: E 549 ARG cc_start: 0.7813 (tpp-160) cc_final: 0.7468 (mmm-85) REVERT: E 592 SER cc_start: 0.6485 (m) cc_final: 0.6076 (p) REVERT: E 596 ILE cc_start: 0.7205 (tt) cc_final: 0.6904 (tt) REVERT: E 597 GLU cc_start: 0.6364 (pm20) cc_final: 0.6016 (mm-30) REVERT: E 661 GLU cc_start: 0.6580 (mt-10) cc_final: 0.6258 (mt-10) REVERT: E 666 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6965 (mt) REVERT: F 319 ASP cc_start: 0.5527 (t0) cc_final: 0.5242 (t0) REVERT: F 338 CYS cc_start: 0.2665 (OUTLIER) cc_final: 0.1333 (m) REVERT: F 421 LEU cc_start: 0.7192 (OUTLIER) cc_final: 0.6621 (mm) REVERT: F 700 ASN cc_start: 0.6651 (OUTLIER) cc_final: 0.6180 (p0) REVERT: F 715 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7750 (mt) REVERT: F 719 CYS cc_start: 0.5357 (m) cc_final: 0.5125 (t) REVERT: F 837 ARG cc_start: 0.4322 (mtp85) cc_final: 0.3828 (ttp-170) REVERT: G 15 ASN cc_start: 0.7511 (m-40) cc_final: 0.7264 (m-40) REVERT: G 130 LYS cc_start: 0.7078 (pttp) cc_final: 0.6835 (ptpt) REVERT: G 247 ARG cc_start: 0.8029 (ttt90) cc_final: 0.7538 (ttp80) REVERT: G 291 GLN cc_start: 0.7930 (mt0) cc_final: 0.7589 (mt0) REVERT: G 297 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7340 (tt0) REVERT: G 402 MET cc_start: 0.4613 (mmm) cc_final: 0.3890 (tmm) REVERT: G 412 ASN cc_start: 0.7625 (t0) cc_final: 0.7141 (m-40) REVERT: G 435 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7597 (tp) REVERT: G 475 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7523 (ttmt) REVERT: G 502 VAL cc_start: 0.5862 (OUTLIER) cc_final: 0.5644 (t) REVERT: G 529 MET cc_start: 0.6989 (mtm) cc_final: 0.6693 (OUTLIER) REVERT: G 554 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.7833 (t0) REVERT: G 556 THR cc_start: 0.8160 (OUTLIER) cc_final: 0.7734 (m) REVERT: G 659 TYR cc_start: 0.7905 (t80) cc_final: 0.7598 (t80) REVERT: G 690 LEU cc_start: 0.8454 (mt) cc_final: 0.8112 (mt) REVERT: H 31 ASN cc_start: 0.3848 (OUTLIER) cc_final: 0.3574 (m-40) REVERT: H 34 LYS cc_start: 0.3762 (tttt) cc_final: 0.3505 (tptp) REVERT: H 135 LEU cc_start: 0.2516 (OUTLIER) cc_final: 0.2211 (tp) REVERT: H 141 LYS cc_start: 0.2808 (mmmt) cc_final: 0.2528 (mmtm) REVERT: H 143 TYR cc_start: 0.3380 (t80) cc_final: 0.2841 (t80) REVERT: H 152 LYS cc_start: 0.4930 (pttp) cc_final: 0.4664 (pptt) REVERT: H 172 ASN cc_start: 0.3415 (p0) cc_final: 0.3156 (p0) REVERT: H 183 PHE cc_start: 0.5370 (m-10) cc_final: 0.5127 (m-10) REVERT: H 281 THR cc_start: 0.6559 (OUTLIER) cc_final: 0.6120 (m) REVERT: H 284 PHE cc_start: 0.5482 (m-80) cc_final: 0.4803 (m-80) REVERT: H 329 LEU cc_start: 0.7483 (mm) cc_final: 0.7127 (mm) REVERT: H 331 GLU cc_start: 0.5692 (mt-10) cc_final: 0.5418 (mt-10) REVERT: H 332 LEU cc_start: 0.6166 (mt) cc_final: 0.5728 (tp) REVERT: H 342 ARG cc_start: 0.5195 (mtm180) cc_final: 0.4993 (ttm-80) REVERT: H 371 GLU cc_start: 0.3616 (OUTLIER) cc_final: 0.2862 (pm20) REVERT: H 389 TYR cc_start: 0.1094 (m-80) cc_final: 0.0863 (m-80) REVERT: I 120 MET cc_start: 0.2317 (pp-130) cc_final: 0.0762 (mpt) REVERT: I 125 ARG cc_start: 0.3750 (OUTLIER) cc_final: 0.3278 (mmm-85) REVERT: I 152 LYS cc_start: 0.3866 (mttt) cc_final: 0.3533 (tppt) REVERT: I 158 LEU cc_start: 0.2946 (tt) cc_final: 0.2135 (mm) REVERT: I 199 MET cc_start: 0.5240 (mtt) cc_final: 0.4830 (mtm) REVERT: I 365 ILE cc_start: 0.2859 (tt) cc_final: 0.2566 (mp) REVERT: I 382 MET cc_start: 0.2196 (mmp) cc_final: 0.1140 (tpt) REVERT: I 519 VAL cc_start: 0.7364 (m) cc_final: 0.6918 (t) REVERT: I 662 GLU cc_start: 0.6506 (tt0) cc_final: 0.6274 (tp30) outliers start: 262 outliers final: 151 residues processed: 1064 average time/residue: 1.5731 time to fit residues: 2173.5368 Evaluate side-chains 1073 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 862 time to evaluate : 5.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 196 GLU Chi-restraints excluded: chain 2 residue 312 SER Chi-restraints excluded: chain 2 residue 326 ARG Chi-restraints excluded: chain 2 residue 374 ARG Chi-restraints excluded: chain 2 residue 418 SER Chi-restraints excluded: chain 2 residue 422 GLU Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 527 VAL Chi-restraints excluded: chain 2 residue 590 THR Chi-restraints excluded: chain 2 residue 656 ARG Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 670 THR Chi-restraints excluded: chain 2 residue 684 ARG Chi-restraints excluded: chain 2 residue 697 THR Chi-restraints excluded: chain 2 residue 783 MET Chi-restraints excluded: chain 2 residue 786 VAL Chi-restraints excluded: chain 2 residue 797 SER Chi-restraints excluded: chain 2 residue 851 VAL Chi-restraints excluded: chain 2 residue 857 LEU Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 117 GLU Chi-restraints excluded: chain 3 residue 189 THR Chi-restraints excluded: chain 3 residue 208 ARG Chi-restraints excluded: chain 3 residue 234 GLU Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 353 LEU Chi-restraints excluded: chain 3 residue 440 VAL Chi-restraints excluded: chain 3 residue 667 VAL Chi-restraints excluded: chain 3 residue 670 GLN Chi-restraints excluded: chain 3 residue 701 THR Chi-restraints excluded: chain 4 residue 232 GLU Chi-restraints excluded: chain 4 residue 284 ILE Chi-restraints excluded: chain 4 residue 296 ILE Chi-restraints excluded: chain 4 residue 411 THR Chi-restraints excluded: chain 4 residue 436 THR Chi-restraints excluded: chain 4 residue 592 SER Chi-restraints excluded: chain 4 residue 636 LYS Chi-restraints excluded: chain 4 residue 661 ILE Chi-restraints excluded: chain 4 residue 674 SER Chi-restraints excluded: chain 4 residue 686 LEU Chi-restraints excluded: chain 4 residue 699 LEU Chi-restraints excluded: chain 4 residue 749 MET Chi-restraints excluded: chain 4 residue 797 GLN Chi-restraints excluded: chain 5 residue 5 ARG Chi-restraints excluded: chain 5 residue 102 SER Chi-restraints excluded: chain 5 residue 148 LEU Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 190 THR Chi-restraints excluded: chain 5 residue 205 VAL Chi-restraints excluded: chain 5 residue 253 GLN Chi-restraints excluded: chain 5 residue 366 LEU Chi-restraints excluded: chain 5 residue 420 THR Chi-restraints excluded: chain 5 residue 484 LYS Chi-restraints excluded: chain 5 residue 495 GLU Chi-restraints excluded: chain 5 residue 544 THR Chi-restraints excluded: chain 5 residue 624 SER Chi-restraints excluded: chain 5 residue 633 LEU Chi-restraints excluded: chain 5 residue 661 GLU Chi-restraints excluded: chain 6 residue 313 MET Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 446 ARG Chi-restraints excluded: chain 6 residue 460 ILE Chi-restraints excluded: chain 6 residue 462 ILE Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 6 residue 598 THR Chi-restraints excluded: chain 6 residue 647 SER Chi-restraints excluded: chain 6 residue 659 GLN Chi-restraints excluded: chain 6 residue 660 THR Chi-restraints excluded: chain 6 residue 831 LEU Chi-restraints excluded: chain 6 residue 833 GLN Chi-restraints excluded: chain 7 residue 141 VAL Chi-restraints excluded: chain 7 residue 207 LEU Chi-restraints excluded: chain 7 residue 244 ILE Chi-restraints excluded: chain 7 residue 283 GLU Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 288 GLU Chi-restraints excluded: chain 7 residue 410 VAL Chi-restraints excluded: chain 7 residue 483 THR Chi-restraints excluded: chain 7 residue 484 THR Chi-restraints excluded: chain 7 residue 502 VAL Chi-restraints excluded: chain 7 residue 556 THR Chi-restraints excluded: chain 7 residue 557 LEU Chi-restraints excluded: chain 7 residue 570 LEU Chi-restraints excluded: chain 7 residue 592 SER Chi-restraints excluded: chain 7 residue 624 LYS Chi-restraints excluded: chain 7 residue 670 ASP Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 581 ARG Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 694 ARG Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain B residue 789 VAL Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 502 ILE Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 572 LEU Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 656 LEU Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 681 LYS Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain D residue 445 ARG Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 649 MET Chi-restraints excluded: chain D residue 674 SER Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 726 ASN Chi-restraints excluded: chain D residue 800 SER Chi-restraints excluded: chain D residue 819 LEU Chi-restraints excluded: chain D residue 847 MET Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 25 THR Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 102 SER Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 280 ARG Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 368 GLU Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain E residue 483 ASP Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain E residue 546 ILE Chi-restraints excluded: chain E residue 599 MET Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 666 LEU Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 338 CYS Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 501 GLN Chi-restraints excluded: chain F residue 519 MET Chi-restraints excluded: chain F residue 645 ASP Chi-restraints excluded: chain F residue 700 ASN Chi-restraints excluded: chain F residue 706 MET Chi-restraints excluded: chain F residue 715 ILE Chi-restraints excluded: chain F residue 727 LEU Chi-restraints excluded: chain F residue 796 THR Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 282 SER Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 297 GLN Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 382 ARG Chi-restraints excluded: chain G residue 435 LEU Chi-restraints excluded: chain G residue 475 LYS Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 554 ASN Chi-restraints excluded: chain G residue 556 THR Chi-restraints excluded: chain G residue 561 THR Chi-restraints excluded: chain G residue 656 VAL Chi-restraints excluded: chain G residue 685 THR Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 277 ASN Chi-restraints excluded: chain H residue 281 THR Chi-restraints excluded: chain H residue 298 THR Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 322 SER Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 347 LEU Chi-restraints excluded: chain H residue 371 GLU Chi-restraints excluded: chain I residue 119 ILE Chi-restraints excluded: chain I residue 125 ARG Chi-restraints excluded: chain I residue 174 ILE Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain I residue 675 ILE Chi-restraints excluded: chain I residue 696 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 501 optimal weight: 1.9990 chunk 807 optimal weight: 9.9990 chunk 492 optimal weight: 2.9990 chunk 382 optimal weight: 4.9990 chunk 561 optimal weight: 0.3980 chunk 846 optimal weight: 5.9990 chunk 779 optimal weight: 1.9990 chunk 674 optimal weight: 0.0040 chunk 70 optimal weight: 0.7980 chunk 520 optimal weight: 1.9990 chunk 413 optimal weight: 4.9990 overall best weight: 1.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 641 ASN ** 3 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 253 GLN ** 5 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 587 GLN 6 156 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 623 ASN ** B 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 GLN ** C 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN D 253 GLN E 560 HIS E 685 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 ASN ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 ASN H 367 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 69476 Z= 0.186 Angle : 0.540 14.208 93996 Z= 0.274 Chirality : 0.043 0.322 10834 Planarity : 0.004 0.056 12062 Dihedral : 7.048 173.683 9630 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.40 % Favored : 97.56 % Rotamer: Outliers : 3.19 % Allowed : 19.74 % Favored : 77.08 % 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: 0.54 (0.09), residues: 8483 helix: 1.17 (0.09), residues: 3491 sheet: -0.18 (0.13), residues: 1576 loop : -0.07 (0.10), residues: 3416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 112 HIS 0.014 0.001 HIS F 653 PHE 0.026 0.001 PHE F 142 TYR 0.022 0.001 TYR B 769 ARG 0.011 0.000 ARG G 162 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16966 Ramachandran restraints generated. 8483 Oldfield, 0 Emsley, 8483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1123 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 881 time to evaluate : 5.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 196 GLU cc_start: 0.5747 (OUTLIER) cc_final: 0.5470 (mt-10) REVERT: 2 232 ARG cc_start: 0.6573 (mmm-85) cc_final: 0.5944 (mtp180) REVERT: 2 326 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.6580 (pmt170) REVERT: 2 374 ARG cc_start: 0.6131 (OUTLIER) cc_final: 0.5315 (ttm110) REVERT: 2 422 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6863 (pp20) REVERT: 2 651 ASN cc_start: 0.8214 (m-40) cc_final: 0.7700 (m-40) REVERT: 2 667 VAL cc_start: 0.7471 (OUTLIER) cc_final: 0.7059 (p) REVERT: 2 684 ARG cc_start: 0.4049 (OUTLIER) cc_final: 0.3348 (ptp90) REVERT: 2 690 GLU cc_start: 0.5433 (pm20) cc_final: 0.4961 (pm20) REVERT: 2 783 MET cc_start: 0.6753 (OUTLIER) cc_final: 0.6442 (ttp) REVERT: 3 23 ASP cc_start: 0.7296 (m-30) cc_final: 0.7030 (m-30) REVERT: 3 52 ASN cc_start: 0.5100 (m-40) cc_final: 0.4887 (m110) REVERT: 3 188 LYS cc_start: 0.7930 (mtmm) cc_final: 0.7254 (ttpt) REVERT: 3 208 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7135 (mtp180) REVERT: 3 234 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.6181 (tm-30) REVERT: 3 274 ILE cc_start: 0.8696 (pt) cc_final: 0.8322 (tp) REVERT: 3 349 ASN cc_start: 0.8020 (m-40) cc_final: 0.7647 (m-40) REVERT: 3 353 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8648 (mm) REVERT: 3 455 ARG cc_start: 0.5907 (mmm160) cc_final: 0.5636 (mtt180) REVERT: 3 535 LEU cc_start: 0.7889 (tp) cc_final: 0.7575 (tp) REVERT: 3 587 ASN cc_start: 0.6636 (m-40) cc_final: 0.4762 (t0) REVERT: 4 178 ARG cc_start: 0.7261 (mmm160) cc_final: 0.6980 (mmm-85) REVERT: 4 232 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7692 (pt0) REVERT: 4 266 GLN cc_start: 0.7618 (tp40) cc_final: 0.7405 (tp-100) REVERT: 4 296 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7679 (mm) REVERT: 4 341 ASP cc_start: 0.8201 (p0) cc_final: 0.7899 (p0) REVERT: 4 404 ASP cc_start: 0.6904 (m-30) cc_final: 0.6574 (m-30) REVERT: 4 411 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.7890 (p) REVERT: 4 477 ASP cc_start: 0.7441 (t0) cc_final: 0.7173 (t0) REVERT: 4 579 GLN cc_start: 0.7719 (mm-40) cc_final: 0.7363 (mm-40) REVERT: 4 583 LYS cc_start: 0.8286 (mmpt) cc_final: 0.7663 (mtmm) REVERT: 4 612 LYS cc_start: 0.7731 (mmpt) cc_final: 0.7083 (mmtp) REVERT: 4 636 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.7556 (mppt) REVERT: 4 715 LYS cc_start: 0.7289 (pttp) cc_final: 0.6631 (mmtp) REVERT: 4 726 ASN cc_start: 0.7708 (m-40) cc_final: 0.7255 (t0) REVERT: 4 756 GLU cc_start: 0.7666 (tt0) cc_final: 0.7412 (tp30) REVERT: 4 772 ARG cc_start: 0.7145 (mtp-110) cc_final: 0.6820 (ttm-80) REVERT: 5 5 ARG cc_start: 0.6990 (OUTLIER) cc_final: 0.6663 (tmm-80) REVERT: 5 29 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7262 (mtmp) REVERT: 5 362 ARG cc_start: 0.6243 (mpp80) cc_final: 0.6032 (mmt180) REVERT: 5 388 ILE cc_start: 0.8172 (mt) cc_final: 0.7929 (mm) REVERT: 5 404 MET cc_start: 0.7011 (ptp) cc_final: 0.5724 (mmp) REVERT: 5 495 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7523 (tt0) REVERT: 5 556 VAL cc_start: 0.6646 (t) cc_final: 0.6300 (p) REVERT: 5 689 MET cc_start: 0.6938 (mmm) cc_final: 0.6633 (mmm) REVERT: 6 174 TYR cc_start: 0.7999 (t80) cc_final: 0.7435 (t80) REVERT: 6 299 GLU cc_start: 0.7137 (pm20) cc_final: 0.6687 (tp30) REVERT: 6 347 ASN cc_start: 0.6567 (t0) cc_final: 0.5864 (m-40) REVERT: 6 753 ARG cc_start: 0.6940 (mtm110) cc_final: 0.6678 (ttm-80) REVERT: 6 764 ILE cc_start: 0.7263 (mt) cc_final: 0.6640 (pp) REVERT: 6 767 LYS cc_start: 0.5592 (tppt) cc_final: 0.4985 (ptpp) REVERT: 6 783 ASP cc_start: 0.5951 (t0) cc_final: 0.5694 (t0) REVERT: 6 833 GLN cc_start: 0.7230 (OUTLIER) cc_final: 0.6428 (mp10) REVERT: 7 69 LYS cc_start: 0.7967 (mtmm) cc_final: 0.7706 (mtpt) REVERT: 7 76 ASN cc_start: 0.7829 (t0) cc_final: 0.7352 (m110) REVERT: 7 81 ASP cc_start: 0.7682 (m-30) cc_final: 0.7374 (t0) REVERT: 7 151 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6920 (mp0) REVERT: 7 159 ASN cc_start: 0.7326 (m-40) cc_final: 0.6965 (m110) REVERT: 7 162 ARG cc_start: 0.7288 (ttm-80) cc_final: 0.6933 (ttt90) REVERT: 7 188 GLU cc_start: 0.6215 (tt0) cc_final: 0.5940 (tt0) REVERT: 7 207 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7458 (pt) REVERT: 7 244 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8476 (tp) REVERT: 7 247 ARG cc_start: 0.8189 (ttm170) cc_final: 0.7518 (ttp-110) REVERT: 7 288 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7069 (tt0) REVERT: 7 449 LYS cc_start: 0.7394 (mtmt) cc_final: 0.6861 (tmtp) REVERT: 7 499 LYS cc_start: 0.7055 (tptm) cc_final: 0.6419 (ttmt) REVERT: 7 502 VAL cc_start: 0.4830 (OUTLIER) cc_final: 0.4299 (t) REVERT: B 198 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7650 (mp) REVERT: B 199 THR cc_start: 0.6571 (t) cc_final: 0.6304 (p) REVERT: B 220 ASP cc_start: 0.4947 (p0) cc_final: 0.4641 (t70) REVERT: B 247 ARG cc_start: 0.6966 (OUTLIER) cc_final: 0.6678 (mtm180) REVERT: B 269 LYS cc_start: 0.6496 (ttmm) cc_final: 0.5083 (mppt) REVERT: B 290 HIS cc_start: 0.5886 (m-70) cc_final: 0.5177 (m170) REVERT: B 413 ASP cc_start: 0.7042 (OUTLIER) cc_final: 0.6738 (m-30) REVERT: B 495 ASP cc_start: 0.5640 (m-30) cc_final: 0.5371 (m-30) REVERT: B 506 TYR cc_start: 0.6371 (t80) cc_final: 0.6051 (t80) REVERT: B 509 ARG cc_start: 0.6845 (OUTLIER) cc_final: 0.6120 (ttt90) REVERT: B 633 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.6944 (mptt) REVERT: B 694 ARG cc_start: 0.6504 (OUTLIER) cc_final: 0.6160 (mtm110) REVERT: B 705 ARG cc_start: 0.6269 (OUTLIER) cc_final: 0.5726 (mtp180) REVERT: B 834 LEU cc_start: 0.6883 (mm) cc_final: 0.6349 (tp) REVERT: C 36 THR cc_start: 0.7349 (p) cc_final: 0.7079 (m) REVERT: C 43 ARG cc_start: 0.6750 (OUTLIER) cc_final: 0.6184 (ttt180) REVERT: C 188 LYS cc_start: 0.8091 (mtmt) cc_final: 0.7592 (mttt) REVERT: C 222 THR cc_start: 0.8748 (OUTLIER) cc_final: 0.8261 (p) REVERT: C 234 GLU cc_start: 0.6875 (mt-10) cc_final: 0.5941 (mp0) REVERT: C 235 ASP cc_start: 0.6738 (p0) cc_final: 0.6372 (p0) REVERT: C 237 GLU cc_start: 0.7102 (mp0) cc_final: 0.6699 (mt-10) REVERT: C 348 ARG cc_start: 0.6996 (mtm110) cc_final: 0.6406 (mtt90) REVERT: C 464 LEU cc_start: 0.7950 (mt) cc_final: 0.7623 (mt) REVERT: C 477 LYS cc_start: 0.7370 (mttm) cc_final: 0.6871 (mttp) REVERT: C 505 THR cc_start: 0.8538 (t) cc_final: 0.8085 (m) REVERT: C 556 ILE cc_start: 0.7235 (pt) cc_final: 0.6838 (mm) REVERT: C 664 LYS cc_start: 0.7606 (mtpp) cc_final: 0.7164 (mtpt) REVERT: C 667 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.8154 (t) REVERT: C 681 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7545 (tmmm) REVERT: C 723 LYS cc_start: 0.7339 (pttt) cc_final: 0.6831 (ttmm) REVERT: D 235 GLU cc_start: 0.6408 (mt-10) cc_final: 0.5802 (tp30) REVERT: D 302 LYS cc_start: 0.7679 (mmtp) cc_final: 0.7078 (mtpp) REVERT: D 327 ASN cc_start: 0.8150 (OUTLIER) cc_final: 0.7293 (m-40) REVERT: D 394 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8528 (tmtp) REVERT: D 408 ASP cc_start: 0.7463 (m-30) cc_final: 0.7170 (m-30) REVERT: D 434 GLU cc_start: 0.7727 (tp30) cc_final: 0.7452 (tm-30) REVERT: D 445 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.6992 (mtt180) REVERT: D 483 GLN cc_start: 0.6818 (tp40) cc_final: 0.6006 (mt0) REVERT: D 503 ASP cc_start: 0.6352 (m-30) cc_final: 0.6023 (m-30) REVERT: D 649 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7781 (mtt) REVERT: D 651 GLN cc_start: 0.8119 (mt0) cc_final: 0.7795 (pm20) REVERT: D 661 ILE cc_start: 0.7025 (OUTLIER) cc_final: 0.6655 (mt) REVERT: D 690 GLU cc_start: 0.6553 (tt0) cc_final: 0.6062 (tp30) REVERT: D 715 LYS cc_start: 0.6926 (OUTLIER) cc_final: 0.6035 (ptmm) REVERT: D 819 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7232 (mm) REVERT: D 847 MET cc_start: 0.5523 (OUTLIER) cc_final: 0.4998 (mmm) REVERT: E 3 PHE cc_start: 0.7617 (m-80) cc_final: 0.7394 (m-80) REVERT: E 5 ARG cc_start: 0.7345 (ttp80) cc_final: 0.6743 (ttm110) REVERT: E 77 LYS cc_start: 0.8044 (mttm) cc_final: 0.7781 (mtpp) REVERT: E 146 ILE cc_start: 0.7615 (pt) cc_final: 0.7367 (pt) REVERT: E 182 MET cc_start: 0.8501 (ttm) cc_final: 0.8161 (ttp) REVERT: E 209 ARG cc_start: 0.6909 (mmm-85) cc_final: 0.6616 (mmt180) REVERT: E 221 MET cc_start: 0.3547 (OUTLIER) cc_final: 0.2870 (pmm) REVERT: E 249 LYS cc_start: 0.7729 (mmtp) cc_final: 0.7315 (mppt) REVERT: E 280 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7576 (mtp85) REVERT: E 354 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6168 (mt-10) REVERT: E 368 GLU cc_start: 0.6434 (OUTLIER) cc_final: 0.6219 (tt0) REVERT: E 379 PHE cc_start: 0.7406 (t80) cc_final: 0.7150 (t80) REVERT: E 431 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.6876 (mtmp) REVERT: E 458 MET cc_start: 0.6223 (mtp) cc_final: 0.5803 (mtm) REVERT: E 469 MET cc_start: 0.7999 (mmm) cc_final: 0.7448 (mmm) REVERT: E 497 MET cc_start: 0.8386 (mtm) cc_final: 0.8172 (mtm) REVERT: E 513 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7896 (pp) REVERT: E 546 ILE cc_start: 0.7356 (OUTLIER) cc_final: 0.6911 (mm) REVERT: E 549 ARG cc_start: 0.7859 (tpp-160) cc_final: 0.7535 (mmm-85) REVERT: E 592 SER cc_start: 0.6428 (m) cc_final: 0.6028 (p) REVERT: E 596 ILE cc_start: 0.7260 (tt) cc_final: 0.6947 (tt) REVERT: E 597 GLU cc_start: 0.6349 (pm20) cc_final: 0.6003 (mm-30) REVERT: E 661 GLU cc_start: 0.6588 (mt-10) cc_final: 0.6256 (mt-10) REVERT: E 666 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.6958 (mt) REVERT: F 338 CYS cc_start: 0.2306 (OUTLIER) cc_final: 0.0931 (m) REVERT: F 421 LEU cc_start: 0.7177 (OUTLIER) cc_final: 0.6615 (mm) REVERT: F 446 ARG cc_start: 0.7146 (ptt90) cc_final: 0.6937 (ptt90) REVERT: F 521 LYS cc_start: 0.4761 (mmpt) cc_final: 0.4505 (mmtt) REVERT: F 700 ASN cc_start: 0.6655 (OUTLIER) cc_final: 0.6176 (p0) REVERT: F 715 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7717 (mt) REVERT: F 837 ARG cc_start: 0.4207 (mtp85) cc_final: 0.3720 (ttp-170) REVERT: G 15 ASN cc_start: 0.7377 (m-40) cc_final: 0.6110 (t0) REVERT: G 130 LYS cc_start: 0.7038 (pttp) cc_final: 0.6810 (ptpt) REVERT: G 247 ARG cc_start: 0.8018 (ttt90) cc_final: 0.7536 (ttp80) REVERT: G 291 GLN cc_start: 0.7909 (mt0) cc_final: 0.7573 (mt0) REVERT: G 297 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7346 (tt0) REVERT: G 402 MET cc_start: 0.4608 (mmm) cc_final: 0.4108 (tmm) REVERT: G 412 ASN cc_start: 0.7606 (t0) cc_final: 0.7125 (m-40) REVERT: G 441 ASP cc_start: 0.7225 (p0) cc_final: 0.7007 (p0) REVERT: G 475 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7493 (ttmt) REVERT: G 502 VAL cc_start: 0.5825 (OUTLIER) cc_final: 0.5578 (t) REVERT: G 508 LEU cc_start: 0.6851 (tp) cc_final: 0.6644 (mt) REVERT: G 529 MET cc_start: 0.6909 (mtm) cc_final: 0.6596 (OUTLIER) REVERT: G 554 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.7849 (t0) REVERT: G 556 THR cc_start: 0.8158 (OUTLIER) cc_final: 0.7644 (m) REVERT: G 659 TYR cc_start: 0.7895 (t80) cc_final: 0.7593 (t80) REVERT: G 690 LEU cc_start: 0.8439 (mt) cc_final: 0.8081 (mt) REVERT: H 15 ILE cc_start: 0.3259 (OUTLIER) cc_final: 0.2162 (mp) REVERT: H 31 ASN cc_start: 0.3878 (OUTLIER) cc_final: 0.3592 (m-40) REVERT: H 34 LYS cc_start: 0.3675 (tttt) cc_final: 0.3451 (tptp) REVERT: H 135 LEU cc_start: 0.2760 (OUTLIER) cc_final: 0.2475 (tp) REVERT: H 137 ILE cc_start: 0.4461 (mm) cc_final: 0.4071 (pp) REVERT: H 141 LYS cc_start: 0.2804 (mmmt) cc_final: 0.2513 (mmtm) REVERT: H 143 TYR cc_start: 0.3363 (t80) cc_final: 0.2813 (t80) REVERT: H 152 LYS cc_start: 0.4999 (pttp) cc_final: 0.4734 (pptt) REVERT: H 172 ASN cc_start: 0.3457 (p0) cc_final: 0.3147 (p0) REVERT: H 183 PHE cc_start: 0.5377 (m-10) cc_final: 0.5101 (m-10) REVERT: H 281 THR cc_start: 0.6575 (OUTLIER) cc_final: 0.6128 (m) REVERT: H 284 PHE cc_start: 0.5458 (m-80) cc_final: 0.4776 (m-80) REVERT: H 329 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7097 (mm) REVERT: H 331 GLU cc_start: 0.5893 (mt-10) cc_final: 0.5594 (mt-10) REVERT: H 332 LEU cc_start: 0.6144 (mt) cc_final: 0.5725 (tp) REVERT: H 342 ARG cc_start: 0.5246 (mtm180) cc_final: 0.5028 (ttm-80) REVERT: H 371 GLU cc_start: 0.3649 (OUTLIER) cc_final: 0.2863 (pm20) REVERT: H 389 TYR cc_start: 0.1187 (m-80) cc_final: 0.0964 (m-80) REVERT: I 120 MET cc_start: 0.2271 (pp-130) cc_final: 0.0702 (mpt) REVERT: I 125 ARG cc_start: 0.3895 (OUTLIER) cc_final: 0.3433 (mmm-85) REVERT: I 152 LYS cc_start: 0.3857 (mttt) cc_final: 0.3567 (tppt) REVERT: I 158 LEU cc_start: 0.3033 (tt) cc_final: 0.2239 (mm) REVERT: I 199 MET cc_start: 0.5012 (mtt) cc_final: 0.4554 (mtm) REVERT: I 344 PHE cc_start: 0.4225 (m-80) cc_final: 0.4020 (m-10) REVERT: I 365 ILE cc_start: 0.2864 (tt) cc_final: 0.2578 (mp) REVERT: I 382 MET cc_start: 0.2286 (mmp) cc_final: 0.1203 (tpp) REVERT: I 519 VAL cc_start: 0.7345 (m) cc_final: 0.6895 (t) REVERT: I 662 GLU cc_start: 0.6501 (tt0) cc_final: 0.6249 (tp30) outliers start: 242 outliers final: 139 residues processed: 1049 average time/residue: 1.5541 time to fit residues: 2119.8166 Evaluate side-chains 1058 residues out of total 7605 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 855 time to evaluate : 5.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 196 GLU Chi-restraints excluded: chain 2 residue 312 SER Chi-restraints excluded: chain 2 residue 326 ARG Chi-restraints excluded: chain 2 residue 374 ARG Chi-restraints excluded: chain 2 residue 418 SER Chi-restraints excluded: chain 2 residue 422 GLU Chi-restraints excluded: chain 2 residue 426 VAL Chi-restraints excluded: chain 2 residue 590 THR Chi-restraints excluded: chain 2 residue 656 ARG Chi-restraints excluded: chain 2 residue 667 VAL Chi-restraints excluded: chain 2 residue 670 THR Chi-restraints excluded: chain 2 residue 684 ARG Chi-restraints excluded: chain 2 residue 697 THR Chi-restraints excluded: chain 2 residue 783 MET Chi-restraints excluded: chain 2 residue 857 LEU Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 117 GLU Chi-restraints excluded: chain 3 residue 189 THR Chi-restraints excluded: chain 3 residue 208 ARG Chi-restraints excluded: chain 3 residue 234 GLU Chi-restraints excluded: chain 3 residue 242 THR Chi-restraints excluded: chain 3 residue 353 LEU Chi-restraints excluded: chain 3 residue 440 VAL Chi-restraints excluded: chain 3 residue 667 VAL Chi-restraints excluded: chain 3 residue 701 THR Chi-restraints excluded: chain 4 residue 232 GLU Chi-restraints excluded: chain 4 residue 284 ILE Chi-restraints excluded: chain 4 residue 296 ILE Chi-restraints excluded: chain 4 residue 411 THR Chi-restraints excluded: chain 4 residue 431 ASP Chi-restraints excluded: chain 4 residue 436 THR Chi-restraints excluded: chain 4 residue 592 SER Chi-restraints excluded: chain 4 residue 636 LYS Chi-restraints excluded: chain 4 residue 661 ILE Chi-restraints excluded: chain 4 residue 674 SER Chi-restraints excluded: chain 4 residue 699 LEU Chi-restraints excluded: chain 4 residue 749 MET Chi-restraints excluded: chain 4 residue 797 GLN Chi-restraints excluded: chain 5 residue 5 ARG Chi-restraints excluded: chain 5 residue 29 LYS Chi-restraints excluded: chain 5 residue 162 LEU Chi-restraints excluded: chain 5 residue 342 ILE Chi-restraints excluded: chain 5 residue 366 LEU Chi-restraints excluded: chain 5 residue 484 LYS Chi-restraints excluded: chain 5 residue 495 GLU Chi-restraints excluded: chain 5 residue 544 THR Chi-restraints excluded: chain 5 residue 624 SER Chi-restraints excluded: chain 5 residue 661 GLU Chi-restraints excluded: chain 6 residue 313 MET Chi-restraints excluded: chain 6 residue 359 VAL Chi-restraints excluded: chain 6 residue 379 VAL Chi-restraints excluded: chain 6 residue 446 ARG Chi-restraints excluded: chain 6 residue 462 ILE Chi-restraints excluded: chain 6 residue 574 VAL Chi-restraints excluded: chain 6 residue 598 THR Chi-restraints excluded: chain 6 residue 647 SER Chi-restraints excluded: chain 6 residue 659 GLN Chi-restraints excluded: chain 6 residue 660 THR Chi-restraints excluded: chain 6 residue 831 LEU Chi-restraints excluded: chain 6 residue 833 GLN Chi-restraints excluded: chain 7 residue 141 VAL Chi-restraints excluded: chain 7 residue 207 LEU Chi-restraints excluded: chain 7 residue 244 ILE Chi-restraints excluded: chain 7 residue 257 VAL Chi-restraints excluded: chain 7 residue 283 GLU Chi-restraints excluded: chain 7 residue 285 THR Chi-restraints excluded: chain 7 residue 288 GLU Chi-restraints excluded: chain 7 residue 410 VAL Chi-restraints excluded: chain 7 residue 483 THR Chi-restraints excluded: chain 7 residue 502 VAL Chi-restraints excluded: chain 7 residue 556 THR Chi-restraints excluded: chain 7 residue 557 LEU Chi-restraints excluded: chain 7 residue 570 LEU Chi-restraints excluded: chain 7 residue 592 SER Chi-restraints excluded: chain 7 residue 624 LYS Chi-restraints excluded: chain 7 residue 670 ASP Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 509 ARG Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 581 ARG Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain B residue 694 ARG Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain B residue 789 VAL Chi-restraints excluded: chain C residue 43 ARG Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 519 VAL Chi-restraints excluded: chain C residue 561 ILE Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 678 VAL Chi-restraints excluded: chain C residue 681 LYS Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 327 ASN Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain D residue 394 LYS Chi-restraints excluded: chain D residue 445 ARG Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 624 SER Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 644 VAL Chi-restraints excluded: chain D residue 649 MET Chi-restraints excluded: chain D residue 661 ILE Chi-restraints excluded: chain D residue 674 SER Chi-restraints excluded: chain D residue 715 LYS Chi-restraints excluded: chain D residue 724 LEU Chi-restraints excluded: chain D residue 800 SER Chi-restraints excluded: chain D residue 819 LEU Chi-restraints excluded: chain D residue 847 MET Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 280 ARG Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 300 ILE Chi-restraints excluded: chain E residue 321 VAL Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 368 GLU Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 431 LYS Chi-restraints excluded: chain E residue 439 THR Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain E residue 546 ILE Chi-restraints excluded: chain E residue 599 MET Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 666 LEU Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 338 CYS Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 419 SER Chi-restraints excluded: chain F residue 421 LEU Chi-restraints excluded: chain F residue 501 GLN Chi-restraints excluded: chain F residue 519 MET Chi-restraints excluded: chain F residue 645 ASP Chi-restraints excluded: chain F residue 653 HIS Chi-restraints excluded: chain F residue 700 ASN Chi-restraints excluded: chain F residue 706 MET Chi-restraints excluded: chain F residue 715 ILE Chi-restraints excluded: chain F residue 727 LEU Chi-restraints excluded: chain F residue 796 THR Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain G residue 257 VAL Chi-restraints excluded: chain G residue 282 SER Chi-restraints excluded: chain G residue 285 THR Chi-restraints excluded: chain G residue 294 THR Chi-restraints excluded: chain G residue 297 GLN Chi-restraints excluded: chain G residue 308 SER Chi-restraints excluded: chain G residue 382 ARG Chi-restraints excluded: chain G residue 473 ILE Chi-restraints excluded: chain G residue 475 LYS Chi-restraints excluded: chain G residue 502 VAL Chi-restraints excluded: chain G residue 554 ASN Chi-restraints excluded: chain G residue 556 THR Chi-restraints excluded: chain G residue 561 THR Chi-restraints excluded: chain G residue 601 LEU Chi-restraints excluded: chain G residue 656 VAL Chi-restraints excluded: chain G residue 685 THR Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 277 ASN Chi-restraints excluded: chain H residue 281 THR Chi-restraints excluded: chain H residue 298 THR Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 322 SER Chi-restraints excluded: chain H residue 329 LEU Chi-restraints excluded: chain H residue 330 LEU Chi-restraints excluded: chain H residue 358 ILE Chi-restraints excluded: chain H residue 371 GLU Chi-restraints excluded: chain I residue 119 ILE Chi-restraints excluded: chain I residue 125 ARG Chi-restraints excluded: chain I residue 174 ILE Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain I residue 280 THR Chi-restraints excluded: chain I residue 675 ILE Chi-restraints excluded: chain I residue 696 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 535 optimal weight: 6.9990 chunk 718 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 621 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 187 optimal weight: 0.9980 chunk 675 optimal weight: 0.9980 chunk 282 optimal weight: 0.1980 chunk 693 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 641 ASN ** 3 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 613 GLN ** 5 585 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 587 GLN 5 625 ASN 6 156 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 GLN ** C 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN D 253 GLN E 560 HIS E 685 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 ASN ** F 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 274 ASN H 367 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.185508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.157132 restraints weight = 738502.927| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 6.94 r_work: 0.3174 rms_B_bonded: 6.37 restraints_weight: 2.0000 r_work: 0.3205 rms_B_bonded: 5.26 restraints_weight: 4.0000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 69476 Z= 0.162 Angle : 0.523 13.353 93996 Z= 0.265 Chirality : 0.042 0.310 10834 Planarity : 0.004 0.057 12062 Dihedral : 6.958 175.471 9630 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.31 % Favored : 97.65 % Rotamer: Outliers : 2.80 % Allowed : 20.20 % Favored : 77.00 % 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: 0.63 (0.09), residues: 8483 helix: 1.25 (0.09), residues: 3488 sheet: -0.15 (0.13), residues: 1572 loop : -0.04 (0.10), residues: 3423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP 5 343 HIS 0.014 0.001 HIS F 653 PHE 0.030 0.001 PHE C 345 TYR 0.022 0.001 TYR B 769 ARG 0.011 0.000 ARG G 162 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30391.85 seconds wall clock time: 525 minutes 50.73 seconds (31550.73 seconds total)