Starting phenix.real_space_refine on Sun Feb 18 02:31:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egq_31138/02_2024/7egq_31138_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egq_31138/02_2024/7egq_31138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egq_31138/02_2024/7egq_31138.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egq_31138/02_2024/7egq_31138.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egq_31138/02_2024/7egq_31138_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7egq_31138/02_2024/7egq_31138_neut.pdb" } resolution = 3.35 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= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 17521 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 26 6.06 5 P 116 5.49 5 Mg 3 5.21 5 S 416 5.16 5 C 34193 2.51 5 N 9243 2.21 5 O 10550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 10": "NH1" <-> "NH2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A GLU 180": "OE1" <-> "OE2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A GLU 350": "OE1" <-> "OE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A GLU 436": "OE1" <-> "OE2" Residue "A GLU 796": "OE1" <-> "OE2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A ASP 846": "OD1" <-> "OD2" Residue "A GLU 857": "OE1" <-> "OE2" Residue "A GLU 876": "OE1" <-> "OE2" Residue "A GLU 917": "OE1" <-> "OE2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D GLU 48": "OE1" <-> "OE2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D GLU 77": "OE1" <-> "OE2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "E GLU 142": "OE1" <-> "OE2" Residue "E TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "E GLU 201": "OE1" <-> "OE2" Residue "E GLU 244": "OE1" <-> "OE2" Residue "E GLU 261": "OE1" <-> "OE2" Residue "E GLU 319": "OE1" <-> "OE2" Residue "E GLU 365": "OE1" <-> "OE2" Residue "E GLU 418": "OE1" <-> "OE2" Residue "E ARG 442": "NH1" <-> "NH2" Residue "E GLU 447": "OE1" <-> "OE2" Residue "E GLU 498": "OE1" <-> "OE2" Residue "E ARG 507": "NH1" <-> "NH2" Residue "G GLU 3": "OE1" <-> "OE2" Residue "G ASP 26": "OD1" <-> "OD2" Residue "G GLU 68": "OE1" <-> "OE2" Residue "G GLU 70": "OE1" <-> "OE2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H GLU 66": "OE1" <-> "OE2" Residue "K ARG 76": "NH1" <-> "NH2" Residue "K GLU 78": "OE1" <-> "OE2" Residue "K GLU 99": "OE1" <-> "OE2" Residue "K PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 347": "OE1" <-> "OE2" Residue "K ARG 525": "NH1" <-> "NH2" Residue "N ARG 10": "NH1" <-> "NH2" Residue "N ARG 18": "NH1" <-> "NH2" Residue "N GLU 83": "OE1" <-> "OE2" Residue "N GLU 167": "OE1" <-> "OE2" Residue "N GLU 180": "OE1" <-> "OE2" Residue "N GLU 277": "OE1" <-> "OE2" Residue "N GLU 278": "OE1" <-> "OE2" Residue "N GLU 350": "OE1" <-> "OE2" Residue "N GLU 370": "OE1" <-> "OE2" Residue "N GLU 436": "OE1" <-> "OE2" Residue "N GLU 796": "OE1" <-> "OE2" Residue "N ARG 836": "NH1" <-> "NH2" Residue "N GLU 857": "OE1" <-> "OE2" Residue "N GLU 876": "OE1" <-> "OE2" Residue "N GLU 917": "OE1" <-> "OE2" Residue "O GLU 23": "OE1" <-> "OE2" Residue "O GLU 60": "OE1" <-> "OE2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "P GLU 50": "OE1" <-> "OE2" Residue "Q GLU 32": "OE1" <-> "OE2" Residue "Q ARG 57": "NH1" <-> "NH2" Residue "Q GLU 155": "OE1" <-> "OE2" Residue "Q GLU 171": "OE1" <-> "OE2" Residue "R GLU 128": "OE1" <-> "OE2" Residue "R ARG 129": "NH1" <-> "NH2" Residue "R GLU 143": "OE1" <-> "OE2" Residue "R GLU 168": "OE1" <-> "OE2" Residue "R ARG 178": "NH1" <-> "NH2" Residue "R GLU 197": "OE1" <-> "OE2" Residue "R GLU 261": "OE1" <-> "OE2" Residue "R GLU 341": "OE1" <-> "OE2" Residue "R GLU 365": "OE1" <-> "OE2" Residue "R GLU 418": "OE1" <-> "OE2" Residue "R GLU 420": "OE1" <-> "OE2" Residue "R ARG 442": "NH1" <-> "NH2" Residue "R ARG 507": "NH1" <-> "NH2" Residue "R GLU 540": "OE1" <-> "OE2" Residue "T GLU 3": "OE1" <-> "OE2" Residue "T GLU 68": "OE1" <-> "OE2" Residue "T GLU 70": "OE1" <-> "OE2" Residue "U GLU 6": "OE1" <-> "OE2" Residue "X GLU 2": "OE1" <-> "OE2" Residue "X ARG 76": "NH1" <-> "NH2" Residue "X GLU 77": "OE1" <-> "OE2" Residue "X GLU 78": "OE1" <-> "OE2" Residue "X GLU 191": "OE1" <-> "OE2" Residue "X GLU 295": "OE1" <-> "OE2" Residue "X GLU 347": "OE1" <-> "OE2" Residue "X GLU 365": "OE1" <-> "OE2" Residue "X GLU 453": "OE1" <-> "OE2" Residue "X GLU 490": "OE1" <-> "OE2" Residue "F GLU 128": "OE1" <-> "OE2" Residue "F GLU 136": "OE1" <-> "OE2" Residue "F GLU 142": "OE1" <-> "OE2" Residue "F GLU 156": "OE1" <-> "OE2" Residue "F ASP 223": "OD1" <-> "OD2" Residue "F GLU 319": "OE1" <-> "OE2" Residue "F GLU 375": "OE1" <-> "OE2" Residue "F GLU 498": "OE1" <-> "OE2" Residue "S GLU 142": "OE1" <-> "OE2" Residue "S GLU 143": "OE1" <-> "OE2" Residue "S GLU 156": "OE1" <-> "OE2" Residue "S GLU 162": "OE1" <-> "OE2" Residue "S GLU 168": "OE1" <-> "OE2" Residue "S GLU 201": "OE1" <-> "OE2" Residue "S GLU 244": "OE1" <-> "OE2" Residue "S GLU 319": "OE1" <-> "OE2" Residue "S GLU 341": "OE1" <-> "OE2" Residue "S GLU 375": "OE1" <-> "OE2" Residue "S GLU 447": "OE1" <-> "OE2" Residue "S GLU 540": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 54547 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 7462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 926, 7462 Classifications: {'peptide': 926} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 895} Chain: "B" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1400 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 553 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "D" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1418 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 179} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 4567 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 588, 4559 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 2, 'PTRANS': 29, 'TRANS': 556} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Conformer: "B" Number of residues, atoms: 588, 4559 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 2, 'PTRANS': 29, 'TRANS': 556} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 bond proxies already assigned to first conformer: 4653 Chain: "G" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 868 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "H" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 955 Classifications: {'peptide': 131} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 121} Chain: "K" Number of atoms: 4169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4169 Classifications: {'peptide': 523} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 4, 'PTRANS': 26, 'TRANS': 492} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 7462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 926, 7462 Classifications: {'peptide': 926} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 895} Chain: "O" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1400 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "P" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 553 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "Q" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1418 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 179} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "R" Number of atoms: 4567 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 588, 4559 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 2, 'PTRANS': 29, 'TRANS': 556} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Conformer: "B" Number of residues, atoms: 588, 4559 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 2, 'PTRANS': 29, 'TRANS': 556} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 bond proxies already assigned to first conformer: 4653 Chain: "T" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 868 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "U" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 947 Classifications: {'peptide': 130} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 121} Chain: "X" Number of atoms: 4177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4177 Classifications: {'peptide': 524} Link IDs: {'CIS': 5, 'PTRANS': 26, 'TRANS': 492} Chain: "F" Number of atoms: 4630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4630 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 5, 'PTRANS': 30, 'TRANS': 560} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "S" Number of atoms: 4630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4630 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 5, 'PTRANS': 30, 'TRANS': 560} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "I" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 545 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 16, 'rna3p_pyr': 8} Link IDs: {'rna3p': 24} Chain: "J" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 692 Classifications: {'RNA': 33} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 19} Link IDs: {'rna2p': 2, 'rna3p': 30} Chain: "L" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 545 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 16, 'rna3p_pyr': 8} Link IDs: {'rna3p': 24} Chain: "M" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 692 Classifications: {'RNA': 33} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 12, 'rna3p_pyr': 18} Link IDs: {'rna2p': 3, 'rna3p': 29} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 2, ' ZN': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 1, ' ZN': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2446 SG CYS A 301 65.490 68.697 176.860 1.00 55.74 S ATOM 2487 SG CYS A 306 66.286 68.110 173.167 1.00 53.32 S ATOM 2519 SG CYS A 310 62.714 68.903 174.340 1.00 49.59 S ATOM 3927 SG CYS A 487 80.661 75.931 189.877 1.00 51.82 S ATOM 5180 SG CYS A 645 81.798 75.317 186.237 1.00 57.87 S ATOM 5186 SG CYS A 646 78.785 73.434 187.678 1.00 61.40 S ATOM 10937 SG CYS E 16 78.491 121.771 244.477 1.00243.61 S ATOM 10952 SG CYS E 19 75.010 120.289 245.496 1.00249.46 S ATOM 10855 SG CYS E 5 73.085 131.165 240.359 1.00247.81 S ATOM 10876 SG CYS E 8 72.312 134.666 241.819 1.00250.69 S ATOM 11014 SG CYS E 26 75.953 133.722 240.625 1.00246.27 S ATOM 11031 SG CYS E 29 74.427 132.436 243.660 1.00246.73 S ATOM 11196 SG CYS E 50 98.173 120.253 238.814 1.00233.68 S ATOM 11226 SG CYS E 55 99.254 118.079 241.896 1.00242.96 S ATOM 11359 SG CYS E 72 100.288 121.848 241.913 1.00232.45 S ATOM 16788 SG CYS H 74 39.543 40.119 115.225 1.00 79.74 S ATOM 16814 SG CYS H 77 39.047 42.783 117.881 1.00 79.74 S ATOM 16919 SG CYS H 90 36.074 40.913 116.442 1.00 91.16 S ATOM 17122 SG CYS H 117 24.815 26.980 109.500 1.00159.18 S ATOM 17142 SG CYS H 120 24.201 25.972 110.284 1.00169.69 S ATOM 17215 SG CYS H 130 22.377 25.808 106.454 1.00202.41 S ATOM 18840 SG CYS K 207 57.079 48.951 89.738 1.00 79.74 S ATOM 18860 SG CYS K 210 58.226 50.781 87.155 1.00 79.74 S ATOM 18981 SG CYS K 226 60.566 51.647 89.814 1.00 79.74 S ATOM 19281 SG CYS K 261 84.088 62.095 111.841 1.00 79.74 S ATOM 19411 SG CYS K 279 82.504 58.673 110.606 1.00 79.74 S ATOM 20801 SG CYS K 452 104.169 61.577 59.938 1.00108.12 S ATOM 21028 SG CYS K 484 101.170 64.406 60.832 1.00 93.58 S ATOM 23838 SG CYS N 301 59.381 129.390 110.662 1.00 46.56 S ATOM 23879 SG CYS N 306 60.006 130.130 114.361 1.00 46.29 S ATOM 23911 SG CYS N 310 56.683 128.622 113.159 1.00 40.34 S ATOM 25319 SG CYS N 487 75.830 125.404 97.798 1.00 48.93 S ATOM 26572 SG CYS N 645 76.783 126.241 101.446 1.00 53.10 S ATOM 26578 SG CYS N 646 73.463 127.466 99.974 1.00 52.49 S ATOM 32329 SG CYS R 16 84.414 80.250 43.627 1.00170.29 S ATOM 32344 SG CYS R 19 80.901 80.039 42.081 1.00172.43 S ATOM 32247 SG CYS R 5 80.068 69.401 47.992 1.00171.68 S ATOM 32268 SG CYS R 8 80.074 65.830 46.423 1.00175.29 S ATOM 32406 SG CYS R 26 83.268 67.508 47.283 1.00171.25 S ATOM 32423 SG CYS R 29 81.357 68.710 44.362 1.00169.36 S ATOM 32588 SG CYS R 50 102.498 86.034 49.244 1.00156.57 S ATOM 32618 SG CYS R 55 102.116 87.719 45.880 1.00179.22 S ATOM 32751 SG CYS R 72 104.722 85.004 46.261 1.00161.23 S ATOM 38180 SG CYS U 74 27.606 152.095 172.061 1.00103.80 S ATOM 38206 SG CYS U 77 28.124 149.358 169.483 1.00 99.95 S ATOM 38311 SG CYS U 90 24.678 150.768 170.150 1.00126.49 S ATOM 38514 SG CYS U 117 10.285 160.545 179.106 1.00193.93 S ATOM 38534 SG CYS U 120 9.983 162.879 177.105 1.00202.41 S ATOM 38607 SG CYS U 130 7.877 163.003 180.427 1.00228.75 S ATOM 40238 SG CYS X 207 47.202 147.519 197.699 1.00 79.74 S ATOM 40258 SG CYS X 210 49.146 147.425 200.688 1.00 79.74 S ATOM 40379 SG CYS X 226 50.396 145.277 197.816 1.00 79.74 S ATOM 40679 SG CYS X 261 76.297 139.908 176.697 1.00 83.92 S ATOM 40809 SG CYS X 279 73.647 142.860 176.940 1.00 79.74 S ATOM 42199 SG CYS X 452 95.966 144.369 227.709 1.00156.03 S ATOM 42431 SG CYS X 484 92.646 142.177 228.637 1.00151.49 S ATOM 42811 SG CYS F 5 91.002 73.398 236.317 1.00275.65 S ATOM 42832 SG CYS F 8 91.728 75.710 239.006 1.00278.91 S ATOM 42970 SG CYS F 26 94.467 75.571 236.534 1.00291.20 S ATOM 42991 SG CYS F 29 94.193 72.502 238.028 1.00294.83 S ATOM 43156 SG CYS F 50 104.359 74.205 212.662 1.00290.42 S ATOM 43186 SG CYS F 55 106.588 71.274 211.799 1.00282.78 S ATOM 43319 SG CYS F 72 108.080 74.392 213.206 1.00292.75 S ATOM 42893 SG CYS F 16 94.031 66.730 229.199 1.00296.46 S ATOM 42908 SG CYS F 19 93.580 63.086 229.977 1.00301.84 S ATOM 47441 SG CYS S 5 86.019 129.997 51.719 1.00244.24 S ATOM 47462 SG CYS S 8 87.351 127.766 49.144 1.00247.73 S ATOM 47600 SG CYS S 26 89.847 128.738 51.561 1.00247.83 S ATOM 47621 SG CYS S 29 89.148 131.443 49.836 1.00248.91 S ATOM 47786 SG CYS S 50 98.901 131.785 75.289 1.00262.30 S ATOM 47816 SG CYS S 55 100.384 135.149 76.132 1.00272.21 S ATOM 47949 SG CYS S 72 102.688 132.616 75.079 1.00265.36 S ATOM 47523 SG CYS S 16 88.223 137.641 59.452 1.00250.57 S ATOM 47538 SG CYS S 19 85.825 140.283 57.850 1.00253.85 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AMET E 474 " occ=0.41 ... (14 atoms not shown) pdb=" CE BMET E 474 " occ=0.59 residue: pdb=" N AMET R 474 " occ=0.41 ... (14 atoms not shown) pdb=" CE BMET R 474 " occ=0.59 Time building chain proxies: 25.12, per 1000 atoms: 0.46 Number of scatterers: 54547 At special positions: 0 Unit cell: (149.46, 200.34, 288.32, 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 26 29.99 S 416 16.00 P 116 15.00 Mg 3 11.99 O 10550 8.00 N 9243 7.00 C 34193 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.30 Conformation dependent library (CDL) restraints added in 8.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 701 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 16 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 19 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 26 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 5 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 29 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 55 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 72 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 50 " pdb=" ZN F1000 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 26 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 5 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 29 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 8 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" ND1 HIS F 75 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 72 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 55 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 50 " pdb=" ZN F1002 " pdb="ZN ZN F1002 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 16 " pdb="ZN ZN F1002 " - pdb=" ND1 HIS F 33 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 19 " pdb=" ZN H 200 " pdb="ZN ZN H 200 " - pdb=" NE2 HIS H 83 " pdb="ZN ZN H 200 " - pdb=" SG CYS H 90 " pdb="ZN ZN H 200 " - pdb=" SG CYS H 74 " pdb="ZN ZN H 200 " - pdb=" SG CYS H 77 " pdb=" ZN H 201 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 120 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 130 " pdb="ZN ZN H 201 " - pdb=" SG CYS H 117 " pdb=" ZN K 600 " pdb="ZN ZN K 600 " - pdb=" SG CYS K 226 " pdb="ZN ZN K 600 " - pdb=" SG CYS K 210 " pdb="ZN ZN K 600 " - pdb=" ND1 HIS K 229 " pdb="ZN ZN K 600 " - pdb=" SG CYS K 207 " pdb=" ZN K 601 " pdb="ZN ZN K 601 " - pdb=" ND1 HIS K 264 " pdb="ZN ZN K 601 " - pdb=" NE2 HIS K 257 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 261 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 279 " pdb=" ZN K 602 " pdb="ZN ZN K 602 " - pdb=" ND1 HIS K 487 " pdb="ZN ZN K 602 " - pdb=" SG CYS K 452 " pdb="ZN ZN K 602 " - pdb=" SG CYS K 484 " pdb=" ZN N1001 " pdb="ZN ZN N1001 " - pdb=" ND1 HIS N 295 " pdb="ZN ZN N1001 " - pdb=" SG CYS N 310 " pdb="ZN ZN N1001 " - pdb=" SG CYS N 301 " pdb="ZN ZN N1001 " - pdb=" SG CYS N 306 " pdb=" ZN N1002 " pdb="ZN ZN N1002 " - pdb=" ND1 HIS N 642 " pdb="ZN ZN N1002 " - pdb=" SG CYS N 487 " pdb="ZN ZN N1002 " - pdb=" SG CYS N 646 " pdb="ZN ZN N1002 " - pdb=" SG CYS N 645 " pdb=" ZN R 701 " pdb="ZN ZN R 701 " - pdb=" NE2 HIS R 33 " pdb="ZN ZN R 701 " - pdb=" ND1 HIS R 39 " pdb="ZN ZN R 701 " - pdb=" SG CYS R 16 " pdb="ZN ZN R 701 " - pdb=" SG CYS R 19 " pdb=" ZN R 702 " pdb="ZN ZN R 702 " - pdb=" SG CYS R 26 " pdb="ZN ZN R 702 " - pdb=" SG CYS R 8 " pdb="ZN ZN R 702 " - pdb=" SG CYS R 29 " pdb="ZN ZN R 702 " - pdb=" SG CYS R 5 " pdb=" ZN R 703 " pdb="ZN ZN R 703 " - pdb=" ND1 HIS R 75 " pdb="ZN ZN R 703 " - pdb=" SG CYS R 55 " pdb="ZN ZN R 703 " - pdb=" SG CYS R 50 " pdb="ZN ZN R 703 " - pdb=" SG CYS R 72 " pdb=" ZN S1000 " pdb="ZN ZN S1000 " - pdb=" SG CYS S 26 " pdb="ZN ZN S1000 " - pdb=" SG CYS S 8 " pdb="ZN ZN S1000 " - pdb=" SG CYS S 29 " pdb="ZN ZN S1000 " - pdb=" SG CYS S 5 " pdb=" ZN S1001 " pdb="ZN ZN S1001 " - pdb=" ND1 HIS S 75 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 55 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 72 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 50 " pdb=" ZN S1002 " pdb="ZN ZN S1002 " - pdb=" ND1 HIS S 39 " pdb="ZN ZN S1002 " - pdb=" ND1 HIS S 33 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 19 " pdb="ZN ZN S1002 " - pdb=" SG CYS S 16 " pdb=" ZN U 200 " pdb="ZN ZN U 200 " - pdb=" NE2 HIS U 83 " pdb="ZN ZN U 200 " - pdb=" SG CYS U 74 " pdb="ZN ZN U 200 " - pdb=" SG CYS U 90 " pdb="ZN ZN U 200 " - pdb=" SG CYS U 77 " pdb=" ZN U 201 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 120 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 130 " pdb="ZN ZN U 201 " - pdb=" SG CYS U 117 " pdb=" ZN X 600 " pdb="ZN ZN X 600 " - pdb=" SG CYS X 210 " pdb="ZN ZN X 600 " - pdb=" NE2 HIS X 229 " pdb="ZN ZN X 600 " - pdb=" SG CYS X 226 " pdb="ZN ZN X 600 " - pdb=" SG CYS X 207 " pdb=" ZN X 601 " pdb="ZN ZN X 601 " - pdb=" NE2 HIS X 257 " pdb="ZN ZN X 601 " - pdb=" NE2 HIS X 264 " pdb="ZN ZN X 601 " - pdb=" SG CYS X 261 " pdb="ZN ZN X 601 " - pdb=" SG CYS X 279 " pdb=" ZN X 602 " pdb="ZN ZN X 602 " - pdb=" SG CYS X 484 " pdb="ZN ZN X 602 " - pdb=" SG CYS X 452 " pdb="ZN ZN X 602 " - pdb=" NE2 HIS X 487 " Number of angles added : 71 13220 Ramachandran restraints generated. 6610 Oldfield, 0 Emsley, 6610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12620 Finding SS restraints... Secondary structure from input PDB file: 235 helices and 76 sheets defined 39.6% alpha, 11.8% beta 42 base pairs and 81 stacking pairs defined. Time for finding SS restraints: 14.29 Creating SS restraints... Processing helix chain 'A' and resid 6 through 13 removed outlier: 3.863A pdb=" N CYS A 12 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 76 through 91 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.548A pdb=" N ASN A 158 " --> pdb=" O ASP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 178 through 199 Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.987A pdb=" N ASN A 209 " --> pdb=" O THR A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 248 Proline residue: A 243 - end of helix removed outlier: 4.059A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 254 removed outlier: 3.636A pdb=" N THR A 252 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 288 removed outlier: 3.892A pdb=" N ARG A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS A 288 " --> pdb=" O ASP A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.880A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.657A pdb=" N SER A 325 " --> pdb=" O PRO A 322 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 322 through 326' Processing helix chain 'A' and resid 367 through 376 Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.611A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 455 through 459 removed outlier: 3.781A pdb=" N TYR A 458 " --> pdb=" O TYR A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 479 removed outlier: 4.038A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.702A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 518 removed outlier: 4.085A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 Processing helix chain 'A' and resid 561 through 580 removed outlier: 3.628A pdb=" N THR A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 Processing helix chain 'A' and resid 621 through 626 removed outlier: 3.604A pdb=" N MET A 626 " --> pdb=" O CYS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 640 removed outlier: 3.503A pdb=" N ARG A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 663 Processing helix chain 'A' and resid 686 through 709 Processing helix chain 'A' and resid 717 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.514A pdb=" N PHE A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 799 removed outlier: 3.690A pdb=" N CYS A 799 " --> pdb=" O GLU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 855 through 867 removed outlier: 4.021A pdb=" N PHE A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 875 through 903 removed outlier: 3.535A pdb=" N ASP A 879 " --> pdb=" O GLN A 875 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 917 removed outlier: 3.687A pdb=" N TRP A 916 " --> pdb=" O SER A 913 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU A 917 " --> pdb=" O ARG A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 926 Processing helix chain 'B' and resid 9 through 28 Processing helix chain 'B' and resid 31 through 52 removed outlier: 3.664A pdb=" N LEU B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 96 Processing helix chain 'B' and resid 100 through 109 removed outlier: 3.737A pdb=" N ASN B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 21 through 25 Processing helix chain 'C' and resid 26 through 42 removed outlier: 3.690A pdb=" N LEU C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 61 removed outlier: 3.724A pdb=" N ALA C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 71 removed outlier: 3.842A pdb=" N LYS C 70 " --> pdb=" O VAL C 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 28 Processing helix chain 'D' and resid 33 through 82 removed outlier: 3.724A pdb=" N LEU D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS D 82 " --> pdb=" O ASP D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 99 removed outlier: 4.324A pdb=" N GLN D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 135 through 141 Processing helix chain 'D' and resid 176 through 180 Processing helix chain 'E' and resid 26 through 37 Processing helix chain 'E' and resid 59 through 63 removed outlier: 3.926A pdb=" N LEU E 63 " --> pdb=" O VAL E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 111 removed outlier: 3.612A pdb=" N THR E 111 " --> pdb=" O ASN E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 125 removed outlier: 3.687A pdb=" N TYR E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 145 Processing helix chain 'E' and resid 259 through 264 removed outlier: 3.861A pdb=" N SER E 264 " --> pdb=" O ASP E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 274 Processing helix chain 'E' and resid 287 through 299 removed outlier: 3.950A pdb=" N ALA E 296 " --> pdb=" O ALA E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 325 removed outlier: 3.596A pdb=" N VAL E 314 " --> pdb=" O SER E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 328 No H-bonds generated for 'chain 'E' and resid 326 through 328' Processing helix chain 'E' and resid 361 through 363 No H-bonds generated for 'chain 'E' and resid 361 through 363' Processing helix chain 'E' and resid 380 through 390 Processing helix chain 'E' and resid 418 through 422 Processing helix chain 'E' and resid 424 through 431 Processing helix chain 'E' and resid 445 through 457 Processing helix chain 'E' and resid 490 through 503 Processing helix chain 'E' and resid 504 through 508 removed outlier: 3.995A pdb=" N LYS E 508 " --> pdb=" O ALA E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 516 through 526 Processing helix chain 'E' and resid 533 through 537 Processing helix chain 'E' and resid 557 through 566 Processing helix chain 'E' and resid 579 through 585 Processing helix chain 'G' and resid 95 through 110 Processing helix chain 'H' and resid 7 through 9 No H-bonds generated for 'chain 'H' and resid 7 through 9' Processing helix chain 'H' and resid 10 through 19 Processing helix chain 'H' and resid 22 through 33 Processing helix chain 'H' and resid 74 through 80 Processing helix chain 'H' and resid 106 through 114 removed outlier: 3.650A pdb=" N PHE H 110 " --> pdb=" O ASP H 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 23 Processing helix chain 'K' and resid 76 through 82 removed outlier: 3.724A pdb=" N HIS K 82 " --> pdb=" O GLU K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 155 removed outlier: 4.153A pdb=" N HIS K 148 " --> pdb=" O GLN K 145 " (cutoff:3.500A) Proline residue: K 151 - end of helix removed outlier: 3.748A pdb=" N TYR K 154 " --> pdb=" O PRO K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 158 through 175 removed outlier: 3.502A pdb=" N VAL K 162 " --> pdb=" O PRO K 158 " (cutoff:3.500A) Processing helix chain 'K' and resid 187 through 195 removed outlier: 3.942A pdb=" N GLU K 191 " --> pdb=" O ALA K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 245 through 248 removed outlier: 3.582A pdb=" N GLY K 248 " --> pdb=" O GLN K 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 245 through 248' Processing helix chain 'K' and resid 252 through 258 Processing helix chain 'K' and resid 270 through 287 removed outlier: 3.711A pdb=" N CYS K 285 " --> pdb=" O ALA K 281 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL K 287 " --> pdb=" O HIS K 283 " (cutoff:3.500A) Processing helix chain 'K' and resid 301 through 325 removed outlier: 3.963A pdb=" N ILE K 305 " --> pdb=" O ASP K 301 " (cutoff:3.500A) Processing helix chain 'K' and resid 369 through 374 removed outlier: 3.827A pdb=" N SER K 374 " --> pdb=" O TYR K 370 " (cutoff:3.500A) Processing helix chain 'K' and resid 433 through 437 removed outlier: 3.508A pdb=" N VAL K 437 " --> pdb=" O SER K 434 " (cutoff:3.500A) Processing helix chain 'K' and resid 485 through 504 Processing helix chain 'K' and resid 516 through 524 removed outlier: 3.699A pdb=" N TRP K 520 " --> pdb=" O THR K 516 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 12 Processing helix chain 'N' and resid 61 through 63 No H-bonds generated for 'chain 'N' and resid 61 through 63' Processing helix chain 'N' and resid 76 through 91 Processing helix chain 'N' and resid 123 through 133 Processing helix chain 'N' and resid 139 through 149 Processing helix chain 'N' and resid 153 through 159 removed outlier: 3.548A pdb=" N ASN N 158 " --> pdb=" O ASP N 155 " (cutoff:3.500A) Processing helix chain 'N' and resid 170 through 177 Processing helix chain 'N' and resid 178 through 199 Processing helix chain 'N' and resid 206 through 210 removed outlier: 3.988A pdb=" N ASN N 209 " --> pdb=" O THR N 206 " (cutoff:3.500A) Processing helix chain 'N' and resid 235 through 248 Proline residue: N 243 - end of helix removed outlier: 4.059A pdb=" N THR N 246 " --> pdb=" O MET N 242 " (cutoff:3.500A) Processing helix chain 'N' and resid 249 through 254 removed outlier: 3.635A pdb=" N THR N 252 " --> pdb=" O ARG N 249 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA N 253 " --> pdb=" O ALA N 250 " (cutoff:3.500A) Processing helix chain 'N' and resid 275 through 288 removed outlier: 3.892A pdb=" N ARG N 279 " --> pdb=" O PHE N 275 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS N 288 " --> pdb=" O ASP N 284 " (cutoff:3.500A) Processing helix chain 'N' and resid 297 through 301 Processing helix chain 'N' and resid 303 through 318 removed outlier: 3.881A pdb=" N PHE N 313 " --> pdb=" O HIS N 309 " (cutoff:3.500A) Processing helix chain 'N' and resid 322 through 326 removed outlier: 3.656A pdb=" N SER N 325 " --> pdb=" O PRO N 322 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE N 326 " --> pdb=" O PRO N 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 322 through 326' Processing helix chain 'N' and resid 367 through 376 Processing helix chain 'N' and resid 377 through 384 removed outlier: 4.611A pdb=" N HIS N 381 " --> pdb=" O ASP N 377 " (cutoff:3.500A) Processing helix chain 'N' and resid 416 through 426 Processing helix chain 'N' and resid 448 through 454 Processing helix chain 'N' and resid 455 through 459 removed outlier: 3.780A pdb=" N TYR N 458 " --> pdb=" O TYR N 455 " (cutoff:3.500A) Processing helix chain 'N' and resid 465 through 479 removed outlier: 4.038A pdb=" N GLU N 474 " --> pdb=" O LEU N 470 " (cutoff:3.500A) Processing helix chain 'N' and resid 489 through 493 removed outlier: 3.702A pdb=" N VAL N 493 " --> pdb=" O ALA N 490 " (cutoff:3.500A) Processing helix chain 'N' and resid 505 through 509 Processing helix chain 'N' and resid 511 through 518 removed outlier: 4.085A pdb=" N TYR N 515 " --> pdb=" O LYS N 511 " (cutoff:3.500A) Processing helix chain 'N' and resid 520 through 532 Processing helix chain 'N' and resid 561 through 580 removed outlier: 3.628A pdb=" N THR N 565 " --> pdb=" O SER N 561 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR N 567 " --> pdb=" O CYS N 563 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLN N 570 " --> pdb=" O MET N 566 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LYS N 574 " --> pdb=" O GLN N 570 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU N 575 " --> pdb=" O PHE N 571 " (cutoff:3.500A) Processing helix chain 'N' and resid 596 through 606 Processing helix chain 'N' and resid 621 through 626 removed outlier: 3.605A pdb=" N MET N 626 " --> pdb=" O CYS N 622 " (cutoff:3.500A) Processing helix chain 'N' and resid 627 through 640 removed outlier: 3.503A pdb=" N ARG N 631 " --> pdb=" O PRO N 627 " (cutoff:3.500A) Processing helix chain 'N' and resid 647 through 663 Processing helix chain 'N' and resid 686 through 709 Processing helix chain 'N' and resid 717 through 733 Processing helix chain 'N' and resid 738 through 753 Processing helix chain 'N' and resid 768 through 774 Processing helix chain 'N' and resid 778 through 791 removed outlier: 3.514A pdb=" N PHE N 782 " --> pdb=" O SER N 778 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN N 791 " --> pdb=" O TYR N 787 " (cutoff:3.500A) Processing helix chain 'N' and resid 795 through 799 removed outlier: 3.689A pdb=" N CYS N 799 " --> pdb=" O GLU N 796 " (cutoff:3.500A) Processing helix chain 'N' and resid 833 through 842 Processing helix chain 'N' and resid 856 through 867 Processing helix chain 'N' and resid 868 through 872 Processing helix chain 'N' and resid 875 through 903 removed outlier: 3.535A pdb=" N ASP N 879 " --> pdb=" O GLN N 875 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE N 881 " --> pdb=" O TYR N 877 " (cutoff:3.500A) Processing helix chain 'N' and resid 912 through 917 removed outlier: 3.687A pdb=" N TRP N 916 " --> pdb=" O SER N 913 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU N 917 " --> pdb=" O ARG N 914 " (cutoff:3.500A) Processing helix chain 'N' and resid 921 through 926 Processing helix chain 'O' and resid 9 through 29 Processing helix chain 'O' and resid 31 through 96 removed outlier: 3.752A pdb=" N ARG O 51 " --> pdb=" O SER O 47 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N GLN O 56 " --> pdb=" O ASP O 52 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG O 57 " --> pdb=" O ALA O 53 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG O 96 " --> pdb=" O PHE O 92 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 110 removed outlier: 4.283A pdb=" N ASN O 104 " --> pdb=" O ASN O 100 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA O 110 " --> pdb=" O ILE O 106 " (cutoff:3.500A) Processing helix chain 'O' and resid 118 through 125 removed outlier: 4.022A pdb=" N LEU O 122 " --> pdb=" O ASN O 118 " (cutoff:3.500A) Processing helix chain 'O' and resid 134 through 142 removed outlier: 3.588A pdb=" N TYR O 138 " --> pdb=" O ASP O 134 " (cutoff:3.500A) Processing helix chain 'O' and resid 168 through 172 removed outlier: 3.521A pdb=" N ILE O 172 " --> pdb=" O LEU O 169 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 180 Processing helix chain 'P' and resid 3 through 20 Processing helix chain 'P' and resid 21 through 25 Processing helix chain 'P' and resid 26 through 42 removed outlier: 3.562A pdb=" N ALA P 30 " --> pdb=" O SER P 26 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU P 41 " --> pdb=" O ASN P 37 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 61 removed outlier: 3.724A pdb=" N ALA P 48 " --> pdb=" O ASP P 44 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL P 58 " --> pdb=" O SER P 54 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU P 59 " --> pdb=" O LEU P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 66 through 71 removed outlier: 3.841A pdb=" N LYS P 70 " --> pdb=" O VAL P 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 28 Processing helix chain 'Q' and resid 32 through 41 removed outlier: 3.960A pdb=" N LEU Q 38 " --> pdb=" O VAL Q 34 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS Q 39 " --> pdb=" O LEU Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 81 removed outlier: 3.564A pdb=" N ARG Q 80 " --> pdb=" O SER Q 76 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 99 removed outlier: 3.848A pdb=" N GLN Q 88 " --> pdb=" O THR Q 84 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP Q 99 " --> pdb=" O LEU Q 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 100 through 112 removed outlier: 4.467A pdb=" N ILE Q 106 " --> pdb=" O ALA Q 102 " (cutoff:3.500A) Processing helix chain 'Q' and resid 134 through 141 removed outlier: 3.646A pdb=" N TYR Q 138 " --> pdb=" O ASP Q 134 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN Q 140 " --> pdb=" O ASN Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 176 through 180 removed outlier: 3.783A pdb=" N LEU Q 180 " --> pdb=" O SER Q 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 36 Processing helix chain 'R' and resid 59 through 61 No H-bonds generated for 'chain 'R' and resid 59 through 61' Processing helix chain 'R' and resid 102 through 112 removed outlier: 4.071A pdb=" N PHE R 106 " --> pdb=" O ASN R 102 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 125 removed outlier: 3.910A pdb=" N TYR R 120 " --> pdb=" O ASN R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 145 Processing helix chain 'R' and resid 265 through 274 Processing helix chain 'R' and resid 287 through 299 Processing helix chain 'R' and resid 310 through 325 removed outlier: 4.189A pdb=" N VAL R 314 " --> pdb=" O SER R 310 " (cutoff:3.500A) Processing helix chain 'R' and resid 326 through 328 No H-bonds generated for 'chain 'R' and resid 326 through 328' Processing helix chain 'R' and resid 380 through 391 Processing helix chain 'R' and resid 423 through 431 Processing helix chain 'R' and resid 445 through 456 Processing helix chain 'R' and resid 490 through 503 Processing helix chain 'R' and resid 504 through 507 Processing helix chain 'R' and resid 515 through 526 Processing helix chain 'R' and resid 557 through 566 Processing helix chain 'R' and resid 579 through 585 Processing helix chain 'T' and resid 95 through 110 Processing helix chain 'U' and resid 7 through 9 No H-bonds generated for 'chain 'U' and resid 7 through 9' Processing helix chain 'U' and resid 10 through 20 removed outlier: 3.823A pdb=" N ALA U 20 " --> pdb=" O PHE U 16 " (cutoff:3.500A) Processing helix chain 'U' and resid 22 through 33 Processing helix chain 'U' and resid 70 through 74 removed outlier: 3.813A pdb=" N CYS U 74 " --> pdb=" O GLY U 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 70 through 74' Processing helix chain 'U' and resid 74 through 80 Processing helix chain 'U' and resid 106 through 114 removed outlier: 3.647A pdb=" N PHE U 110 " --> pdb=" O ASP U 106 " (cutoff:3.500A) Processing helix chain 'X' and resid 77 through 82 Processing helix chain 'X' and resid 143 through 155 removed outlier: 4.110A pdb=" N HIS X 148 " --> pdb=" O GLN X 145 " (cutoff:3.500A) Proline residue: X 151 - end of helix removed outlier: 3.579A pdb=" N LYS X 155 " --> pdb=" O LEU X 152 " (cutoff:3.500A) Processing helix chain 'X' and resid 158 through 175 removed outlier: 4.330A pdb=" N ILE X 164 " --> pdb=" O ASN X 160 " (cutoff:3.500A) Processing helix chain 'X' and resid 187 through 195 removed outlier: 3.719A pdb=" N GLU X 191 " --> pdb=" O ALA X 187 " (cutoff:3.500A) Processing helix chain 'X' and resid 196 through 198 No H-bonds generated for 'chain 'X' and resid 196 through 198' Processing helix chain 'X' and resid 245 through 248 removed outlier: 3.564A pdb=" N GLY X 248 " --> pdb=" O GLN X 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 245 through 248' Processing helix chain 'X' and resid 252 through 258 Processing helix chain 'X' and resid 269 through 287 removed outlier: 3.757A pdb=" N ASP X 273 " --> pdb=" O VAL X 269 " (cutoff:3.500A) Processing helix chain 'X' and resid 302 through 325 Processing helix chain 'X' and resid 372 through 376 removed outlier: 3.612A pdb=" N ASP X 375 " --> pdb=" O THR X 372 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS X 376 " --> pdb=" O HIS X 373 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 372 through 376' Processing helix chain 'X' and resid 484 through 504 Processing helix chain 'X' and resid 516 through 524 removed outlier: 3.584A pdb=" N TRP X 520 " --> pdb=" O THR X 516 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR X 524 " --> pdb=" O TRP X 520 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 37 removed outlier: 3.506A pdb=" N SER F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR F 37 " --> pdb=" O HIS F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 61 No H-bonds generated for 'chain 'F' and resid 59 through 61' Processing helix chain 'F' and resid 102 through 111 removed outlier: 3.719A pdb=" N PHE F 106 " --> pdb=" O ASN F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 125 removed outlier: 4.072A pdb=" N TYR F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 148 Processing helix chain 'F' and resid 259 through 261 No H-bonds generated for 'chain 'F' and resid 259 through 261' Processing helix chain 'F' and resid 262 through 273 removed outlier: 4.467A pdb=" N ASN F 268 " --> pdb=" O SER F 264 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS F 271 " --> pdb=" O ALA F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 299 removed outlier: 3.611A pdb=" N ALA F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 322 removed outlier: 5.149A pdb=" N LYS F 320 " --> pdb=" O ALA F 316 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA F 321 " --> pdb=" O LEU F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 363 No H-bonds generated for 'chain 'F' and resid 361 through 363' Processing helix chain 'F' and resid 380 through 391 Processing helix chain 'F' and resid 418 through 422 Processing helix chain 'F' and resid 423 through 432 Processing helix chain 'F' and resid 445 through 449 Processing helix chain 'F' and resid 451 through 455 removed outlier: 3.606A pdb=" N ALA F 454 " --> pdb=" O THR F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 494 Processing helix chain 'F' and resid 515 through 525 removed outlier: 3.811A pdb=" N ILE F 525 " --> pdb=" O VAL F 521 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 536 Processing helix chain 'F' and resid 557 through 566 Processing helix chain 'F' and resid 580 through 585 removed outlier: 4.021A pdb=" N LYS F 584 " --> pdb=" O ASP F 580 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU F 585 " --> pdb=" O LEU F 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 580 through 585' Processing helix chain 'S' and resid 26 through 37 removed outlier: 3.665A pdb=" N THR S 37 " --> pdb=" O HIS S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 112 Processing helix chain 'S' and resid 116 through 125 Processing helix chain 'S' and resid 127 through 149 removed outlier: 3.680A pdb=" N TYR S 149 " --> pdb=" O PHE S 145 " (cutoff:3.500A) Processing helix chain 'S' and resid 259 through 261 No H-bonds generated for 'chain 'S' and resid 259 through 261' Processing helix chain 'S' and resid 262 through 275 removed outlier: 4.066A pdb=" N ALA S 267 " --> pdb=" O SER S 263 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASN S 268 " --> pdb=" O SER S 264 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS S 271 " --> pdb=" O ALA S 267 " (cutoff:3.500A) Processing helix chain 'S' and resid 289 through 299 Processing helix chain 'S' and resid 310 through 319 Processing helix chain 'S' and resid 361 through 363 No H-bonds generated for 'chain 'S' and resid 361 through 363' Processing helix chain 'S' and resid 380 through 391 Processing helix chain 'S' and resid 418 through 422 Processing helix chain 'S' and resid 423 through 432 Processing helix chain 'S' and resid 445 through 449 Processing helix chain 'S' and resid 489 through 494 Processing helix chain 'S' and resid 515 through 525 removed outlier: 3.682A pdb=" N ILE S 525 " --> pdb=" O VAL S 521 " (cutoff:3.500A) Processing helix chain 'S' and resid 532 through 537 removed outlier: 3.817A pdb=" N GLN S 537 " --> pdb=" O VAL S 533 " (cutoff:3.500A) Processing helix chain 'S' and resid 557 through 566 Processing helix chain 'S' and resid 580 through 584 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 38 Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 59 removed outlier: 5.191A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 removed outlier: 7.233A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.665A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 334 through 335 Processing sheet with id=AA6, first strand: chain 'A' and resid 387 through 390 removed outlier: 6.815A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 397 through 400 removed outlier: 6.565A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA9, first strand: chain 'A' and resid 540 through 544 Processing sheet with id=AB1, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AB2, first strand: chain 'A' and resid 816 through 822 Processing sheet with id=AB3, first strand: chain 'D' and resid 128 through 132 removed outlier: 3.682A pdb=" N GLN D 158 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AB5, first strand: chain 'E' and resid 15 through 16 Processing sheet with id=AB6, first strand: chain 'E' and resid 64 through 66 removed outlier: 3.572A pdb=" N GLY E 66 " --> pdb=" O SER E 69 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 156 through 159 removed outlier: 3.620A pdb=" N GLU E 156 " --> pdb=" O HIS E 164 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLU E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N GLY E 184 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLU E 197 " --> pdb=" O PHE E 182 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE E 182 " --> pdb=" O GLU E 197 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 347 through 348 removed outlier: 7.442A pdb=" N CYS E 330 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N SER E 331 " --> pdb=" O PHE E 357 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N THR E 359 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA E 308 " --> pdb=" O CYS E 358 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR E 367 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ALA E 393 " --> pdb=" O THR E 367 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASP E 369 " --> pdb=" O ALA E 393 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER E 278 " --> pdb=" O TYR E 398 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N GLY E 400 " --> pdb=" O SER E 278 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LEU E 280 " --> pdb=" O GLY E 400 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 530 through 532 removed outlier: 6.296A pdb=" N PHE E 511 " --> pdb=" O GLN E 531 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASP E 542 " --> pdb=" O LYS E 569 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 480 through 481 Processing sheet with id=AC2, first strand: chain 'G' and resid 67 through 68 removed outlier: 3.549A pdb=" N THR G 67 " --> pdb=" O ALA G 54 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA G 15 " --> pdb=" O ARG G 55 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ALA G 16 " --> pdb=" O ASP G 26 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASP G 26 " --> pdb=" O ALA G 16 " (cutoff:3.500A) removed outlier: 10.639A pdb=" N ASN G 27 " --> pdb=" O SER G 46 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N SER G 46 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU G 29 " --> pdb=" O LEU G 44 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU G 44 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR G 31 " --> pdb=" O LEU G 42 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY G 38 " --> pdb=" O THR G 35 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE G 75 " --> pdb=" O LYS G 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 65 through 69 Processing sheet with id=AC4, first strand: chain 'K' and resid 34 through 35 Processing sheet with id=AC5, first strand: chain 'K' and resid 116 through 118 removed outlier: 3.700A pdb=" N GLN K 108 " --> pdb=" O GLU K 92 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE K 87 " --> pdb=" O VAL K 184 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 95 through 96 Processing sheet with id=AC7, first strand: chain 'K' and resid 122 through 126 Processing sheet with id=AC8, first strand: chain 'K' and resid 216 through 218 removed outlier: 3.536A pdb=" N ALA K 225 " --> pdb=" O CYS K 216 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR K 223 " --> pdb=" O SER K 218 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 347 through 348 removed outlier: 3.685A pdb=" N ILE K 332 " --> pdb=" O LEU K 383 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 351 through 352 Processing sheet with id=AD2, first strand: chain 'K' and resid 399 through 401 Processing sheet with id=AD3, first strand: chain 'K' and resid 411 through 412 Processing sheet with id=AD4, first strand: chain 'K' and resid 439 through 440 Processing sheet with id=AD5, first strand: chain 'K' and resid 446 through 447 removed outlier: 6.385A pdb=" N TYR K 446 " --> pdb=" O ILE K 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'N' and resid 18 through 21 removed outlier: 4.407A pdb=" N ARG N 18 " --> pdb=" O LYS N 59 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N SER N 68 " --> pdb=" O GLU N 58 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 31 through 38 Processing sheet with id=AD8, first strand: chain 'N' and resid 223 through 224 removed outlier: 7.233A pdb=" N VAL N 233 " --> pdb=" O ILE N 201 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLY N 203 " --> pdb=" O VAL N 233 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'N' and resid 353 through 355 removed outlier: 6.665A pdb=" N LEU N 329 " --> pdb=" O THR N 344 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 334 through 335 Processing sheet with id=AE2, first strand: chain 'N' and resid 387 through 390 removed outlier: 6.864A pdb=" N ILE O 185 " --> pdb=" O VAL O 159 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N VAL O 159 " --> pdb=" O ILE O 185 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N THR O 187 " --> pdb=" O GLN O 157 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU O 153 " --> pdb=" O ALA O 191 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'N' and resid 397 through 400 removed outlier: 6.564A pdb=" N SER N 397 " --> pdb=" O VAL N 675 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N VAL N 675 " --> pdb=" O SER N 397 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA N 399 " --> pdb=" O LEU N 673 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 414 through 415 Processing sheet with id=AE5, first strand: chain 'N' and resid 540 through 544 Processing sheet with id=AE6, first strand: chain 'N' and resid 755 through 758 Processing sheet with id=AE7, first strand: chain 'N' and resid 816 through 822 Processing sheet with id=AE8, first strand: chain 'Q' and resid 115 through 116 removed outlier: 3.785A pdb=" N VAL Q 115 " --> pdb=" O VAL Q 131 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL Q 130 " --> pdb=" O VAL Q 186 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'R' and resid 3 through 4 Processing sheet with id=AF1, first strand: chain 'R' and resid 15 through 16 Processing sheet with id=AF2, first strand: chain 'R' and resid 63 through 66 Processing sheet with id=AF3, first strand: chain 'R' and resid 84 through 85 Processing sheet with id=AF4, first strand: chain 'R' and resid 193 through 198 removed outlier: 5.830A pdb=" N GLN R 194 " --> pdb=" O ARG R 186 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ARG R 186 " --> pdb=" O GLN R 194 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLY R 196 " --> pdb=" O GLY R 184 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ASP R 223 " --> pdb=" O VAL R 154 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N HIS R 164 " --> pdb=" O ARG R 155 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N VAL R 157 " --> pdb=" O GLU R 162 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N GLU R 162 " --> pdb=" O VAL R 157 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'R' and resid 277 through 279 removed outlier: 6.767A pdb=" N SER R 278 " --> pdb=" O TYR R 398 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL R 305 " --> pdb=" O VAL R 372 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA R 308 " --> pdb=" O CYS R 358 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N SER R 331 " --> pdb=" O PHE R 357 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N THR R 359 " --> pdb=" O SER R 331 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N CYS R 330 " --> pdb=" O LYS R 347 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'R' and resid 440 through 441 removed outlier: 7.078A pdb=" N LYS R 462 " --> pdb=" O CYS R 441 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'R' and resid 530 through 531 removed outlier: 5.985A pdb=" N PHE R 511 " --> pdb=" O GLN R 531 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N CYS R 471 " --> pdb=" O THR R 588 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'R' and resid 480 through 483 removed outlier: 3.685A pdb=" N SER R 486 " --> pdb=" O ASP R 483 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'T' and resid 67 through 68 removed outlier: 3.549A pdb=" N THR T 67 " --> pdb=" O ALA T 54 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA T 15 " --> pdb=" O ARG T 55 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG T 10 " --> pdb=" O TYR T 32 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR T 32 " --> pdb=" O ARG T 10 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ALA T 16 " --> pdb=" O ASP T 26 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASP T 26 " --> pdb=" O ALA T 16 " (cutoff:3.500A) removed outlier: 10.717A pdb=" N ASN T 27 " --> pdb=" O SER T 46 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N SER T 46 " --> pdb=" O ASN T 27 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU T 29 " --> pdb=" O LEU T 44 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU T 44 " --> pdb=" O LEU T 29 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR T 31 " --> pdb=" O LEU T 42 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY T 38 " --> pdb=" O THR T 35 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE T 75 " --> pdb=" O LYS T 86 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'U' and resid 65 through 69 Processing sheet with id=AG2, first strand: chain 'X' and resid 53 through 54 removed outlier: 3.591A pdb=" N ARG X 53 " --> pdb=" O ASP X 126 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'X' and resid 117 through 118 removed outlier: 7.732A pdb=" N ASN X 104 " --> pdb=" O ALA X 96 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA X 96 " --> pdb=" O ASN X 104 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N CYS X 94 " --> pdb=" O PRO X 106 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP X 90 " --> pdb=" O GLY X 110 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'X' and resid 184 through 185 Processing sheet with id=AG5, first strand: chain 'X' and resid 216 through 218 removed outlier: 3.587A pdb=" N SER X 218 " --> pdb=" O THR X 223 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR X 223 " --> pdb=" O SER X 218 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'X' and resid 347 through 348 removed outlier: 6.328A pdb=" N VAL X 328 " --> pdb=" O VAL X 381 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'X' and resid 351 through 352 Processing sheet with id=AG8, first strand: chain 'X' and resid 398 through 401 removed outlier: 3.705A pdb=" N VAL X 398 " --> pdb=" O TRP X 509 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'X' and resid 418 through 421 Processing sheet with id=AH1, first strand: chain 'F' and resid 3 through 4 Processing sheet with id=AH2, first strand: chain 'F' and resid 70 through 72 removed outlier: 3.563A pdb=" N PHE F 81 " --> pdb=" O LEU F 65 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 84 through 85 removed outlier: 3.688A pdb=" N ALA F 85 " --> pdb=" O GLN F 88 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 154 through 156 removed outlier: 7.127A pdb=" N HIS F 164 " --> pdb=" O ARG F 155 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLN F 194 " --> pdb=" O ARG F 186 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ARG F 186 " --> pdb=" O GLN F 194 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY F 196 " --> pdb=" O GLY F 184 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 277 through 280 removed outlier: 6.230A pdb=" N VAL F 371 " --> pdb=" O VAL F 397 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE F 399 " --> pdb=" O VAL F 371 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N PHE F 373 " --> pdb=" O ILE F 399 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR F 307 " --> pdb=" O VAL F 372 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'F' and resid 472 through 473 removed outlier: 6.355A pdb=" N PHE F 472 " --> pdb=" O LEU F 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'F' and resid 511 through 512 removed outlier: 6.239A pdb=" N ILE F 512 " --> pdb=" O THR F 547 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N LEU F 573 " --> pdb=" O PHE F 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'S' and resid 3 through 4 Processing sheet with id=AH9, first strand: chain 'S' and resid 15 through 16 Processing sheet with id=AI1, first strand: chain 'S' and resid 70 through 71 Processing sheet with id=AI2, first strand: chain 'S' and resid 154 through 156 removed outlier: 3.565A pdb=" N ARG S 212 " --> pdb=" O THR S 199 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLN S 194 " --> pdb=" O ARG S 186 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG S 186 " --> pdb=" O GLN S 194 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY S 196 " --> pdb=" O GLY S 184 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'S' and resid 277 through 280 removed outlier: 6.379A pdb=" N VAL S 371 " --> pdb=" O VAL S 397 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ILE S 399 " --> pdb=" O VAL S 371 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N PHE S 373 " --> pdb=" O ILE S 399 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE S 304 " --> pdb=" O VAL S 356 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N CYS S 358 " --> pdb=" O ILE S 304 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N TYR S 306 " --> pdb=" O CYS S 358 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'S' and resid 511 through 512 removed outlier: 5.977A pdb=" N ILE S 512 " --> pdb=" O THR S 547 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE S 575 " --> pdb=" O PHE S 546 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS S 574 " --> pdb=" O CYS S 471 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE S 472 " --> pdb=" O LEU S 590 " (cutoff:3.500A) 2041 hydrogen bonds defined for protein. 5670 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 100 hydrogen bonds 192 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 81 stacking parallelities Total time for adding SS restraints: 20.48 Time building geometry restraints manager: 19.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 8617 1.29 - 1.42: 15445 1.42 - 1.56: 31114 1.56 - 1.69: 239 1.69 - 1.83: 578 Bond restraints: 55993 Sorted by residual: bond pdb=" CA HIS A 810 " pdb=" C HIS A 810 " ideal model delta sigma weight residual 1.525 1.414 0.111 1.29e-02 6.01e+03 7.40e+01 bond pdb=" N HIS A 810 " pdb=" CA HIS A 810 " ideal model delta sigma weight residual 1.458 1.360 0.098 1.27e-02 6.20e+03 5.92e+01 bond pdb=" CA SER A 607 " pdb=" C SER A 607 " ideal model delta sigma weight residual 1.526 1.423 0.103 1.35e-02 5.49e+03 5.78e+01 bond pdb=" C1' G M 21 " pdb=" N9 G M 21 " ideal model delta sigma weight residual 1.475 1.371 0.104 1.50e-02 4.44e+03 4.83e+01 bond pdb=" C HIS A 810 " pdb=" O HIS A 810 " ideal model delta sigma weight residual 1.235 1.149 0.085 1.23e-02 6.61e+03 4.82e+01 ... (remaining 55988 not shown) Histogram of bond angle deviations from ideal: 70.96 - 88.49: 34 88.49 - 106.02: 2066 106.02 - 123.56: 72549 123.56 - 141.09: 1971 141.09 - 158.62: 16 Bond angle restraints: 76636 Sorted by residual: angle pdb=" N ASP T 25 " pdb=" CA ASP T 25 " pdb=" C ASP T 25 " ideal model delta sigma weight residual 110.97 157.46 -46.49 1.09e+00 8.42e-01 1.82e+03 angle pdb=" N GLY R 170 " pdb=" CA GLY R 170 " pdb=" C GLY R 170 " ideal model delta sigma weight residual 112.64 158.62 -45.98 1.21e+00 6.83e-01 1.44e+03 angle pdb=" N CYS X 208 " pdb=" CA CYS X 208 " pdb=" C CYS X 208 " ideal model delta sigma weight residual 111.11 152.10 -40.99 1.20e+00 6.94e-01 1.17e+03 angle pdb=" N TYR A 217 " pdb=" CA TYR A 217 " pdb=" C TYR A 217 " ideal model delta sigma weight residual 114.04 154.65 -40.61 1.24e+00 6.50e-01 1.07e+03 angle pdb=" N SER S 536 " pdb=" CA SER S 536 " pdb=" C SER S 536 " ideal model delta sigma weight residual 113.23 148.46 -35.23 1.24e+00 6.50e-01 8.07e+02 ... (remaining 76631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.95: 31873 33.95 - 67.89: 1629 67.89 - 101.84: 121 101.84 - 135.79: 2 135.79 - 169.73: 1 Dihedral angle restraints: 33626 sinusoidal: 14036 harmonic: 19590 Sorted by residual: dihedral pdb=" C MET N 855 " pdb=" N MET N 855 " pdb=" CA MET N 855 " pdb=" CB MET N 855 " ideal model delta harmonic sigma weight residual -122.60 -77.65 -44.95 0 2.50e+00 1.60e-01 3.23e+02 dihedral pdb=" C SER F 536 " pdb=" N SER F 536 " pdb=" CA SER F 536 " pdb=" CB SER F 536 " ideal model delta harmonic sigma weight residual -122.60 -79.39 -43.21 0 2.50e+00 1.60e-01 2.99e+02 dihedral pdb=" C LYS K 469 " pdb=" N LYS K 469 " pdb=" CA LYS K 469 " pdb=" CB LYS K 469 " ideal model delta harmonic sigma weight residual -122.60 -79.52 -43.08 0 2.50e+00 1.60e-01 2.97e+02 ... (remaining 33623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.352: 8649 0.352 - 0.704: 96 0.704 - 1.056: 11 1.056 - 1.409: 6 1.409 - 1.761: 8 Chirality restraints: 8770 Sorted by residual: chirality pdb=" CA LYS X 423 " pdb=" N LYS X 423 " pdb=" C LYS X 423 " pdb=" CB LYS X 423 " both_signs ideal model delta sigma weight residual False 2.51 0.75 1.76 2.00e-01 2.50e+01 7.75e+01 chirality pdb=" CA LEU R 147 " pdb=" N LEU R 147 " pdb=" C LEU R 147 " pdb=" CB LEU R 147 " both_signs ideal model delta sigma weight residual False 2.51 0.77 1.74 2.00e-01 2.50e+01 7.58e+01 chirality pdb=" CA CYS X 208 " pdb=" N CYS X 208 " pdb=" C CYS X 208 " pdb=" CB CYS X 208 " both_signs ideal model delta sigma weight residual False 2.51 0.84 1.67 2.00e-01 2.50e+01 6.97e+01 ... (remaining 8767 not shown) Planarity restraints: 9378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY N 808 " -0.094 5.00e-02 4.00e+02 1.39e-01 3.10e+01 pdb=" N PRO N 809 " 0.241 5.00e-02 4.00e+02 pdb=" CA PRO N 809 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO N 809 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 808 " 0.023 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C GLY A 808 " -0.079 2.00e-02 2.50e+03 pdb=" O GLY A 808 " 0.030 2.00e-02 2.50e+03 pdb=" N PRO A 809 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP O 182 " 0.073 5.00e-02 4.00e+02 1.09e-01 1.91e+01 pdb=" N PRO O 183 " -0.189 5.00e-02 4.00e+02 pdb=" CA PRO O 183 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO O 183 " 0.059 5.00e-02 4.00e+02 ... (remaining 9375 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.12: 41 2.12 - 2.81: 18176 2.81 - 3.51: 77754 3.51 - 4.20: 131738 4.20 - 4.90: 218617 Nonbonded interactions: 446326 Sorted by model distance: nonbonded pdb=" OE1 GLU N 83 " pdb=" O PHE N 219 " model vdw 1.423 3.040 nonbonded pdb=" OE1 GLN A 822 " pdb=" OG1 THR A 926 " model vdw 1.511 2.440 nonbonded pdb=" CE1 TYR A 606 " pdb=" CD2 LEU A 805 " model vdw 1.637 3.760 nonbonded pdb=" N GLY N 23 " pdb=" O GLY N 23 " model vdw 1.721 2.496 nonbonded pdb=" O ASP T 26 " pdb=" OD1 ASP T 26 " model vdw 1.730 3.040 ... (remaining 446321 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 'A' selection = chain 'N' } ncs_group { reference = (chain 'B' and ((resid 6 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 191)) selection = (chain 'D' and (resid 6 through 21 or (resid 22 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 34 or (resi \ d 35 through 37 and (name N or name CA or name C or name O or name CB )) or resi \ d 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 191)) selection = (chain 'O' and ((resid 6 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 191)) selection = (chain 'Q' and (resid 6 through 21 or (resid 22 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 34 or (resi \ d 35 through 37 and (name N or name CA or name C or name O or name CB )) or resi \ d 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 191)) } ncs_group { reference = chain 'C' selection = chain 'P' } ncs_group { reference = (chain 'E' and (resid 2 through 148 or (resid 149 and (name N or name CA or name \ C or name O or name CB )) or resid 150 through 226 or (resid 227 and (name N or \ name CA or name C or name O or name CB )) or resid 228 through 287 or (resid 28 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 289 through \ 441 or (resid 442 through 443 and (name N or name CA or name C or name O or name \ CB )) or resid 444 through 473 or resid 475 through 592 or resid 701 through 70 \ 3)) selection = (chain 'F' and (resid 2 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 93 or (resid 94 and (name N or name \ CA or name C or name O or name CB )) or resid 95 through 100 or (resid 101 thro \ ugh 102 and (name N or name CA or name C or name O or name CB )) or resid 103 th \ rough 336 or resid 340 through 391 or (resid 392 through 393 and (name N or name \ CA or name C or name O or name CB )) or resid 394 through 473 or resid 475 thro \ ugh 523 or (resid 524 and (name N or name CA or name C or name O or name CB )) o \ r resid 525 through 590 or (resid 591 and (name N or name CA or name C or name O \ or name CB )) or resid 592 or resid 1000 through 1002)) selection = (chain 'R' and (resid 2 through 148 or (resid 149 and (name N or name CA or name \ C or name O or name CB )) or resid 150 through 226 or (resid 227 and (name N or \ name CA or name C or name O or name CB )) or resid 228 through 287 or (resid 28 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 289 through \ 441 or (resid 442 through 443 and (name N or name CA or name C or name O or name \ CB )) or resid 444 through 473 or resid 475 through 592 or resid 701 through 70 \ 3)) selection = (chain 'S' and (resid 2 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 93 or (resid 94 and (name N or name \ CA or name C or name O or name CB )) or resid 95 through 100 or (resid 101 thro \ ugh 102 and (name N or name CA or name C or name O or name CB )) or resid 103 th \ rough 336 or resid 340 through 391 or (resid 392 through 393 and (name N or name \ CA or name C or name O or name CB )) or resid 394 through 473 or resid 475 thro \ ugh 523 or (resid 524 and (name N or name CA or name C or name O or name CB )) o \ r resid 525 through 590 or (resid 591 and (name N or name CA or name C or name O \ or name CB )) or resid 592 or resid 1000 through 1002)) } ncs_group { reference = chain 'G' selection = chain 'T' } ncs_group { reference = (chain 'H' and (resid 1 through 130 or resid 200 through 201)) selection = chain 'U' } ncs_group { reference = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'J' selection = chain 'M' } ncs_group { reference = (chain 'K' and (resid 3 through 524 or resid 601 through 602 or resid 604)) selection = (chain 'X' and (resid 3 through 454 or (resid 455 and (name N or name CA or name \ C or name O or name CB )) or resid 456 through 524 or resid 600 through 601 or \ resid 603)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.41 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: 3.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.320 Construct map_model_manager: 0.040 Extract box with map and model: 19.020 Check model and map are aligned: 0.620 Set scattering table: 0.380 Process input model: 137.680 Find NCS groups from input model: 2.850 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 167.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 : 0.008 0.111 55993 Z= 0.506 Angle : 1.560 46.492 76636 Z= 0.968 Chirality : 0.101 1.761 8770 Planarity : 0.006 0.139 9378 Dihedral : 18.689 169.732 21006 Min Nonbonded Distance : 1.423 Molprobity Statistics. All-atom Clashscore : 23.53 Ramachandran Plot: Outliers : 0.58 % Allowed : 10.49 % Favored : 88.93 % Rotamer: Outliers : 9.99 % Allowed : 17.51 % Favored : 72.51 % Cbeta Deviations : 2.46 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.41 % Twisted Proline : 1.07 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.09), residues: 6610 helix: -1.63 (0.09), residues: 2317 sheet: -2.48 (0.15), residues: 905 loop : -3.31 (0.09), residues: 3388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 182 HIS 0.016 0.002 HIS X 229 PHE 0.047 0.003 PHE A 881 TYR 0.038 0.002 TYR N 595 ARG 0.018 0.001 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13220 Ramachandran restraints generated. 6610 Oldfield, 0 Emsley, 6610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13220 Ramachandran restraints generated. 6610 Oldfield, 0 Emsley, 6610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 997 residues out of total 5781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 571 poor density : 426 time to evaluate : 4.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.8219 (p0) REVERT: A 63 ASP cc_start: 0.8569 (m-30) cc_final: 0.7673 (t0) REVERT: A 138 ASN cc_start: 0.8767 (p0) cc_final: 0.8546 (p0) REVERT: A 583 ARG cc_start: 0.9120 (OUTLIER) cc_final: 0.8763 (mpt180) REVERT: A 609 VAL cc_start: 0.8183 (OUTLIER) cc_final: 0.7956 (t) REVERT: A 721 ARG cc_start: 0.8786 (OUTLIER) cc_final: 0.8091 (mtp85) REVERT: A 847 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8924 (tt) REVERT: A 848 VAL cc_start: 0.9483 (OUTLIER) cc_final: 0.9237 (t) REVERT: A 899 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8291 (ttp) REVERT: A 904 SER cc_start: 0.7909 (OUTLIER) cc_final: 0.7367 (t) REVERT: B 69 GLN cc_start: 0.8412 (tm130) cc_final: 0.8109 (tm-30) REVERT: B 72 LYS cc_start: 0.8834 (mmmt) cc_final: 0.8594 (pttm) REVERT: B 174 MET cc_start: 0.8502 (tpt) cc_final: 0.8163 (tpt) REVERT: D 49 PHE cc_start: 0.6903 (t80) cc_final: 0.6615 (t80) REVERT: D 55 MET cc_start: 0.8169 (ppp) cc_final: 0.7934 (ppp) REVERT: D 56 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7720 (tt0) REVERT: D 69 GLN cc_start: 0.8492 (tm-30) cc_final: 0.7976 (tm-30) REVERT: E 167 TRP cc_start: 0.7220 (m-90) cc_final: 0.6963 (m-90) REVERT: G 66 TYR cc_start: 0.8050 (m-10) cc_final: 0.7425 (m-80) REVERT: G 92 LYS cc_start: 0.7786 (ttmt) cc_final: 0.7428 (ttmm) REVERT: K 170 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8581 (mp) REVERT: K 241 MET cc_start: 0.9042 (mtt) cc_final: 0.8661 (mtt) REVERT: K 493 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8643 (mp) REVERT: N 103 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7526 (mtpp) REVERT: N 154 ASP cc_start: 0.8160 (t70) cc_final: 0.7809 (t0) REVERT: N 219 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.7641 (m-80) REVERT: N 624 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.8783 (mtt90) REVERT: N 714 LYS cc_start: 0.8968 (mmtm) cc_final: 0.8504 (mmtm) REVERT: N 729 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8032 (mt-10) REVERT: O 42 LEU cc_start: 0.4214 (OUTLIER) cc_final: 0.3929 (tt) REVERT: O 51 ARG cc_start: 0.3624 (OUTLIER) cc_final: 0.3142 (mmt180) REVERT: T 50 ASP cc_start: 0.6591 (OUTLIER) cc_final: 0.5520 (p0) REVERT: X 395 ASN cc_start: 0.7742 (OUTLIER) cc_final: 0.7469 (p0) REVERT: X 400 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7616 (tpp80) REVERT: X 457 LYS cc_start: 0.6995 (tptt) cc_final: 0.6534 (tptt) REVERT: F 233 MET cc_start: 0.4745 (ptp) cc_final: 0.4517 (ppp) REVERT: S 164 HIS cc_start: 0.3590 (OUTLIER) cc_final: 0.3015 (m90) REVERT: S 554 HIS cc_start: -0.0049 (OUTLIER) cc_final: -0.0604 (t-170) outliers start: 571 outliers final: 285 residues processed: 934 average time/residue: 0.5348 time to fit residues: 835.6570 Evaluate side-chains 639 residues out of total 5781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 332 time to evaluate : 4.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 102 PHE Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 721 ARG Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 889 ARG Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 50 ASP Chi-restraints excluded: chain G residue 55 ARG Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 74 ARG Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 62 ASN Chi-restraints excluded: chain H residue 64 ASP Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 130 CYS Chi-restraints excluded: chain H residue 131 ASP Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 188 HIS Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 221 SER Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 242 ILE Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain K residue 261 CYS Chi-restraints excluded: chain K residue 269 VAL Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain K residue 291 ASP Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain K residue 303 LEU Chi-restraints excluded: chain K residue 332 ILE Chi-restraints excluded: chain K residue 346 VAL Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 403 THR Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain K residue 428 THR Chi-restraints excluded: chain K residue 462 ASP Chi-restraints excluded: chain K residue 463 ILE Chi-restraints excluded: chain K residue 470 SER Chi-restraints excluded: chain K residue 475 THR Chi-restraints excluded: chain K residue 478 ASN Chi-restraints excluded: chain K residue 484 CYS Chi-restraints excluded: chain K residue 493 LEU Chi-restraints excluded: chain K residue 523 PHE Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 18 ARG Chi-restraints excluded: chain N residue 21 PRO Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 53 CYS Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 102 PHE Chi-restraints excluded: chain N residue 103 LYS Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain N residue 107 ASP Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain N residue 115 SER Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 160 LYS Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain N residue 219 PHE Chi-restraints excluded: chain N residue 226 THR Chi-restraints excluded: chain N residue 262 THR Chi-restraints excluded: chain N residue 277 GLU Chi-restraints excluded: chain N residue 293 THR Chi-restraints excluded: chain N residue 295 HIS Chi-restraints excluded: chain N residue 299 VAL Chi-restraints excluded: chain N residue 325 SER Chi-restraints excluded: chain N residue 335 VAL Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 496 ASN Chi-restraints excluded: chain N residue 504 PHE Chi-restraints excluded: chain N residue 621 LYS Chi-restraints excluded: chain N residue 624 ARG Chi-restraints excluded: chain N residue 644 THR Chi-restraints excluded: chain N residue 667 VAL Chi-restraints excluded: chain N residue 680 THR Chi-restraints excluded: chain N residue 686 THR Chi-restraints excluded: chain N residue 708 LEU Chi-restraints excluded: chain N residue 710 THR Chi-restraints excluded: chain N residue 715 ILE Chi-restraints excluded: chain N residue 718 LYS Chi-restraints excluded: chain N residue 729 GLU Chi-restraints excluded: chain N residue 737 VAL Chi-restraints excluded: chain N residue 740 ASP Chi-restraints excluded: chain N residue 744 GLU Chi-restraints excluded: chain N residue 807 LYS Chi-restraints excluded: chain N residue 820 VAL Chi-restraints excluded: chain N residue 835 SER Chi-restraints excluded: chain N residue 900 LEU Chi-restraints excluded: chain N residue 919 GLU Chi-restraints excluded: chain N residue 926 THR Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 51 ARG Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain P residue 4 SER Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain Q residue 50 ASP Chi-restraints excluded: chain Q residue 89 THR Chi-restraints excluded: chain Q residue 114 CYS Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 153 LEU Chi-restraints excluded: chain Q residue 159 VAL Chi-restraints excluded: chain R residue 7 LEU Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 116 ASN Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 288 LYS Chi-restraints excluded: chain R residue 383 ASP Chi-restraints excluded: chain R residue 413 THR Chi-restraints excluded: chain R residue 458 ASP Chi-restraints excluded: chain R residue 488 ILE Chi-restraints excluded: chain R residue 495 VAL Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 29 LEU Chi-restraints excluded: chain T residue 50 ASP Chi-restraints excluded: chain T residue 55 ARG Chi-restraints excluded: chain T residue 68 GLU Chi-restraints excluded: chain T residue 75 PHE Chi-restraints excluded: chain T residue 81 LYS Chi-restraints excluded: chain U residue 12 THR Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 47 THR Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 72 SER Chi-restraints excluded: chain U residue 90 CYS Chi-restraints excluded: chain U residue 97 VAL Chi-restraints excluded: chain U residue 102 THR Chi-restraints excluded: chain U residue 108 VAL Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 14 VAL Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain X residue 74 ILE Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain X residue 112 SER Chi-restraints excluded: chain X residue 113 THR Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 127 THR Chi-restraints excluded: chain X residue 182 VAL Chi-restraints excluded: chain X residue 193 THR Chi-restraints excluded: chain X residue 194 SER Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 207 CYS Chi-restraints excluded: chain X residue 212 ARG Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain X residue 223 THR Chi-restraints excluded: chain X residue 264 HIS Chi-restraints excluded: chain X residue 268 HIS Chi-restraints excluded: chain X residue 317 VAL Chi-restraints excluded: chain X residue 345 ASP Chi-restraints excluded: chain X residue 387 CYS Chi-restraints excluded: chain X residue 395 ASN Chi-restraints excluded: chain X residue 396 SER Chi-restraints excluded: chain X residue 398 VAL Chi-restraints excluded: chain X residue 400 ARG Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 407 SER Chi-restraints excluded: chain X residue 414 CYS Chi-restraints excluded: chain X residue 415 ASP Chi-restraints excluded: chain X residue 437 VAL Chi-restraints excluded: chain X residue 466 VAL Chi-restraints excluded: chain X residue 470 SER Chi-restraints excluded: chain X residue 476 ARG Chi-restraints excluded: chain X residue 503 SER Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 309 CYS Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 544 VAL Chi-restraints excluded: chain F residue 582 TYR Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 70 TYR Chi-restraints excluded: chain S residue 74 SER Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 157 VAL Chi-restraints excluded: chain S residue 164 HIS Chi-restraints excluded: chain S residue 183 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 232 VAL Chi-restraints excluded: chain S residue 241 VAL Chi-restraints excluded: chain S residue 250 THR Chi-restraints excluded: chain S residue 255 THR Chi-restraints excluded: chain S residue 286 THR Chi-restraints excluded: chain S residue 315 ASP Chi-restraints excluded: chain S residue 325 LEU Chi-restraints excluded: chain S residue 333 ILE Chi-restraints excluded: chain S residue 350 SER Chi-restraints excluded: chain S residue 351 THR Chi-restraints excluded: chain S residue 383 ASP Chi-restraints excluded: chain S residue 387 VAL Chi-restraints excluded: chain S residue 392 ARG Chi-restraints excluded: chain S residue 449 VAL Chi-restraints excluded: chain S residue 455 LEU Chi-restraints excluded: chain S residue 495 VAL Chi-restraints excluded: chain S residue 549 THR Chi-restraints excluded: chain S residue 554 HIS Chi-restraints excluded: chain S residue 572 ILE Chi-restraints excluded: chain S residue 588 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 562 optimal weight: 6.9990 chunk 504 optimal weight: 0.5980 chunk 280 optimal weight: 4.9990 chunk 172 optimal weight: 20.0000 chunk 340 optimal weight: 0.7980 chunk 269 optimal weight: 8.9990 chunk 522 optimal weight: 5.9990 chunk 202 optimal weight: 0.6980 chunk 317 optimal weight: 0.8980 chunk 388 optimal weight: 20.0000 chunk 604 optimal weight: 6.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN E 164 HIS ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 548 GLN ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 116 ASN ** K 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 408 GLN R 86 ASN ** R 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 562 ASN ** T 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 98 GLN X 104 ASN X 228 HIS ** X 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 478 ASN ** X 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 275 GLN ** S 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 404 GLN ** S 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 55993 Z= 0.252 Angle : 0.710 13.478 76636 Z= 0.370 Chirality : 0.044 0.266 8770 Planarity : 0.005 0.083 9378 Dihedral : 13.794 165.146 9563 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.10 % Favored : 92.78 % Rotamer: Outliers : 6.37 % Allowed : 20.41 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.41 % Twisted Proline : 1.07 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.10), residues: 6610 helix: -0.27 (0.10), residues: 2350 sheet: -1.94 (0.16), residues: 889 loop : -2.67 (0.09), residues: 3371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 520 HIS 0.015 0.001 HIS X 487 PHE 0.028 0.002 PHE X 367 TYR 0.043 0.002 TYR X 465 ARG 0.009 0.001 ARG T 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13220 Ramachandran restraints generated. 6610 Oldfield, 0 Emsley, 6610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13220 Ramachandran restraints generated. 6610 Oldfield, 0 Emsley, 6610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 5781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 364 poor density : 357 time to evaluate : 4.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8517 (m-30) cc_final: 0.7700 (t0) REVERT: A 758 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8084 (tt) REVERT: A 848 VAL cc_start: 0.9344 (OUTLIER) cc_final: 0.9139 (t) REVERT: A 899 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8417 (ttp) REVERT: A 904 SER cc_start: 0.7978 (OUTLIER) cc_final: 0.7250 (t) REVERT: B 48 GLU cc_start: 0.4967 (mt-10) cc_final: 0.4554 (mm-30) REVERT: B 55 MET cc_start: 0.6247 (ptm) cc_final: 0.5892 (mmm) REVERT: B 69 GLN cc_start: 0.8427 (tm130) cc_final: 0.8167 (tm-30) REVERT: B 72 LYS cc_start: 0.8934 (mmmt) cc_final: 0.8676 (pttm) REVERT: B 90 MET cc_start: 0.9332 (tmm) cc_final: 0.8658 (tmm) REVERT: D 55 MET cc_start: 0.8223 (ppp) cc_final: 0.8004 (ppp) REVERT: D 60 GLU cc_start: 0.8331 (tp30) cc_final: 0.7991 (tp30) REVERT: D 64 ASP cc_start: 0.8338 (m-30) cc_final: 0.7953 (m-30) REVERT: D 69 GLN cc_start: 0.8398 (tm-30) cc_final: 0.7908 (tm-30) REVERT: E 164 HIS cc_start: 0.6087 (OUTLIER) cc_final: 0.5842 (m90) REVERT: E 167 TRP cc_start: 0.7198 (m-90) cc_final: 0.6948 (m-90) REVERT: E 240 LEU cc_start: 0.4214 (mp) cc_final: 0.3640 (tp) REVERT: G 66 TYR cc_start: 0.7962 (m-10) cc_final: 0.7375 (m-80) REVERT: G 106 LEU cc_start: 0.8625 (tt) cc_final: 0.8412 (tp) REVERT: K 170 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8495 (mp) REVERT: K 241 MET cc_start: 0.8828 (mtt) cc_final: 0.8560 (mtt) REVERT: N 63 ASP cc_start: 0.8384 (m-30) cc_final: 0.7925 (m-30) REVERT: N 154 ASP cc_start: 0.8188 (t70) cc_final: 0.7780 (t0) REVERT: N 219 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.7763 (m-80) REVERT: N 463 MET cc_start: 0.7935 (ttt) cc_final: 0.7723 (ttt) REVERT: N 714 LYS cc_start: 0.8968 (mmtm) cc_final: 0.8544 (mmtm) REVERT: O 55 MET cc_start: 0.7901 (mtp) cc_final: 0.7603 (ppp) REVERT: Q 155 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7646 (mm-30) REVERT: T 50 ASP cc_start: 0.6787 (OUTLIER) cc_final: 0.5792 (p0) REVERT: X 210 CYS cc_start: 0.6376 (OUTLIER) cc_final: 0.6079 (p) REVERT: X 457 LYS cc_start: 0.6965 (tptt) cc_final: 0.6444 (tptt) REVERT: F 233 MET cc_start: 0.4671 (ptp) cc_final: 0.4454 (ppp) REVERT: F 333 ILE cc_start: 0.1106 (OUTLIER) cc_final: -0.0871 (tp) REVERT: F 511 PHE cc_start: -0.0502 (OUTLIER) cc_final: -0.0825 (m-80) REVERT: S 70 TYR cc_start: 0.7975 (OUTLIER) cc_final: 0.7525 (p90) REVERT: S 315 ASP cc_start: 0.2817 (OUTLIER) cc_final: 0.2612 (p0) REVERT: S 554 HIS cc_start: 0.0053 (OUTLIER) cc_final: -0.0432 (t-170) outliers start: 364 outliers final: 236 residues processed: 692 average time/residue: 0.5080 time to fit residues: 605.0316 Evaluate side-chains 583 residues out of total 5781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 333 time to evaluate : 4.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 367 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 904 SER Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 148 SER Chi-restraints excluded: chain E residue 164 HIS Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 185 LEU Chi-restraints excluded: chain K residue 188 HIS Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 242 ILE Chi-restraints excluded: chain K residue 291 ASP Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain K residue 345 ASP Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 403 THR Chi-restraints excluded: chain K residue 428 THR Chi-restraints excluded: chain K residue 463 ILE Chi-restraints excluded: chain K residue 468 LEU Chi-restraints excluded: chain K residue 475 THR Chi-restraints excluded: chain K residue 478 ASN Chi-restraints excluded: chain K residue 484 CYS Chi-restraints excluded: chain K residue 489 ASN Chi-restraints excluded: chain K residue 523 PHE Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 160 LYS Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain N residue 219 PHE Chi-restraints excluded: chain N residue 226 THR Chi-restraints excluded: chain N residue 293 THR Chi-restraints excluded: chain N residue 295 HIS Chi-restraints excluded: chain N residue 335 VAL Chi-restraints excluded: chain N residue 361 LEU Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 468 GLN Chi-restraints excluded: chain N residue 496 ASN Chi-restraints excluded: chain N residue 561 SER Chi-restraints excluded: chain N residue 680 THR Chi-restraints excluded: chain N residue 715 ILE Chi-restraints excluded: chain N residue 731 LEU Chi-restraints excluded: chain N residue 737 VAL Chi-restraints excluded: chain N residue 740 ASP Chi-restraints excluded: chain N residue 744 GLU Chi-restraints excluded: chain N residue 807 LYS Chi-restraints excluded: chain N residue 820 VAL Chi-restraints excluded: chain N residue 835 SER Chi-restraints excluded: chain N residue 865 ASP Chi-restraints excluded: chain N residue 883 LEU Chi-restraints excluded: chain N residue 899 MET Chi-restraints excluded: chain N residue 900 LEU Chi-restraints excluded: chain N residue 907 LEU Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 60 GLU Chi-restraints excluded: chain O residue 87 MET Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 179 ASN Chi-restraints excluded: chain P residue 18 GLN Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain Q residue 15 PHE Chi-restraints excluded: chain Q residue 50 ASP Chi-restraints excluded: chain Q residue 64 ASP Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain Q residue 145 THR Chi-restraints excluded: chain Q residue 180 LEU Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 116 ASN Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 290 HIS Chi-restraints excluded: chain R residue 413 THR Chi-restraints excluded: chain R residue 458 ASP Chi-restraints excluded: chain R residue 488 ILE Chi-restraints excluded: chain R residue 495 VAL Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 42 LEU Chi-restraints excluded: chain T residue 50 ASP Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 75 PHE Chi-restraints excluded: chain T residue 92 LYS Chi-restraints excluded: chain T residue 102 VAL Chi-restraints excluded: chain U residue 3 ASN Chi-restraints excluded: chain U residue 12 THR Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 72 SER Chi-restraints excluded: chain U residue 97 VAL Chi-restraints excluded: chain U residue 102 THR Chi-restraints excluded: chain U residue 108 VAL Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain X residue 112 SER Chi-restraints excluded: chain X residue 113 THR Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 182 VAL Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 207 CYS Chi-restraints excluded: chain X residue 210 CYS Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain X residue 223 THR Chi-restraints excluded: chain X residue 236 VAL Chi-restraints excluded: chain X residue 264 HIS Chi-restraints excluded: chain X residue 268 HIS Chi-restraints excluded: chain X residue 269 VAL Chi-restraints excluded: chain X residue 279 CYS Chi-restraints excluded: chain X residue 317 VAL Chi-restraints excluded: chain X residue 398 VAL Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 415 ASP Chi-restraints excluded: chain X residue 450 SER Chi-restraints excluded: chain X residue 466 VAL Chi-restraints excluded: chain X residue 470 SER Chi-restraints excluded: chain X residue 518 ASN Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 198 TYR Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 344 ASP Chi-restraints excluded: chain F residue 429 MET Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 511 PHE Chi-restraints excluded: chain F residue 544 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain F residue 582 TYR Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 70 TYR Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 157 VAL Chi-restraints excluded: chain S residue 164 HIS Chi-restraints excluded: chain S residue 183 THR Chi-restraints excluded: chain S residue 188 THR Chi-restraints excluded: chain S residue 204 ASP Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 232 VAL Chi-restraints excluded: chain S residue 250 THR Chi-restraints excluded: chain S residue 270 GLN Chi-restraints excluded: chain S residue 315 ASP Chi-restraints excluded: chain S residue 382 TYR Chi-restraints excluded: chain S residue 383 ASP Chi-restraints excluded: chain S residue 392 ARG Chi-restraints excluded: chain S residue 486 SER Chi-restraints excluded: chain S residue 495 VAL Chi-restraints excluded: chain S residue 496 VAL Chi-restraints excluded: chain S residue 544 VAL Chi-restraints excluded: chain S residue 549 THR Chi-restraints excluded: chain S residue 554 HIS Chi-restraints excluded: chain S residue 572 ILE Chi-restraints excluded: chain S residue 575 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 336 optimal weight: 3.9990 chunk 187 optimal weight: 9.9990 chunk 503 optimal weight: 2.9990 chunk 411 optimal weight: 7.9990 chunk 166 optimal weight: 4.9990 chunk 605 optimal weight: 9.9990 chunk 654 optimal weight: 30.0000 chunk 539 optimal weight: 5.9990 chunk 600 optimal weight: 9.9990 chunk 206 optimal weight: 5.9990 chunk 486 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 725 HIS A 898 HIS ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN E 107 ASN ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 65 GLN ** K 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 256 HIS ** N 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 347 HIS ** N 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 599 HIS N 725 HIS N 790 ASN ** R 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 290 HIS ** T 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 82 HIS ** X 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 455 HIS X 478 ASN ** X 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 519 ASN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 275 GLN ** S 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.098 55993 Z= 0.533 Angle : 0.784 15.327 76636 Z= 0.411 Chirality : 0.048 0.307 8770 Planarity : 0.005 0.061 9378 Dihedral : 13.204 168.020 9303 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.09 % Favored : 90.84 % Rotamer: Outliers : 7.80 % Allowed : 21.04 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.41 % Twisted Proline : 1.07 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.10), residues: 6610 helix: -0.11 (0.11), residues: 2315 sheet: -1.83 (0.16), residues: 915 loop : -2.50 (0.10), residues: 3380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 154 HIS 0.015 0.002 HIS N 256 PHE 0.044 0.003 PHE A 429 TYR 0.034 0.002 TYR X 465 ARG 0.011 0.001 ARG N 279 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13220 Ramachandran restraints generated. 6610 Oldfield, 0 Emsley, 6610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13220 Ramachandran restraints generated. 6610 Oldfield, 0 Emsley, 6610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 5781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 446 poor density : 342 time to evaluate : 4.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8675 (m-30) cc_final: 0.7769 (t0) REVERT: A 545 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8325 (ttmt) REVERT: A 666 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.7611 (mtt) REVERT: A 758 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8318 (tt) REVERT: B 12 TYR cc_start: 0.6641 (t80) cc_final: 0.5944 (t80) REVERT: B 55 MET cc_start: 0.6507 (ptm) cc_final: 0.6195 (mmp) REVERT: B 69 GLN cc_start: 0.8456 (tm130) cc_final: 0.8112 (tm-30) REVERT: B 72 LYS cc_start: 0.8973 (mmmt) cc_final: 0.8713 (pttm) REVERT: B 174 MET cc_start: 0.8663 (tpt) cc_final: 0.8421 (tpt) REVERT: D 69 GLN cc_start: 0.8454 (tm-30) cc_final: 0.7970 (tm-30) REVERT: E 167 TRP cc_start: 0.7152 (m-90) cc_final: 0.6828 (m-90) REVERT: G 66 TYR cc_start: 0.7900 (m-10) cc_final: 0.7371 (m-80) REVERT: G 74 ARG cc_start: 0.8413 (tpt90) cc_final: 0.8076 (tpt90) REVERT: K 58 MET cc_start: 0.8744 (mtt) cc_final: 0.8494 (mtt) REVERT: K 490 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8176 (mm-30) REVERT: N 63 ASP cc_start: 0.8672 (m-30) cc_final: 0.8282 (m-30) REVERT: N 154 ASP cc_start: 0.8476 (t70) cc_final: 0.8071 (t0) REVERT: N 219 PHE cc_start: 0.9075 (OUTLIER) cc_final: 0.8021 (m-80) REVERT: N 372 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9254 (mp) REVERT: N 815 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8098 (mm110) REVERT: O 55 MET cc_start: 0.7886 (mtp) cc_final: 0.7419 (ppp) REVERT: Q 155 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7775 (mm-30) REVERT: T 12 MET cc_start: 0.6309 (tmm) cc_final: 0.6048 (tmm) REVERT: T 50 ASP cc_start: 0.6996 (OUTLIER) cc_final: 0.5735 (p0) REVERT: X 210 CYS cc_start: 0.6089 (OUTLIER) cc_final: 0.5778 (p) REVERT: X 390 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7721 (t0) REVERT: X 457 LYS cc_start: 0.7279 (tptt) cc_final: 0.6636 (tptt) REVERT: X 460 VAL cc_start: 0.7911 (OUTLIER) cc_final: 0.7605 (p) REVERT: F 332 ARG cc_start: 0.0888 (OUTLIER) cc_final: -0.1891 (mtm110) REVERT: F 333 ILE cc_start: 0.1198 (OUTLIER) cc_final: -0.0948 (tp) REVERT: F 511 PHE cc_start: -0.0645 (OUTLIER) cc_final: -0.1032 (m-80) REVERT: S 70 TYR cc_start: 0.7650 (OUTLIER) cc_final: 0.7035 (p90) outliers start: 446 outliers final: 324 residues processed: 749 average time/residue: 0.5085 time to fit residues: 657.7684 Evaluate side-chains 658 residues out of total 5781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 339 poor density : 319 time to evaluate : 4.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain A residue 929 THR Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain H residue 62 ASN Chi-restraints excluded: chain H residue 64 ASP Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 130 CYS Chi-restraints excluded: chain K residue 3 ASN Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 188 HIS Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 206 THR Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 242 ILE Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain K residue 291 ASP Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain K residue 345 ASP Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 403 THR Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain K residue 428 THR Chi-restraints excluded: chain K residue 462 ASP Chi-restraints excluded: chain K residue 463 ILE Chi-restraints excluded: chain K residue 468 LEU Chi-restraints excluded: chain K residue 475 THR Chi-restraints excluded: chain K residue 478 ASN Chi-restraints excluded: chain K residue 484 CYS Chi-restraints excluded: chain K residue 489 ASN Chi-restraints excluded: chain K residue 490 GLU Chi-restraints excluded: chain K residue 523 PHE Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 62 ASP Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 160 LYS Chi-restraints excluded: chain N residue 174 VAL Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain N residue 219 PHE Chi-restraints excluded: chain N residue 226 THR Chi-restraints excluded: chain N residue 293 THR Chi-restraints excluded: chain N residue 295 HIS Chi-restraints excluded: chain N residue 299 VAL Chi-restraints excluded: chain N residue 335 VAL Chi-restraints excluded: chain N residue 361 LEU Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain N residue 372 LEU Chi-restraints excluded: chain N residue 388 LEU Chi-restraints excluded: chain N residue 394 THR Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 468 GLN Chi-restraints excluded: chain N residue 482 CYS Chi-restraints excluded: chain N residue 496 ASN Chi-restraints excluded: chain N residue 518 SER Chi-restraints excluded: chain N residue 561 SER Chi-restraints excluded: chain N residue 565 THR Chi-restraints excluded: chain N residue 640 ARG Chi-restraints excluded: chain N residue 644 THR Chi-restraints excluded: chain N residue 667 VAL Chi-restraints excluded: chain N residue 686 THR Chi-restraints excluded: chain N residue 709 SER Chi-restraints excluded: chain N residue 710 THR Chi-restraints excluded: chain N residue 731 LEU Chi-restraints excluded: chain N residue 737 VAL Chi-restraints excluded: chain N residue 740 ASP Chi-restraints excluded: chain N residue 744 GLU Chi-restraints excluded: chain N residue 758 LEU Chi-restraints excluded: chain N residue 790 ASN Chi-restraints excluded: chain N residue 815 GLN Chi-restraints excluded: chain N residue 820 VAL Chi-restraints excluded: chain N residue 825 ASP Chi-restraints excluded: chain N residue 865 ASP Chi-restraints excluded: chain N residue 883 LEU Chi-restraints excluded: chain N residue 899 MET Chi-restraints excluded: chain N residue 900 LEU Chi-restraints excluded: chain N residue 907 LEU Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 60 GLU Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain O residue 90 MET Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain O residue 164 SER Chi-restraints excluded: chain O residue 170 SER Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 179 ASN Chi-restraints excluded: chain P residue 18 GLN Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain Q residue 9 LEU Chi-restraints excluded: chain Q residue 15 PHE Chi-restraints excluded: chain Q residue 64 ASP Chi-restraints excluded: chain Q residue 141 THR Chi-restraints excluded: chain Q residue 145 THR Chi-restraints excluded: chain Q residue 153 LEU Chi-restraints excluded: chain Q residue 180 LEU Chi-restraints excluded: chain R residue 7 LEU Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 116 ASN Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 223 ASP Chi-restraints excluded: chain R residue 228 THR Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 255 THR Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 288 LYS Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 413 THR Chi-restraints excluded: chain R residue 458 ASP Chi-restraints excluded: chain R residue 488 ILE Chi-restraints excluded: chain R residue 495 VAL Chi-restraints excluded: chain R residue 580 ASP Chi-restraints excluded: chain R residue 581 LEU Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 50 ASP Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 73 CYS Chi-restraints excluded: chain T residue 75 PHE Chi-restraints excluded: chain T residue 102 VAL Chi-restraints excluded: chain U residue 3 ASN Chi-restraints excluded: chain U residue 10 ASN Chi-restraints excluded: chain U residue 12 THR Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 47 THR Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 63 MET Chi-restraints excluded: chain U residue 97 VAL Chi-restraints excluded: chain U residue 102 THR Chi-restraints excluded: chain U residue 112 LEU Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 14 VAL Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 39 CYS Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain X residue 54 LEU Chi-restraints excluded: chain X residue 74 ILE Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain X residue 112 SER Chi-restraints excluded: chain X residue 113 THR Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 182 VAL Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 210 CYS Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain X residue 223 THR Chi-restraints excluded: chain X residue 236 VAL Chi-restraints excluded: chain X residue 264 HIS Chi-restraints excluded: chain X residue 268 HIS Chi-restraints excluded: chain X residue 269 VAL Chi-restraints excluded: chain X residue 279 CYS Chi-restraints excluded: chain X residue 317 VAL Chi-restraints excluded: chain X residue 345 ASP Chi-restraints excluded: chain X residue 390 ASP Chi-restraints excluded: chain X residue 396 SER Chi-restraints excluded: chain X residue 398 VAL Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 406 LEU Chi-restraints excluded: chain X residue 411 LEU Chi-restraints excluded: chain X residue 437 VAL Chi-restraints excluded: chain X residue 438 ASN Chi-restraints excluded: chain X residue 450 SER Chi-restraints excluded: chain X residue 460 VAL Chi-restraints excluded: chain X residue 466 VAL Chi-restraints excluded: chain X residue 478 ASN Chi-restraints excluded: chain X residue 518 ASN Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 30 CYS Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 275 GLN Chi-restraints excluded: chain F residue 309 CYS Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 344 ASP Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 429 MET Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 468 SER Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 511 PHE Chi-restraints excluded: chain F residue 544 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain F residue 582 TYR Chi-restraints excluded: chain S residue 69 SER Chi-restraints excluded: chain S residue 70 TYR Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 157 VAL Chi-restraints excluded: chain S residue 164 HIS Chi-restraints excluded: chain S residue 183 THR Chi-restraints excluded: chain S residue 188 THR Chi-restraints excluded: chain S residue 204 ASP Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 232 VAL Chi-restraints excluded: chain S residue 241 VAL Chi-restraints excluded: chain S residue 249 ILE Chi-restraints excluded: chain S residue 250 THR Chi-restraints excluded: chain S residue 255 THR Chi-restraints excluded: chain S residue 270 GLN Chi-restraints excluded: chain S residue 333 ILE Chi-restraints excluded: chain S residue 350 SER Chi-restraints excluded: chain S residue 382 TYR Chi-restraints excluded: chain S residue 383 ASP Chi-restraints excluded: chain S residue 392 ARG Chi-restraints excluded: chain S residue 416 THR Chi-restraints excluded: chain S residue 449 VAL Chi-restraints excluded: chain S residue 486 SER Chi-restraints excluded: chain S residue 495 VAL Chi-restraints excluded: chain S residue 496 VAL Chi-restraints excluded: chain S residue 544 VAL Chi-restraints excluded: chain S residue 549 THR Chi-restraints excluded: chain S residue 572 ILE Chi-restraints excluded: chain S residue 575 ILE Chi-restraints excluded: chain S residue 588 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 598 optimal weight: 20.0000 chunk 455 optimal weight: 20.0000 chunk 314 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 289 optimal weight: 2.9990 chunk 406 optimal weight: 6.9990 chunk 608 optimal weight: 20.0000 chunk 643 optimal weight: 0.1980 chunk 317 optimal weight: 3.9990 chunk 576 optimal weight: 20.0000 chunk 173 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 ASN E 107 ASN ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 ASN ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 209 ASN ** N 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 356 ASN ** N 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 790 ASN R 107 ASN ** R 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 82 HIS ** X 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 ASN F 220 ASN ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 531 GLN ** S 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 55993 Z= 0.267 Angle : 0.650 13.449 76636 Z= 0.338 Chirality : 0.043 0.242 8770 Planarity : 0.004 0.060 9378 Dihedral : 12.847 166.479 9259 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.12 % Favored : 92.81 % Rotamer: Outliers : 6.68 % Allowed : 22.56 % Favored : 70.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.41 % Twisted Proline : 1.07 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.10), residues: 6610 helix: 0.22 (0.11), residues: 2349 sheet: -1.64 (0.16), residues: 885 loop : -2.28 (0.10), residues: 3376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP Q 182 HIS 0.007 0.001 HIS P 36 PHE 0.017 0.002 PHE A 275 TYR 0.039 0.002 TYR X 465 ARG 0.009 0.001 ARG G 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13220 Ramachandran restraints generated. 6610 Oldfield, 0 Emsley, 6610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13220 Ramachandran restraints generated. 6610 Oldfield, 0 Emsley, 6610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 5781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 382 poor density : 334 time to evaluate : 4.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8621 (m-30) cc_final: 0.7797 (t0) REVERT: A 758 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8261 (tt) REVERT: B 55 MET cc_start: 0.6426 (ptm) cc_final: 0.6104 (mmp) REVERT: B 69 GLN cc_start: 0.8433 (tm130) cc_final: 0.8208 (tm-30) REVERT: B 72 LYS cc_start: 0.9020 (mmmt) cc_final: 0.8749 (pttm) REVERT: B 174 MET cc_start: 0.8579 (tpt) cc_final: 0.8314 (tpt) REVERT: D 60 GLU cc_start: 0.8064 (tp30) cc_final: 0.7602 (tp30) REVERT: D 64 ASP cc_start: 0.8309 (m-30) cc_final: 0.7998 (m-30) REVERT: D 69 GLN cc_start: 0.8429 (tm-30) cc_final: 0.7934 (tm-30) REVERT: D 127 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8310 (ptpp) REVERT: E 167 TRP cc_start: 0.7051 (m-90) cc_final: 0.6730 (m-90) REVERT: G 9 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7587 (mt) REVERT: G 66 TYR cc_start: 0.7914 (m-10) cc_final: 0.7374 (m-80) REVERT: N 63 ASP cc_start: 0.8554 (m-30) cc_final: 0.8021 (m-30) REVERT: N 154 ASP cc_start: 0.8396 (t70) cc_final: 0.8041 (t0) REVERT: N 219 PHE cc_start: 0.9104 (OUTLIER) cc_final: 0.8120 (m-80) REVERT: N 366 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.7820 (pp) REVERT: N 714 LYS cc_start: 0.8864 (mmtm) cc_final: 0.8388 (mmtm) REVERT: O 55 MET cc_start: 0.7920 (mtp) cc_final: 0.7486 (ppp) REVERT: O 90 MET cc_start: 0.8484 (tmm) cc_final: 0.8191 (tmm) REVERT: P 2 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7566 (tptm) REVERT: Q 155 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7792 (mm-30) REVERT: R 475 PHE cc_start: 0.8852 (p90) cc_final: 0.8435 (p90) REVERT: T 50 ASP cc_start: 0.6983 (OUTLIER) cc_final: 0.5879 (p0) REVERT: X 210 CYS cc_start: 0.6100 (OUTLIER) cc_final: 0.5782 (p) REVERT: X 390 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7632 (t0) REVERT: X 400 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7048 (tpt90) REVERT: X 457 LYS cc_start: 0.7251 (tptt) cc_final: 0.6574 (tptt) REVERT: X 460 VAL cc_start: 0.7855 (OUTLIER) cc_final: 0.7544 (p) REVERT: X 517 TYR cc_start: 0.7056 (OUTLIER) cc_final: 0.6265 (t80) REVERT: F 332 ARG cc_start: 0.0956 (OUTLIER) cc_final: -0.1697 (mtm110) REVERT: F 511 PHE cc_start: -0.0525 (OUTLIER) cc_final: -0.0759 (m-80) REVERT: S 70 TYR cc_start: 0.7509 (OUTLIER) cc_final: 0.6903 (p90) REVERT: S 347 LYS cc_start: 0.5962 (OUTLIER) cc_final: 0.5565 (pptt) REVERT: S 525 ILE cc_start: 0.1157 (OUTLIER) cc_final: 0.0894 (mt) REVERT: S 554 HIS cc_start: -0.0056 (OUTLIER) cc_final: -0.0545 (t-170) outliers start: 382 outliers final: 289 residues processed: 685 average time/residue: 0.5102 time to fit residues: 601.0246 Evaluate side-chains 623 residues out of total 5781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 316 time to evaluate : 4.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain H residue 40 ASN Chi-restraints excluded: chain H residue 62 ASN Chi-restraints excluded: chain H residue 64 ASP Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain H residue 131 ASP Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 188 HIS Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 242 ILE Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain K residue 291 ASP Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain K residue 345 ASP Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 403 THR Chi-restraints excluded: chain K residue 428 THR Chi-restraints excluded: chain K residue 463 ILE Chi-restraints excluded: chain K residue 468 LEU Chi-restraints excluded: chain K residue 475 THR Chi-restraints excluded: chain K residue 478 ASN Chi-restraints excluded: chain K residue 489 ASN Chi-restraints excluded: chain K residue 518 ASN Chi-restraints excluded: chain K residue 523 PHE Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 30 VAL Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 37 ILE Chi-restraints excluded: chain N residue 62 ASP Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 140 ASP Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 160 LYS Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain N residue 219 PHE Chi-restraints excluded: chain N residue 226 THR Chi-restraints excluded: chain N residue 269 ASP Chi-restraints excluded: chain N residue 293 THR Chi-restraints excluded: chain N residue 295 HIS Chi-restraints excluded: chain N residue 335 VAL Chi-restraints excluded: chain N residue 361 LEU Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain N residue 393 THR Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 468 GLN Chi-restraints excluded: chain N residue 496 ASN Chi-restraints excluded: chain N residue 518 SER Chi-restraints excluded: chain N residue 561 SER Chi-restraints excluded: chain N residue 640 ARG Chi-restraints excluded: chain N residue 644 THR Chi-restraints excluded: chain N residue 667 VAL Chi-restraints excluded: chain N residue 709 SER Chi-restraints excluded: chain N residue 731 LEU Chi-restraints excluded: chain N residue 737 VAL Chi-restraints excluded: chain N residue 740 ASP Chi-restraints excluded: chain N residue 744 GLU Chi-restraints excluded: chain N residue 758 LEU Chi-restraints excluded: chain N residue 820 VAL Chi-restraints excluded: chain N residue 825 ASP Chi-restraints excluded: chain N residue 865 ASP Chi-restraints excluded: chain N residue 883 LEU Chi-restraints excluded: chain N residue 900 LEU Chi-restraints excluded: chain N residue 907 LEU Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 42 LEU Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 60 GLU Chi-restraints excluded: chain O residue 87 MET Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain O residue 164 SER Chi-restraints excluded: chain O residue 170 SER Chi-restraints excluded: chain O residue 179 ASN Chi-restraints excluded: chain P residue 2 LYS Chi-restraints excluded: chain P residue 18 GLN Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain Q residue 15 PHE Chi-restraints excluded: chain Q residue 50 ASP Chi-restraints excluded: chain Q residue 64 ASP Chi-restraints excluded: chain Q residue 180 LEU Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 116 ASN Chi-restraints excluded: chain R residue 160 ASP Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 319 GLU Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 413 THR Chi-restraints excluded: chain R residue 458 ASP Chi-restraints excluded: chain R residue 481 THR Chi-restraints excluded: chain R residue 495 VAL Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 50 ASP Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 73 CYS Chi-restraints excluded: chain T residue 75 PHE Chi-restraints excluded: chain T residue 102 VAL Chi-restraints excluded: chain U residue 3 ASN Chi-restraints excluded: chain U residue 10 ASN Chi-restraints excluded: chain U residue 12 THR Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 47 THR Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 58 THR Chi-restraints excluded: chain U residue 63 MET Chi-restraints excluded: chain U residue 72 SER Chi-restraints excluded: chain U residue 97 VAL Chi-restraints excluded: chain U residue 102 THR Chi-restraints excluded: chain U residue 105 ASN Chi-restraints excluded: chain U residue 112 LEU Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain X residue 14 VAL Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain X residue 54 LEU Chi-restraints excluded: chain X residue 74 ILE Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain X residue 113 THR Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 127 THR Chi-restraints excluded: chain X residue 137 SER Chi-restraints excluded: chain X residue 182 VAL Chi-restraints excluded: chain X residue 206 THR Chi-restraints excluded: chain X residue 210 CYS Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain X residue 223 THR Chi-restraints excluded: chain X residue 236 VAL Chi-restraints excluded: chain X residue 264 HIS Chi-restraints excluded: chain X residue 268 HIS Chi-restraints excluded: chain X residue 269 VAL Chi-restraints excluded: chain X residue 279 CYS Chi-restraints excluded: chain X residue 317 VAL Chi-restraints excluded: chain X residue 390 ASP Chi-restraints excluded: chain X residue 396 SER Chi-restraints excluded: chain X residue 398 VAL Chi-restraints excluded: chain X residue 400 ARG Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 411 LEU Chi-restraints excluded: chain X residue 450 SER Chi-restraints excluded: chain X residue 460 VAL Chi-restraints excluded: chain X residue 466 VAL Chi-restraints excluded: chain X residue 470 SER Chi-restraints excluded: chain X residue 476 ARG Chi-restraints excluded: chain X residue 503 SER Chi-restraints excluded: chain X residue 517 TYR Chi-restraints excluded: chain X residue 518 ASN Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 30 CYS Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 176 LEU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 198 TYR Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 275 GLN Chi-restraints excluded: chain F residue 309 CYS Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 344 ASP Chi-restraints excluded: chain F residue 429 MET Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 511 PHE Chi-restraints excluded: chain F residue 544 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain F residue 582 TYR Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 70 TYR Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 157 VAL Chi-restraints excluded: chain S residue 159 SER Chi-restraints excluded: chain S residue 164 HIS Chi-restraints excluded: chain S residue 183 THR Chi-restraints excluded: chain S residue 188 THR Chi-restraints excluded: chain S residue 204 ASP Chi-restraints excluded: chain S residue 232 VAL Chi-restraints excluded: chain S residue 241 VAL Chi-restraints excluded: chain S residue 249 ILE Chi-restraints excluded: chain S residue 250 THR Chi-restraints excluded: chain S residue 255 THR Chi-restraints excluded: chain S residue 270 GLN Chi-restraints excluded: chain S residue 333 ILE Chi-restraints excluded: chain S residue 347 LYS Chi-restraints excluded: chain S residue 350 SER Chi-restraints excluded: chain S residue 382 TYR Chi-restraints excluded: chain S residue 383 ASP Chi-restraints excluded: chain S residue 392 ARG Chi-restraints excluded: chain S residue 449 VAL Chi-restraints excluded: chain S residue 486 SER Chi-restraints excluded: chain S residue 495 VAL Chi-restraints excluded: chain S residue 496 VAL Chi-restraints excluded: chain S residue 525 ILE Chi-restraints excluded: chain S residue 544 VAL Chi-restraints excluded: chain S residue 549 THR Chi-restraints excluded: chain S residue 554 HIS Chi-restraints excluded: chain S residue 572 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 536 optimal weight: 0.9990 chunk 365 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 479 optimal weight: 0.8980 chunk 265 optimal weight: 2.9990 chunk 549 optimal weight: 30.0000 chunk 444 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 328 optimal weight: 0.7980 chunk 577 optimal weight: 50.0000 chunk 162 optimal weight: 20.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN A 356 ASN A 886 GLN B 56 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN D 108 ASN ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 GLN ** K 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 492 GLN ** R 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 311 HIS ** R 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 82 HIS ** X 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 55993 Z= 0.199 Angle : 0.603 13.476 76636 Z= 0.313 Chirality : 0.042 0.234 8770 Planarity : 0.004 0.062 9378 Dihedral : 12.522 167.837 9240 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.10 % Favored : 92.84 % Rotamer: Outliers : 5.82 % Allowed : 23.38 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.41 % Twisted Proline : 1.07 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.10), residues: 6610 helix: 0.55 (0.11), residues: 2331 sheet: -1.49 (0.16), residues: 888 loop : -2.10 (0.10), residues: 3391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP Q 182 HIS 0.021 0.001 HIS X 487 PHE 0.013 0.001 PHE N 422 TYR 0.037 0.001 TYR B 71 ARG 0.009 0.000 ARG G 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13220 Ramachandran restraints generated. 6610 Oldfield, 0 Emsley, 6610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13220 Ramachandran restraints generated. 6610 Oldfield, 0 Emsley, 6610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 5781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 333 poor density : 342 time to evaluate : 4.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8650 (m-30) cc_final: 0.7865 (t0) REVERT: A 758 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8200 (tt) REVERT: B 55 MET cc_start: 0.6359 (ptm) cc_final: 0.6032 (mmp) REVERT: B 69 GLN cc_start: 0.8433 (tm130) cc_final: 0.8101 (tm-30) REVERT: B 72 LYS cc_start: 0.9052 (mmmt) cc_final: 0.8749 (pttm) REVERT: B 90 MET cc_start: 0.9355 (tmm) cc_final: 0.8802 (tmm) REVERT: B 174 MET cc_start: 0.8518 (tpt) cc_final: 0.8238 (tpt) REVERT: B 180 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7662 (mt) REVERT: D 12 TYR cc_start: 0.5453 (t80) cc_final: 0.5132 (t80) REVERT: D 55 MET cc_start: 0.8169 (ppp) cc_final: 0.7904 (ppp) REVERT: D 60 GLU cc_start: 0.8113 (tp30) cc_final: 0.7576 (tp30) REVERT: D 64 ASP cc_start: 0.8384 (m-30) cc_final: 0.8075 (m-30) REVERT: D 69 GLN cc_start: 0.8444 (tm-30) cc_final: 0.7935 (tm-30) REVERT: E 167 TRP cc_start: 0.7070 (m-90) cc_final: 0.6808 (m-90) REVERT: G 9 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.6585 (mt) REVERT: G 31 TYR cc_start: 0.7719 (OUTLIER) cc_final: 0.6836 (t80) REVERT: N 63 ASP cc_start: 0.8477 (m-30) cc_final: 0.7987 (m-30) REVERT: N 154 ASP cc_start: 0.8306 (t70) cc_final: 0.7898 (t0) REVERT: N 219 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8039 (m-80) REVERT: N 366 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.7818 (pp) REVERT: O 23 GLU cc_start: 0.6230 (mt-10) cc_final: 0.5534 (pp20) REVERT: O 55 MET cc_start: 0.7986 (mtp) cc_final: 0.7534 (ppp) REVERT: P 2 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7522 (tptm) REVERT: Q 65 GLN cc_start: 0.8224 (tm-30) cc_final: 0.8004 (tm-30) REVERT: Q 155 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7823 (mm-30) REVERT: R 233 MET cc_start: 0.6742 (tpp) cc_final: 0.6504 (tpt) REVERT: T 50 ASP cc_start: 0.6980 (OUTLIER) cc_final: 0.5929 (p0) REVERT: T 68 GLU cc_start: 0.7613 (pp20) cc_final: 0.6932 (pp20) REVERT: X 210 CYS cc_start: 0.6205 (OUTLIER) cc_final: 0.5865 (p) REVERT: X 349 LYS cc_start: 0.6567 (ttpt) cc_final: 0.6161 (ttpt) REVERT: X 390 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7570 (t0) REVERT: X 400 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6911 (tpt90) REVERT: X 460 VAL cc_start: 0.7658 (OUTLIER) cc_final: 0.7294 (p) REVERT: X 463 ILE cc_start: 0.4454 (mm) cc_final: 0.3830 (mm) REVERT: X 517 TYR cc_start: 0.7028 (OUTLIER) cc_final: 0.6210 (t80) REVERT: F 319 GLU cc_start: 0.0495 (OUTLIER) cc_final: 0.0120 (pt0) REVERT: F 333 ILE cc_start: 0.1278 (OUTLIER) cc_final: -0.0685 (tp) REVERT: F 511 PHE cc_start: -0.0546 (OUTLIER) cc_final: -0.0782 (m-80) REVERT: S 70 TYR cc_start: 0.7478 (OUTLIER) cc_final: 0.6809 (p90) REVERT: S 554 HIS cc_start: 0.0192 (OUTLIER) cc_final: -0.0301 (t-170) outliers start: 333 outliers final: 245 residues processed: 643 average time/residue: 0.5104 time to fit residues: 566.2309 Evaluate side-chains 583 residues out of total 5781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 320 time to evaluate : 4.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 31 TYR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain H residue 64 ASP Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 188 HIS Chi-restraints excluded: chain K residue 206 THR Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 242 ILE Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 403 THR Chi-restraints excluded: chain K residue 428 THR Chi-restraints excluded: chain K residue 463 ILE Chi-restraints excluded: chain K residue 468 LEU Chi-restraints excluded: chain K residue 475 THR Chi-restraints excluded: chain K residue 478 ASN Chi-restraints excluded: chain K residue 518 ASN Chi-restraints excluded: chain K residue 523 PHE Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 62 ASP Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 140 ASP Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain N residue 219 PHE Chi-restraints excluded: chain N residue 226 THR Chi-restraints excluded: chain N residue 295 HIS Chi-restraints excluded: chain N residue 299 VAL Chi-restraints excluded: chain N residue 361 LEU Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain N residue 372 LEU Chi-restraints excluded: chain N residue 393 THR Chi-restraints excluded: chain N residue 394 THR Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 468 GLN Chi-restraints excluded: chain N residue 482 CYS Chi-restraints excluded: chain N residue 518 SER Chi-restraints excluded: chain N residue 561 SER Chi-restraints excluded: chain N residue 640 ARG Chi-restraints excluded: chain N residue 644 THR Chi-restraints excluded: chain N residue 731 LEU Chi-restraints excluded: chain N residue 737 VAL Chi-restraints excluded: chain N residue 740 ASP Chi-restraints excluded: chain N residue 744 GLU Chi-restraints excluded: chain N residue 758 LEU Chi-restraints excluded: chain N residue 820 VAL Chi-restraints excluded: chain N residue 825 ASP Chi-restraints excluded: chain N residue 865 ASP Chi-restraints excluded: chain N residue 883 LEU Chi-restraints excluded: chain N residue 900 LEU Chi-restraints excluded: chain N residue 907 LEU Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 60 GLU Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain O residue 129 MET Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain P residue 2 LYS Chi-restraints excluded: chain P residue 18 GLN Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain P residue 53 VAL Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain Q residue 50 ASP Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 145 THR Chi-restraints excluded: chain Q residue 180 LEU Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 413 THR Chi-restraints excluded: chain R residue 458 ASP Chi-restraints excluded: chain R residue 481 THR Chi-restraints excluded: chain R residue 495 VAL Chi-restraints excluded: chain R residue 581 LEU Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 50 ASP Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 102 VAL Chi-restraints excluded: chain U residue 3 ASN Chi-restraints excluded: chain U residue 12 THR Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 22 ASP Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 58 THR Chi-restraints excluded: chain U residue 63 MET Chi-restraints excluded: chain U residue 72 SER Chi-restraints excluded: chain U residue 97 VAL Chi-restraints excluded: chain U residue 112 LEU Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 14 VAL Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain X residue 71 ASN Chi-restraints excluded: chain X residue 74 ILE Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain X residue 113 THR Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 127 THR Chi-restraints excluded: chain X residue 182 VAL Chi-restraints excluded: chain X residue 210 CYS Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain X residue 223 THR Chi-restraints excluded: chain X residue 264 HIS Chi-restraints excluded: chain X residue 268 HIS Chi-restraints excluded: chain X residue 269 VAL Chi-restraints excluded: chain X residue 279 CYS Chi-restraints excluded: chain X residue 317 VAL Chi-restraints excluded: chain X residue 345 ASP Chi-restraints excluded: chain X residue 390 ASP Chi-restraints excluded: chain X residue 396 SER Chi-restraints excluded: chain X residue 398 VAL Chi-restraints excluded: chain X residue 400 ARG Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 411 LEU Chi-restraints excluded: chain X residue 438 ASN Chi-restraints excluded: chain X residue 450 SER Chi-restraints excluded: chain X residue 460 VAL Chi-restraints excluded: chain X residue 466 VAL Chi-restraints excluded: chain X residue 470 SER Chi-restraints excluded: chain X residue 503 SER Chi-restraints excluded: chain X residue 517 TYR Chi-restraints excluded: chain X residue 518 ASN Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 30 CYS Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 275 GLN Chi-restraints excluded: chain F residue 309 CYS Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 395 HIS Chi-restraints excluded: chain F residue 429 MET Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 511 PHE Chi-restraints excluded: chain F residue 544 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain F residue 582 TYR Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 70 TYR Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 157 VAL Chi-restraints excluded: chain S residue 164 HIS Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain S residue 183 THR Chi-restraints excluded: chain S residue 188 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 232 VAL Chi-restraints excluded: chain S residue 241 VAL Chi-restraints excluded: chain S residue 249 ILE Chi-restraints excluded: chain S residue 250 THR Chi-restraints excluded: chain S residue 263 SER Chi-restraints excluded: chain S residue 270 GLN Chi-restraints excluded: chain S residue 333 ILE Chi-restraints excluded: chain S residue 350 SER Chi-restraints excluded: chain S residue 382 TYR Chi-restraints excluded: chain S residue 383 ASP Chi-restraints excluded: chain S residue 392 ARG Chi-restraints excluded: chain S residue 449 VAL Chi-restraints excluded: chain S residue 486 SER Chi-restraints excluded: chain S residue 495 VAL Chi-restraints excluded: chain S residue 544 VAL Chi-restraints excluded: chain S residue 549 THR Chi-restraints excluded: chain S residue 554 HIS Chi-restraints excluded: chain S residue 572 ILE Chi-restraints excluded: chain S residue 575 ILE Chi-restraints excluded: chain S residue 588 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 216 optimal weight: 9.9990 chunk 579 optimal weight: 0.8980 chunk 127 optimal weight: 7.9990 chunk 377 optimal weight: 0.9990 chunk 158 optimal weight: 10.0000 chunk 644 optimal weight: 8.9990 chunk 534 optimal weight: 0.8980 chunk 298 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 213 optimal weight: 8.9990 chunk 338 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 GLN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 283 HIS K 306 ASN ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 82 HIS ** X 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 55993 Z= 0.199 Angle : 0.596 17.005 76636 Z= 0.307 Chirality : 0.041 0.246 8770 Planarity : 0.004 0.062 9378 Dihedral : 12.337 168.395 9205 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.56 % Favored : 93.38 % Rotamer: Outliers : 5.88 % Allowed : 23.82 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.41 % Twisted Proline : 1.07 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.10), residues: 6610 helix: 0.67 (0.11), residues: 2332 sheet: -1.36 (0.17), residues: 884 loop : -2.01 (0.10), residues: 3394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP T 53 HIS 0.010 0.001 HIS X 487 PHE 0.013 0.001 PHE A 753 TYR 0.043 0.001 TYR B 71 ARG 0.011 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13220 Ramachandran restraints generated. 6610 Oldfield, 0 Emsley, 6610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13220 Ramachandran restraints generated. 6610 Oldfield, 0 Emsley, 6610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 5781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 336 poor density : 334 time to evaluate : 5.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8617 (m-30) cc_final: 0.7846 (t0) REVERT: A 545 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8308 (ttmt) REVERT: A 758 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8224 (tt) REVERT: B 55 MET cc_start: 0.6477 (ptm) cc_final: 0.6131 (mmp) REVERT: B 69 GLN cc_start: 0.8449 (tm130) cc_final: 0.8207 (tm-30) REVERT: B 72 LYS cc_start: 0.9056 (mmmt) cc_final: 0.8708 (pttm) REVERT: B 90 MET cc_start: 0.9362 (tmm) cc_final: 0.8796 (tmm) REVERT: B 96 ARG cc_start: 0.8521 (mtm110) cc_final: 0.8259 (ttm110) REVERT: B 174 MET cc_start: 0.8499 (tpt) cc_final: 0.8233 (tpt) REVERT: D 60 GLU cc_start: 0.8195 (tp30) cc_final: 0.7664 (tp30) REVERT: D 64 ASP cc_start: 0.8424 (m-30) cc_final: 0.8086 (m-30) REVERT: D 69 GLN cc_start: 0.8449 (tm-30) cc_final: 0.7935 (tm-30) REVERT: D 91 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8696 (tp) REVERT: E 167 TRP cc_start: 0.7075 (m-90) cc_final: 0.6834 (m-90) REVERT: G 9 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.6536 (mt) REVERT: G 31 TYR cc_start: 0.7706 (m-80) cc_final: 0.6850 (t80) REVERT: G 66 TYR cc_start: 0.7866 (m-10) cc_final: 0.7496 (m-10) REVERT: N 63 ASP cc_start: 0.8509 (m-30) cc_final: 0.8025 (m-30) REVERT: N 154 ASP cc_start: 0.8307 (t70) cc_final: 0.7847 (t0) REVERT: N 366 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.7850 (pp) REVERT: O 55 MET cc_start: 0.7887 (mtp) cc_final: 0.7547 (tmm) REVERT: Q 57 ARG cc_start: 0.8125 (ptm-80) cc_final: 0.7707 (ptp-170) REVERT: Q 65 GLN cc_start: 0.8233 (tm-30) cc_final: 0.7966 (tm-30) REVERT: R 233 MET cc_start: 0.6875 (tpp) cc_final: 0.6596 (tpp) REVERT: R 378 MET cc_start: 0.7265 (ttp) cc_final: 0.7013 (ptm) REVERT: R 475 PHE cc_start: 0.8866 (p90) cc_final: 0.8370 (p90) REVERT: T 50 ASP cc_start: 0.7047 (OUTLIER) cc_final: 0.6036 (p0) REVERT: X 210 CYS cc_start: 0.6268 (OUTLIER) cc_final: 0.5869 (p) REVERT: X 390 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7579 (t0) REVERT: X 400 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6886 (tpt90) REVERT: X 460 VAL cc_start: 0.7690 (OUTLIER) cc_final: 0.7377 (p) REVERT: X 463 ILE cc_start: 0.3500 (mm) cc_final: 0.3282 (mm) REVERT: X 517 TYR cc_start: 0.7054 (OUTLIER) cc_final: 0.6268 (t80) REVERT: F 319 GLU cc_start: 0.0490 (OUTLIER) cc_final: 0.0157 (pt0) REVERT: F 333 ILE cc_start: 0.1199 (OUTLIER) cc_final: -0.0744 (tp) REVERT: S 525 ILE cc_start: 0.1106 (OUTLIER) cc_final: 0.0806 (mt) REVERT: S 554 HIS cc_start: -0.0136 (OUTLIER) cc_final: -0.0592 (t-170) outliers start: 336 outliers final: 275 residues processed: 639 average time/residue: 0.5286 time to fit residues: 579.4290 Evaluate side-chains 611 residues out of total 5781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 321 time to evaluate : 4.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 579 ARG Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain H residue 64 ASP Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 130 CYS Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 16 THR Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 131 THR Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 185 LEU Chi-restraints excluded: chain K residue 188 HIS Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 242 ILE Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 403 THR Chi-restraints excluded: chain K residue 463 ILE Chi-restraints excluded: chain K residue 468 LEU Chi-restraints excluded: chain K residue 475 THR Chi-restraints excluded: chain K residue 478 ASN Chi-restraints excluded: chain K residue 518 ASN Chi-restraints excluded: chain K residue 523 PHE Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 140 ASP Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain N residue 226 THR Chi-restraints excluded: chain N residue 269 ASP Chi-restraints excluded: chain N residue 295 HIS Chi-restraints excluded: chain N residue 299 VAL Chi-restraints excluded: chain N residue 330 VAL Chi-restraints excluded: chain N residue 361 LEU Chi-restraints excluded: chain N residue 364 SER Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain N residue 372 LEU Chi-restraints excluded: chain N residue 393 THR Chi-restraints excluded: chain N residue 394 THR Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 468 GLN Chi-restraints excluded: chain N residue 482 CYS Chi-restraints excluded: chain N residue 518 SER Chi-restraints excluded: chain N residue 561 SER Chi-restraints excluded: chain N residue 640 ARG Chi-restraints excluded: chain N residue 644 THR Chi-restraints excluded: chain N residue 709 SER Chi-restraints excluded: chain N residue 731 LEU Chi-restraints excluded: chain N residue 737 VAL Chi-restraints excluded: chain N residue 740 ASP Chi-restraints excluded: chain N residue 758 LEU Chi-restraints excluded: chain N residue 820 VAL Chi-restraints excluded: chain N residue 825 ASP Chi-restraints excluded: chain N residue 865 ASP Chi-restraints excluded: chain N residue 883 LEU Chi-restraints excluded: chain N residue 899 MET Chi-restraints excluded: chain N residue 900 LEU Chi-restraints excluded: chain N residue 907 LEU Chi-restraints excluded: chain O residue 60 GLU Chi-restraints excluded: chain O residue 76 SER Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain O residue 164 SER Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain P residue 18 GLN Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain P residue 53 VAL Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain Q residue 15 PHE Chi-restraints excluded: chain Q residue 50 ASP Chi-restraints excluded: chain Q residue 145 THR Chi-restraints excluded: chain Q residue 180 LEU Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 223 ASP Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 319 GLU Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 413 THR Chi-restraints excluded: chain R residue 458 ASP Chi-restraints excluded: chain R residue 481 THR Chi-restraints excluded: chain R residue 488 ILE Chi-restraints excluded: chain R residue 495 VAL Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 50 ASP Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 73 CYS Chi-restraints excluded: chain T residue 102 VAL Chi-restraints excluded: chain U residue 3 ASN Chi-restraints excluded: chain U residue 10 ASN Chi-restraints excluded: chain U residue 12 THR Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 22 ASP Chi-restraints excluded: chain U residue 63 MET Chi-restraints excluded: chain U residue 97 VAL Chi-restraints excluded: chain U residue 102 THR Chi-restraints excluded: chain U residue 105 ASN Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 39 CYS Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain X residue 54 LEU Chi-restraints excluded: chain X residue 71 ASN Chi-restraints excluded: chain X residue 74 ILE Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain X residue 87 ILE Chi-restraints excluded: chain X residue 113 THR Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 127 THR Chi-restraints excluded: chain X residue 137 SER Chi-restraints excluded: chain X residue 182 VAL Chi-restraints excluded: chain X residue 210 CYS Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain X residue 223 THR Chi-restraints excluded: chain X residue 236 VAL Chi-restraints excluded: chain X residue 264 HIS Chi-restraints excluded: chain X residue 268 HIS Chi-restraints excluded: chain X residue 269 VAL Chi-restraints excluded: chain X residue 279 CYS Chi-restraints excluded: chain X residue 317 VAL Chi-restraints excluded: chain X residue 345 ASP Chi-restraints excluded: chain X residue 390 ASP Chi-restraints excluded: chain X residue 396 SER Chi-restraints excluded: chain X residue 398 VAL Chi-restraints excluded: chain X residue 400 ARG Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 407 SER Chi-restraints excluded: chain X residue 411 LEU Chi-restraints excluded: chain X residue 415 ASP Chi-restraints excluded: chain X residue 450 SER Chi-restraints excluded: chain X residue 460 VAL Chi-restraints excluded: chain X residue 466 VAL Chi-restraints excluded: chain X residue 470 SER Chi-restraints excluded: chain X residue 503 SER Chi-restraints excluded: chain X residue 517 TYR Chi-restraints excluded: chain X residue 518 ASN Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 30 CYS Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 275 GLN Chi-restraints excluded: chain F residue 309 CYS Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 344 ASP Chi-restraints excluded: chain F residue 395 HIS Chi-restraints excluded: chain F residue 429 MET Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 544 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain F residue 582 TYR Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 70 TYR Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 157 VAL Chi-restraints excluded: chain S residue 159 SER Chi-restraints excluded: chain S residue 164 HIS Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain S residue 183 THR Chi-restraints excluded: chain S residue 188 THR Chi-restraints excluded: chain S residue 210 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 232 VAL Chi-restraints excluded: chain S residue 241 VAL Chi-restraints excluded: chain S residue 249 ILE Chi-restraints excluded: chain S residue 250 THR Chi-restraints excluded: chain S residue 255 THR Chi-restraints excluded: chain S residue 270 GLN Chi-restraints excluded: chain S residue 333 ILE Chi-restraints excluded: chain S residue 350 SER Chi-restraints excluded: chain S residue 382 TYR Chi-restraints excluded: chain S residue 383 ASP Chi-restraints excluded: chain S residue 392 ARG Chi-restraints excluded: chain S residue 449 VAL Chi-restraints excluded: chain S residue 486 SER Chi-restraints excluded: chain S residue 495 VAL Chi-restraints excluded: chain S residue 496 VAL Chi-restraints excluded: chain S residue 525 ILE Chi-restraints excluded: chain S residue 544 VAL Chi-restraints excluded: chain S residue 549 THR Chi-restraints excluded: chain S residue 554 HIS Chi-restraints excluded: chain S residue 572 ILE Chi-restraints excluded: chain S residue 575 ILE Chi-restraints excluded: chain S residue 588 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 621 optimal weight: 30.0000 chunk 72 optimal weight: 4.9990 chunk 367 optimal weight: 0.9990 chunk 470 optimal weight: 9.9990 chunk 364 optimal weight: 7.9990 chunk 542 optimal weight: 0.8980 chunk 359 optimal weight: 0.8980 chunk 641 optimal weight: 7.9990 chunk 401 optimal weight: 0.6980 chunk 391 optimal weight: 4.9990 chunk 296 optimal weight: 0.3980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 548 GLN ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 497 ASN Q 158 GLN R 268 ASN ** R 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 48 HIS X 82 HIS ** X 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 518 GLN ** S 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 55993 Z= 0.162 Angle : 0.577 13.459 76636 Z= 0.296 Chirality : 0.041 0.242 8770 Planarity : 0.004 0.062 9378 Dihedral : 12.173 168.051 9192 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.34 % Favored : 93.64 % Rotamer: Outliers : 5.07 % Allowed : 24.71 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.41 % Twisted Proline : 0.71 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.10), residues: 6610 helix: 0.88 (0.11), residues: 2297 sheet: -1.14 (0.17), residues: 870 loop : -1.87 (0.10), residues: 3443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP Q 182 HIS 0.008 0.001 HIS X 487 PHE 0.014 0.001 PHE A 340 TYR 0.041 0.001 TYR B 71 ARG 0.012 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13220 Ramachandran restraints generated. 6610 Oldfield, 0 Emsley, 6610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13220 Ramachandran restraints generated. 6610 Oldfield, 0 Emsley, 6610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 5781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 347 time to evaluate : 4.697 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: A 63 ASP cc_start: 0.8608 (m-30) cc_final: 0.7831 (t0) REVERT: A 758 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8165 (tt) REVERT: B 12 TYR cc_start: 0.6322 (t80) cc_final: 0.6116 (t80) REVERT: B 48 GLU cc_start: 0.4475 (mt-10) cc_final: 0.4011 (mm-30) REVERT: B 55 MET cc_start: 0.6586 (ptm) cc_final: 0.6249 (mmp) REVERT: B 69 GLN cc_start: 0.8443 (tm130) cc_final: 0.8103 (tm-30) REVERT: B 72 LYS cc_start: 0.9056 (mmmt) cc_final: 0.8725 (pttm) REVERT: B 90 MET cc_start: 0.9395 (tmm) cc_final: 0.8964 (tmm) REVERT: B 174 MET cc_start: 0.8526 (tpt) cc_final: 0.8228 (tpt) REVERT: B 180 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7574 (mt) REVERT: D 12 TYR cc_start: 0.5123 (t80) cc_final: 0.4660 (t80) REVERT: D 60 GLU cc_start: 0.8250 (tp30) cc_final: 0.7717 (tp30) REVERT: D 64 ASP cc_start: 0.8443 (m-30) cc_final: 0.8061 (m-30) REVERT: D 69 GLN cc_start: 0.8442 (tm-30) cc_final: 0.7915 (tm-30) REVERT: D 91 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8642 (tp) REVERT: E 573 LEU cc_start: 0.3083 (OUTLIER) cc_final: 0.2882 (tt) REVERT: G 66 TYR cc_start: 0.7818 (m-10) cc_final: 0.7438 (m-10) REVERT: G 106 LEU cc_start: 0.8498 (tt) cc_final: 0.8190 (tp) REVERT: N 63 ASP cc_start: 0.8461 (m-30) cc_final: 0.7975 (m-30) REVERT: N 154 ASP cc_start: 0.8264 (t70) cc_final: 0.7755 (t0) REVERT: N 163 TYR cc_start: 0.9131 (p90) cc_final: 0.8641 (p90) REVERT: N 365 ARG cc_start: 0.6906 (tpt170) cc_final: 0.6680 (tmt-80) REVERT: N 366 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7714 (pp) REVERT: O 55 MET cc_start: 0.7992 (mtp) cc_final: 0.7678 (tmm) REVERT: Q 65 GLN cc_start: 0.8199 (tm-30) cc_final: 0.7895 (tm-30) REVERT: Q 158 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7763 (tm130) REVERT: R 233 MET cc_start: 0.6683 (tpp) cc_final: 0.6412 (tpp) REVERT: R 378 MET cc_start: 0.7236 (ttp) cc_final: 0.6993 (ptm) REVERT: R 429 MET cc_start: 0.6173 (ppp) cc_final: 0.5938 (mmp) REVERT: T 68 GLU cc_start: 0.7317 (pp20) cc_final: 0.6871 (tm-30) REVERT: X 210 CYS cc_start: 0.6252 (OUTLIER) cc_final: 0.5886 (p) REVERT: X 390 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7562 (t0) REVERT: X 460 VAL cc_start: 0.7726 (OUTLIER) cc_final: 0.7393 (p) REVERT: X 465 TYR cc_start: 0.3332 (p90) cc_final: 0.2305 (p90) REVERT: X 517 TYR cc_start: 0.7039 (OUTLIER) cc_final: 0.6180 (t80) REVERT: F 333 ILE cc_start: 0.0997 (OUTLIER) cc_final: -0.0923 (tp) REVERT: F 531 GLN cc_start: 0.2602 (OUTLIER) cc_final: 0.1447 (mm-40) REVERT: S 429 MET cc_start: -0.1461 (ptt) cc_final: -0.3271 (ttp) REVERT: S 554 HIS cc_start: -0.0136 (OUTLIER) cc_final: -0.0582 (t-170) outliers start: 290 outliers final: 248 residues processed: 609 average time/residue: 0.5268 time to fit residues: 550.3222 Evaluate side-chains 592 residues out of total 5781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 331 time to evaluate : 4.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 710 THR Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 573 LEU Chi-restraints excluded: chain E residue 579 ARG Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain H residue 64 ASP Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 130 CYS Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 115 VAL Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 185 LEU Chi-restraints excluded: chain K residue 188 HIS Chi-restraints excluded: chain K residue 193 THR Chi-restraints excluded: chain K residue 206 THR Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 242 ILE Chi-restraints excluded: chain K residue 261 CYS Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 403 THR Chi-restraints excluded: chain K residue 463 ILE Chi-restraints excluded: chain K residue 468 LEU Chi-restraints excluded: chain K residue 475 THR Chi-restraints excluded: chain K residue 478 ASN Chi-restraints excluded: chain K residue 484 CYS Chi-restraints excluded: chain K residue 518 ASN Chi-restraints excluded: chain K residue 523 PHE Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 140 ASP Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 153 ASP Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain N residue 226 THR Chi-restraints excluded: chain N residue 269 ASP Chi-restraints excluded: chain N residue 295 HIS Chi-restraints excluded: chain N residue 361 LEU Chi-restraints excluded: chain N residue 364 SER Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain N residue 372 LEU Chi-restraints excluded: chain N residue 393 THR Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 468 GLN Chi-restraints excluded: chain N residue 482 CYS Chi-restraints excluded: chain N residue 561 SER Chi-restraints excluded: chain N residue 573 GLN Chi-restraints excluded: chain N residue 640 ARG Chi-restraints excluded: chain N residue 709 SER Chi-restraints excluded: chain N residue 731 LEU Chi-restraints excluded: chain N residue 737 VAL Chi-restraints excluded: chain N residue 740 ASP Chi-restraints excluded: chain N residue 758 LEU Chi-restraints excluded: chain N residue 761 ASP Chi-restraints excluded: chain N residue 820 VAL Chi-restraints excluded: chain N residue 825 ASP Chi-restraints excluded: chain N residue 865 ASP Chi-restraints excluded: chain N residue 900 LEU Chi-restraints excluded: chain N residue 902 MET Chi-restraints excluded: chain N residue 907 LEU Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 87 MET Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain O residue 129 MET Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 179 ASN Chi-restraints excluded: chain P residue 18 GLN Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain P residue 53 VAL Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain Q residue 50 ASP Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 145 THR Chi-restraints excluded: chain Q residue 158 GLN Chi-restraints excluded: chain Q residue 180 LEU Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 160 ASP Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 223 ASP Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 458 ASP Chi-restraints excluded: chain R residue 481 THR Chi-restraints excluded: chain R residue 488 ILE Chi-restraints excluded: chain R residue 495 VAL Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 73 CYS Chi-restraints excluded: chain T residue 102 VAL Chi-restraints excluded: chain U residue 3 ASN Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 22 ASP Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 63 MET Chi-restraints excluded: chain U residue 72 SER Chi-restraints excluded: chain U residue 97 VAL Chi-restraints excluded: chain U residue 102 THR Chi-restraints excluded: chain U residue 105 ASN Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 14 VAL Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 39 CYS Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain X residue 71 ASN Chi-restraints excluded: chain X residue 74 ILE Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain X residue 82 HIS Chi-restraints excluded: chain X residue 87 ILE Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 137 SER Chi-restraints excluded: chain X residue 182 VAL Chi-restraints excluded: chain X residue 193 THR Chi-restraints excluded: chain X residue 210 CYS Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain X residue 223 THR Chi-restraints excluded: chain X residue 236 VAL Chi-restraints excluded: chain X residue 264 HIS Chi-restraints excluded: chain X residue 268 HIS Chi-restraints excluded: chain X residue 269 VAL Chi-restraints excluded: chain X residue 317 VAL Chi-restraints excluded: chain X residue 345 ASP Chi-restraints excluded: chain X residue 390 ASP Chi-restraints excluded: chain X residue 396 SER Chi-restraints excluded: chain X residue 398 VAL Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 407 SER Chi-restraints excluded: chain X residue 411 LEU Chi-restraints excluded: chain X residue 450 SER Chi-restraints excluded: chain X residue 460 VAL Chi-restraints excluded: chain X residue 466 VAL Chi-restraints excluded: chain X residue 517 TYR Chi-restraints excluded: chain X residue 518 ASN Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 30 CYS Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 275 GLN Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 344 ASP Chi-restraints excluded: chain F residue 395 HIS Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 544 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain F residue 582 TYR Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 70 TYR Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 157 VAL Chi-restraints excluded: chain S residue 164 HIS Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain S residue 183 THR Chi-restraints excluded: chain S residue 188 THR Chi-restraints excluded: chain S residue 210 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 232 VAL Chi-restraints excluded: chain S residue 241 VAL Chi-restraints excluded: chain S residue 249 ILE Chi-restraints excluded: chain S residue 250 THR Chi-restraints excluded: chain S residue 263 SER Chi-restraints excluded: chain S residue 270 GLN Chi-restraints excluded: chain S residue 333 ILE Chi-restraints excluded: chain S residue 350 SER Chi-restraints excluded: chain S residue 382 TYR Chi-restraints excluded: chain S residue 383 ASP Chi-restraints excluded: chain S residue 392 ARG Chi-restraints excluded: chain S residue 449 VAL Chi-restraints excluded: chain S residue 486 SER Chi-restraints excluded: chain S residue 496 VAL Chi-restraints excluded: chain S residue 544 VAL Chi-restraints excluded: chain S residue 549 THR Chi-restraints excluded: chain S residue 554 HIS Chi-restraints excluded: chain S residue 572 ILE Chi-restraints excluded: chain S residue 575 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 397 optimal weight: 0.9980 chunk 256 optimal weight: 0.7980 chunk 383 optimal weight: 2.9990 chunk 193 optimal weight: 0.8980 chunk 126 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 408 optimal weight: 5.9990 chunk 437 optimal weight: 0.9990 chunk 317 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 504 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 GLN B 43 ASN ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 88 ASN N 133 HIS N 570 GLN ** R 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 586 GLN ** T 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 65 GLN X 82 HIS ** X 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 ASN ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 177 ASN ** S 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 55993 Z= 0.162 Angle : 0.576 13.467 76636 Z= 0.295 Chirality : 0.041 0.243 8770 Planarity : 0.004 0.062 9378 Dihedral : 12.069 168.291 9175 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.18 % Favored : 93.81 % Rotamer: Outliers : 5.30 % Allowed : 24.61 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.41 % Twisted Proline : 0.71 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.10), residues: 6610 helix: 0.95 (0.11), residues: 2289 sheet: -1.05 (0.17), residues: 871 loop : -1.78 (0.10), residues: 3450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP Q 182 HIS 0.030 0.001 HIS X 82 PHE 0.019 0.001 PHE B 49 TYR 0.040 0.001 TYR B 71 ARG 0.012 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13220 Ramachandran restraints generated. 6610 Oldfield, 0 Emsley, 6610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13220 Ramachandran restraints generated. 6610 Oldfield, 0 Emsley, 6610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 5781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 303 poor density : 342 time to evaluate : 4.733 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: A 63 ASP cc_start: 0.8583 (m-30) cc_final: 0.7970 (t0) REVERT: A 545 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8287 (ttmt) REVERT: A 758 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8159 (tt) REVERT: B 48 GLU cc_start: 0.4626 (mt-10) cc_final: 0.4102 (mm-30) REVERT: B 55 MET cc_start: 0.6614 (ptm) cc_final: 0.6293 (mmp) REVERT: B 69 GLN cc_start: 0.8468 (tm130) cc_final: 0.8130 (tm-30) REVERT: B 72 LYS cc_start: 0.9142 (mmmt) cc_final: 0.8788 (pttm) REVERT: B 90 MET cc_start: 0.9404 (tmm) cc_final: 0.8984 (tmm) REVERT: B 174 MET cc_start: 0.8510 (tpt) cc_final: 0.8220 (tpt) REVERT: B 180 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7558 (mt) REVERT: D 12 TYR cc_start: 0.5045 (t80) cc_final: 0.4602 (t80) REVERT: D 60 GLU cc_start: 0.8268 (tp30) cc_final: 0.7717 (tp30) REVERT: D 64 ASP cc_start: 0.8508 (m-30) cc_final: 0.8107 (m-30) REVERT: D 69 GLN cc_start: 0.8448 (tm-30) cc_final: 0.7911 (tm-30) REVERT: D 91 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8635 (tp) REVERT: G 66 TYR cc_start: 0.7875 (m-10) cc_final: 0.7464 (m-10) REVERT: G 106 LEU cc_start: 0.8486 (tt) cc_final: 0.8188 (tp) REVERT: N 63 ASP cc_start: 0.8470 (m-30) cc_final: 0.7992 (m-30) REVERT: N 154 ASP cc_start: 0.8266 (t70) cc_final: 0.7737 (t0) REVERT: N 163 TYR cc_start: 0.9123 (p90) cc_final: 0.8652 (p90) REVERT: N 219 PHE cc_start: 0.9125 (OUTLIER) cc_final: 0.8023 (m-80) REVERT: N 366 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.7668 (pp) REVERT: N 924 MET cc_start: 0.8505 (mmt) cc_final: 0.8019 (mmt) REVERT: O 55 MET cc_start: 0.7997 (mtp) cc_final: 0.7663 (tmm) REVERT: Q 65 GLN cc_start: 0.8197 (tm-30) cc_final: 0.7871 (tm-30) REVERT: R 233 MET cc_start: 0.6652 (tpp) cc_final: 0.6382 (tpp) REVERT: R 378 MET cc_start: 0.7238 (ttp) cc_final: 0.7016 (ptm) REVERT: T 92 LYS cc_start: 0.8319 (tttp) cc_final: 0.7964 (ttmm) REVERT: X 210 CYS cc_start: 0.6276 (OUTLIER) cc_final: 0.5891 (p) REVERT: X 368 TYR cc_start: 0.7788 (t80) cc_final: 0.7337 (t80) REVERT: X 390 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7542 (t0) REVERT: X 460 VAL cc_start: 0.7721 (OUTLIER) cc_final: 0.7386 (p) REVERT: X 517 TYR cc_start: 0.7002 (OUTLIER) cc_final: 0.6159 (t80) REVERT: F 333 ILE cc_start: 0.0944 (OUTLIER) cc_final: -0.0957 (tp) REVERT: F 531 GLN cc_start: 0.2577 (OUTLIER) cc_final: 0.1676 (mm-40) REVERT: S 554 HIS cc_start: -0.0057 (OUTLIER) cc_final: -0.0508 (t-170) outliers start: 303 outliers final: 253 residues processed: 616 average time/residue: 0.5258 time to fit residues: 554.1758 Evaluate side-chains 600 residues out of total 5781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 334 time to evaluate : 4.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 579 ARG Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain H residue 64 ASP Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 130 CYS Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 185 LEU Chi-restraints excluded: chain K residue 206 THR Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 242 ILE Chi-restraints excluded: chain K residue 261 CYS Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain K residue 303 LEU Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 463 ILE Chi-restraints excluded: chain K residue 468 LEU Chi-restraints excluded: chain K residue 475 THR Chi-restraints excluded: chain K residue 478 ASN Chi-restraints excluded: chain K residue 484 CYS Chi-restraints excluded: chain K residue 518 ASN Chi-restraints excluded: chain K residue 523 PHE Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 153 ASP Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain N residue 219 PHE Chi-restraints excluded: chain N residue 269 ASP Chi-restraints excluded: chain N residue 295 HIS Chi-restraints excluded: chain N residue 299 VAL Chi-restraints excluded: chain N residue 330 VAL Chi-restraints excluded: chain N residue 361 LEU Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain N residue 372 LEU Chi-restraints excluded: chain N residue 393 THR Chi-restraints excluded: chain N residue 394 THR Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 468 GLN Chi-restraints excluded: chain N residue 482 CYS Chi-restraints excluded: chain N residue 496 ASN Chi-restraints excluded: chain N residue 499 ASP Chi-restraints excluded: chain N residue 573 GLN Chi-restraints excluded: chain N residue 640 ARG Chi-restraints excluded: chain N residue 644 THR Chi-restraints excluded: chain N residue 692 SER Chi-restraints excluded: chain N residue 709 SER Chi-restraints excluded: chain N residue 731 LEU Chi-restraints excluded: chain N residue 737 VAL Chi-restraints excluded: chain N residue 740 ASP Chi-restraints excluded: chain N residue 744 GLU Chi-restraints excluded: chain N residue 758 LEU Chi-restraints excluded: chain N residue 761 ASP Chi-restraints excluded: chain N residue 825 ASP Chi-restraints excluded: chain N residue 865 ASP Chi-restraints excluded: chain N residue 883 LEU Chi-restraints excluded: chain N residue 900 LEU Chi-restraints excluded: chain N residue 902 MET Chi-restraints excluded: chain N residue 907 LEU Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain O residue 129 MET Chi-restraints excluded: chain O residue 170 SER Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 179 ASN Chi-restraints excluded: chain P residue 18 GLN Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain P residue 53 VAL Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain Q residue 50 ASP Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 145 THR Chi-restraints excluded: chain Q residue 180 LEU Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 160 ASP Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 223 ASP Chi-restraints excluded: chain R residue 227 LEU Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 458 ASP Chi-restraints excluded: chain R residue 481 THR Chi-restraints excluded: chain R residue 495 VAL Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 73 CYS Chi-restraints excluded: chain T residue 102 VAL Chi-restraints excluded: chain U residue 3 ASN Chi-restraints excluded: chain U residue 10 ASN Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 22 ASP Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 63 MET Chi-restraints excluded: chain U residue 72 SER Chi-restraints excluded: chain U residue 97 VAL Chi-restraints excluded: chain U residue 102 THR Chi-restraints excluded: chain U residue 105 ASN Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 14 VAL Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain X residue 71 ASN Chi-restraints excluded: chain X residue 74 ILE Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain X residue 82 HIS Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 127 THR Chi-restraints excluded: chain X residue 137 SER Chi-restraints excluded: chain X residue 182 VAL Chi-restraints excluded: chain X residue 210 CYS Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain X residue 223 THR Chi-restraints excluded: chain X residue 236 VAL Chi-restraints excluded: chain X residue 264 HIS Chi-restraints excluded: chain X residue 268 HIS Chi-restraints excluded: chain X residue 269 VAL Chi-restraints excluded: chain X residue 317 VAL Chi-restraints excluded: chain X residue 345 ASP Chi-restraints excluded: chain X residue 390 ASP Chi-restraints excluded: chain X residue 396 SER Chi-restraints excluded: chain X residue 398 VAL Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 407 SER Chi-restraints excluded: chain X residue 411 LEU Chi-restraints excluded: chain X residue 415 ASP Chi-restraints excluded: chain X residue 450 SER Chi-restraints excluded: chain X residue 460 VAL Chi-restraints excluded: chain X residue 466 VAL Chi-restraints excluded: chain X residue 470 SER Chi-restraints excluded: chain X residue 503 SER Chi-restraints excluded: chain X residue 517 TYR Chi-restraints excluded: chain X residue 518 ASN Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 30 CYS Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 275 GLN Chi-restraints excluded: chain F residue 309 CYS Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 344 ASP Chi-restraints excluded: chain F residue 395 HIS Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 544 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain F residue 554 HIS Chi-restraints excluded: chain F residue 582 TYR Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 70 TYR Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 157 VAL Chi-restraints excluded: chain S residue 159 SER Chi-restraints excluded: chain S residue 164 HIS Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain S residue 183 THR Chi-restraints excluded: chain S residue 188 THR Chi-restraints excluded: chain S residue 210 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 232 VAL Chi-restraints excluded: chain S residue 241 VAL Chi-restraints excluded: chain S residue 249 ILE Chi-restraints excluded: chain S residue 250 THR Chi-restraints excluded: chain S residue 263 SER Chi-restraints excluded: chain S residue 270 GLN Chi-restraints excluded: chain S residue 333 ILE Chi-restraints excluded: chain S residue 350 SER Chi-restraints excluded: chain S residue 382 TYR Chi-restraints excluded: chain S residue 392 ARG Chi-restraints excluded: chain S residue 449 VAL Chi-restraints excluded: chain S residue 486 SER Chi-restraints excluded: chain S residue 496 VAL Chi-restraints excluded: chain S residue 544 VAL Chi-restraints excluded: chain S residue 549 THR Chi-restraints excluded: chain S residue 554 HIS Chi-restraints excluded: chain S residue 572 ILE Chi-restraints excluded: chain S residue 575 ILE Chi-restraints excluded: chain S residue 588 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 583 optimal weight: 0.2980 chunk 614 optimal weight: 3.9990 chunk 561 optimal weight: 40.0000 chunk 598 optimal weight: 8.9990 chunk 360 optimal weight: 2.9990 chunk 260 optimal weight: 2.9990 chunk 469 optimal weight: 5.9990 chunk 183 optimal weight: 30.0000 chunk 540 optimal weight: 7.9990 chunk 565 optimal weight: 20.0000 chunk 596 optimal weight: 0.0020 overall best weight: 2.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 GLN A 773 GLN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 497 ASN Q 158 GLN ** R 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 82 HIS ** X 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 55993 Z= 0.256 Angle : 0.610 13.460 76636 Z= 0.314 Chirality : 0.042 0.246 8770 Planarity : 0.004 0.062 9378 Dihedral : 12.044 169.792 9164 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.83 % Favored : 93.14 % Rotamer: Outliers : 5.37 % Allowed : 24.59 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.41 % Twisted Proline : 0.71 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.10), residues: 6610 helix: 0.86 (0.11), residues: 2324 sheet: -1.05 (0.17), residues: 873 loop : -1.82 (0.10), residues: 3413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP Q 182 HIS 0.041 0.001 HIS X 82 PHE 0.020 0.002 PHE E 262 TYR 0.041 0.001 TYR B 71 ARG 0.014 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13220 Ramachandran restraints generated. 6610 Oldfield, 0 Emsley, 6610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13220 Ramachandran restraints generated. 6610 Oldfield, 0 Emsley, 6610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 5781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 335 time to evaluate : 4.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8661 (m-30) cc_final: 0.7957 (t0) REVERT: A 545 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8330 (ttmt) REVERT: A 758 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8270 (tt) REVERT: B 55 MET cc_start: 0.6490 (ptm) cc_final: 0.6148 (mmp) REVERT: B 69 GLN cc_start: 0.8444 (tm130) cc_final: 0.8084 (tm-30) REVERT: B 72 LYS cc_start: 0.9084 (mmmt) cc_final: 0.8788 (pttm) REVERT: B 90 MET cc_start: 0.9367 (tmm) cc_final: 0.8822 (tmm) REVERT: B 174 MET cc_start: 0.8548 (tpt) cc_final: 0.8256 (tpt) REVERT: B 180 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7637 (mt) REVERT: D 12 TYR cc_start: 0.5102 (t80) cc_final: 0.4664 (t80) REVERT: D 55 MET cc_start: 0.8078 (ppp) cc_final: 0.7862 (ppp) REVERT: D 60 GLU cc_start: 0.8234 (tp30) cc_final: 0.7670 (tp30) REVERT: D 64 ASP cc_start: 0.8508 (m-30) cc_final: 0.8100 (m-30) REVERT: D 69 GLN cc_start: 0.8469 (tm-30) cc_final: 0.7938 (tm-30) REVERT: D 91 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8652 (tp) REVERT: G 66 TYR cc_start: 0.7823 (m-10) cc_final: 0.7435 (m-10) REVERT: N 63 ASP cc_start: 0.8485 (m-30) cc_final: 0.8137 (m-30) REVERT: N 154 ASP cc_start: 0.8297 (t70) cc_final: 0.7755 (t0) REVERT: N 366 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.7904 (pp) REVERT: O 55 MET cc_start: 0.7947 (mtp) cc_final: 0.7725 (tmm) REVERT: O 70 MET cc_start: 0.7774 (ptt) cc_final: 0.7366 (tmm) REVERT: P 2 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7590 (tptm) REVERT: Q 65 GLN cc_start: 0.8171 (tm-30) cc_final: 0.7866 (tm-30) REVERT: Q 158 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7455 (tm130) REVERT: R 233 MET cc_start: 0.6621 (tpp) cc_final: 0.6370 (tpp) REVERT: X 210 CYS cc_start: 0.6299 (OUTLIER) cc_final: 0.5913 (p) REVERT: X 390 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7597 (t0) REVERT: X 400 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.6871 (tpt90) REVERT: X 460 VAL cc_start: 0.7866 (OUTLIER) cc_final: 0.7545 (p) REVERT: X 465 TYR cc_start: 0.3892 (p90) cc_final: 0.2771 (p90) REVERT: X 517 TYR cc_start: 0.7041 (OUTLIER) cc_final: 0.6210 (t80) REVERT: F 319 GLU cc_start: 0.0555 (OUTLIER) cc_final: 0.0219 (pt0) REVERT: F 333 ILE cc_start: 0.0883 (OUTLIER) cc_final: -0.0958 (tp) REVERT: F 531 GLN cc_start: 0.2255 (OUTLIER) cc_final: 0.1314 (mm-40) outliers start: 307 outliers final: 271 residues processed: 613 average time/residue: 0.5347 time to fit residues: 565.4765 Evaluate side-chains 614 residues out of total 5781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 328 time to evaluate : 4.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 579 ARG Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain H residue 62 ASN Chi-restraints excluded: chain H residue 64 ASP Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 130 CYS Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 206 THR Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 242 ILE Chi-restraints excluded: chain K residue 261 CYS Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain K residue 303 LEU Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 463 ILE Chi-restraints excluded: chain K residue 468 LEU Chi-restraints excluded: chain K residue 475 THR Chi-restraints excluded: chain K residue 478 ASN Chi-restraints excluded: chain K residue 484 CYS Chi-restraints excluded: chain K residue 518 ASN Chi-restraints excluded: chain K residue 523 PHE Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 62 ASP Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 153 ASP Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain N residue 226 THR Chi-restraints excluded: chain N residue 269 ASP Chi-restraints excluded: chain N residue 295 HIS Chi-restraints excluded: chain N residue 299 VAL Chi-restraints excluded: chain N residue 330 VAL Chi-restraints excluded: chain N residue 361 LEU Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain N residue 372 LEU Chi-restraints excluded: chain N residue 393 THR Chi-restraints excluded: chain N residue 394 THR Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 468 GLN Chi-restraints excluded: chain N residue 482 CYS Chi-restraints excluded: chain N residue 496 ASN Chi-restraints excluded: chain N residue 499 ASP Chi-restraints excluded: chain N residue 518 SER Chi-restraints excluded: chain N residue 573 GLN Chi-restraints excluded: chain N residue 640 ARG Chi-restraints excluded: chain N residue 644 THR Chi-restraints excluded: chain N residue 692 SER Chi-restraints excluded: chain N residue 709 SER Chi-restraints excluded: chain N residue 731 LEU Chi-restraints excluded: chain N residue 737 VAL Chi-restraints excluded: chain N residue 744 GLU Chi-restraints excluded: chain N residue 758 LEU Chi-restraints excluded: chain N residue 761 ASP Chi-restraints excluded: chain N residue 825 ASP Chi-restraints excluded: chain N residue 865 ASP Chi-restraints excluded: chain N residue 883 LEU Chi-restraints excluded: chain N residue 899 MET Chi-restraints excluded: chain N residue 900 LEU Chi-restraints excluded: chain N residue 907 LEU Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain O residue 129 MET Chi-restraints excluded: chain O residue 170 SER Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain P residue 2 LYS Chi-restraints excluded: chain P residue 18 GLN Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain P residue 53 VAL Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain Q residue 50 ASP Chi-restraints excluded: chain Q residue 64 ASP Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 145 THR Chi-restraints excluded: chain Q residue 158 GLN Chi-restraints excluded: chain Q residue 180 LEU Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 160 ASP Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 223 ASP Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 458 ASP Chi-restraints excluded: chain R residue 481 THR Chi-restraints excluded: chain R residue 488 ILE Chi-restraints excluded: chain R residue 495 VAL Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 73 CYS Chi-restraints excluded: chain T residue 102 VAL Chi-restraints excluded: chain U residue 3 ASN Chi-restraints excluded: chain U residue 10 ASN Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 22 ASP Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 63 MET Chi-restraints excluded: chain U residue 72 SER Chi-restraints excluded: chain U residue 97 VAL Chi-restraints excluded: chain U residue 102 THR Chi-restraints excluded: chain U residue 105 ASN Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 14 VAL Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain X residue 71 ASN Chi-restraints excluded: chain X residue 74 ILE Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain X residue 82 HIS Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 127 THR Chi-restraints excluded: chain X residue 137 SER Chi-restraints excluded: chain X residue 182 VAL Chi-restraints excluded: chain X residue 193 THR Chi-restraints excluded: chain X residue 210 CYS Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain X residue 223 THR Chi-restraints excluded: chain X residue 236 VAL Chi-restraints excluded: chain X residue 264 HIS Chi-restraints excluded: chain X residue 268 HIS Chi-restraints excluded: chain X residue 269 VAL Chi-restraints excluded: chain X residue 345 ASP Chi-restraints excluded: chain X residue 390 ASP Chi-restraints excluded: chain X residue 396 SER Chi-restraints excluded: chain X residue 398 VAL Chi-restraints excluded: chain X residue 400 ARG Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 407 SER Chi-restraints excluded: chain X residue 411 LEU Chi-restraints excluded: chain X residue 415 ASP Chi-restraints excluded: chain X residue 450 SER Chi-restraints excluded: chain X residue 460 VAL Chi-restraints excluded: chain X residue 466 VAL Chi-restraints excluded: chain X residue 470 SER Chi-restraints excluded: chain X residue 503 SER Chi-restraints excluded: chain X residue 517 TYR Chi-restraints excluded: chain X residue 518 ASN Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 30 CYS Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 275 GLN Chi-restraints excluded: chain F residue 309 CYS Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 344 ASP Chi-restraints excluded: chain F residue 395 HIS Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 544 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 70 TYR Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 157 VAL Chi-restraints excluded: chain S residue 159 SER Chi-restraints excluded: chain S residue 164 HIS Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain S residue 183 THR Chi-restraints excluded: chain S residue 188 THR Chi-restraints excluded: chain S residue 210 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 232 VAL Chi-restraints excluded: chain S residue 241 VAL Chi-restraints excluded: chain S residue 249 ILE Chi-restraints excluded: chain S residue 250 THR Chi-restraints excluded: chain S residue 263 SER Chi-restraints excluded: chain S residue 270 GLN Chi-restraints excluded: chain S residue 333 ILE Chi-restraints excluded: chain S residue 350 SER Chi-restraints excluded: chain S residue 382 TYR Chi-restraints excluded: chain S residue 392 ARG Chi-restraints excluded: chain S residue 449 VAL Chi-restraints excluded: chain S residue 486 SER Chi-restraints excluded: chain S residue 495 VAL Chi-restraints excluded: chain S residue 496 VAL Chi-restraints excluded: chain S residue 544 VAL Chi-restraints excluded: chain S residue 549 THR Chi-restraints excluded: chain S residue 554 HIS Chi-restraints excluded: chain S residue 572 ILE Chi-restraints excluded: chain S residue 575 ILE Chi-restraints excluded: chain S residue 582 TYR Chi-restraints excluded: chain S residue 588 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 392 optimal weight: 0.8980 chunk 632 optimal weight: 20.0000 chunk 386 optimal weight: 6.9990 chunk 300 optimal weight: 0.9980 chunk 439 optimal weight: 7.9990 chunk 663 optimal weight: 9.9990 chunk 610 optimal weight: 20.0000 chunk 528 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 408 optimal weight: 7.9990 chunk 323 optimal weight: 0.0670 overall best weight: 1.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 GLN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 82 HIS ** X 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 554 HIS ** S 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 55993 Z= 0.246 Angle : 0.609 13.477 76636 Z= 0.312 Chirality : 0.042 0.245 8770 Planarity : 0.004 0.063 9378 Dihedral : 12.037 170.271 9159 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.62 % Favored : 93.35 % Rotamer: Outliers : 5.05 % Allowed : 24.80 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.41 % Twisted Proline : 0.71 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.10), residues: 6610 helix: 0.89 (0.11), residues: 2316 sheet: -1.08 (0.17), residues: 884 loop : -1.82 (0.10), residues: 3410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP Q 182 HIS 0.016 0.001 HIS X 82 PHE 0.020 0.001 PHE B 49 TYR 0.041 0.001 TYR B 71 ARG 0.015 0.000 ARG B 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13220 Ramachandran restraints generated. 6610 Oldfield, 0 Emsley, 6610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13220 Ramachandran restraints generated. 6610 Oldfield, 0 Emsley, 6610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 5781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 289 poor density : 335 time to evaluate : 4.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ASP cc_start: 0.8650 (m-30) cc_final: 0.8008 (t0) REVERT: A 545 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8325 (ttmt) REVERT: A 758 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8271 (tt) REVERT: B 12 TYR cc_start: 0.6433 (t80) cc_final: 0.6208 (t80) REVERT: B 55 MET cc_start: 0.6664 (ptm) cc_final: 0.6340 (mmp) REVERT: B 69 GLN cc_start: 0.8448 (tm130) cc_final: 0.8066 (tm-30) REVERT: B 72 LYS cc_start: 0.9052 (mmmt) cc_final: 0.8779 (pttm) REVERT: B 90 MET cc_start: 0.9379 (tmm) cc_final: 0.8855 (tmm) REVERT: B 174 MET cc_start: 0.8558 (tpt) cc_final: 0.8305 (tpt) REVERT: B 180 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7641 (mt) REVERT: D 12 TYR cc_start: 0.5212 (t80) cc_final: 0.4765 (t80) REVERT: D 55 MET cc_start: 0.8085 (ppp) cc_final: 0.7864 (ppp) REVERT: D 60 GLU cc_start: 0.8237 (tp30) cc_final: 0.7669 (tp30) REVERT: D 64 ASP cc_start: 0.8491 (m-30) cc_final: 0.8057 (m-30) REVERT: D 69 GLN cc_start: 0.8470 (tm-30) cc_final: 0.7936 (tm-30) REVERT: D 91 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8693 (tp) REVERT: G 66 TYR cc_start: 0.7839 (m-10) cc_final: 0.7448 (m-10) REVERT: N 63 ASP cc_start: 0.8469 (m-30) cc_final: 0.8132 (m-30) REVERT: N 154 ASP cc_start: 0.8317 (t70) cc_final: 0.7756 (t0) REVERT: N 366 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.7853 (pp) REVERT: O 55 MET cc_start: 0.7971 (mtp) cc_final: 0.7720 (tmm) REVERT: P 2 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7660 (tptm) REVERT: Q 65 GLN cc_start: 0.8140 (tm-30) cc_final: 0.7851 (tm-30) REVERT: R 233 MET cc_start: 0.6706 (tpp) cc_final: 0.6467 (tpp) REVERT: X 210 CYS cc_start: 0.6194 (OUTLIER) cc_final: 0.5815 (p) REVERT: X 390 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7631 (t0) REVERT: X 400 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.6863 (tpt90) REVERT: X 460 VAL cc_start: 0.7911 (OUTLIER) cc_final: 0.7584 (p) REVERT: X 517 TYR cc_start: 0.7031 (OUTLIER) cc_final: 0.6207 (t80) REVERT: F 319 GLU cc_start: 0.0519 (OUTLIER) cc_final: 0.0009 (pt0) REVERT: F 333 ILE cc_start: 0.0889 (OUTLIER) cc_final: -0.1003 (tp) REVERT: F 531 GLN cc_start: 0.2180 (OUTLIER) cc_final: 0.1332 (mm-40) outliers start: 289 outliers final: 265 residues processed: 598 average time/residue: 0.5213 time to fit residues: 534.3742 Evaluate side-chains 605 residues out of total 5781 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 326 time to evaluate : 4.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 865 ASP Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 119 ILE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 579 ARG Chi-restraints excluded: chain G residue 4 LEU Chi-restraints excluded: chain G residue 25 ASP Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 73 CYS Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 112 LEU Chi-restraints excluded: chain H residue 62 ASN Chi-restraints excluded: chain H residue 64 ASP Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 89 PHE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 130 CYS Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 136 VAL Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 206 THR Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 242 ILE Chi-restraints excluded: chain K residue 261 CYS Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain K residue 301 ASP Chi-restraints excluded: chain K residue 303 LEU Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 463 ILE Chi-restraints excluded: chain K residue 468 LEU Chi-restraints excluded: chain K residue 475 THR Chi-restraints excluded: chain K residue 478 ASN Chi-restraints excluded: chain K residue 484 CYS Chi-restraints excluded: chain K residue 518 ASN Chi-restraints excluded: chain K residue 523 PHE Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 62 ASP Chi-restraints excluded: chain N residue 141 THR Chi-restraints excluded: chain N residue 153 ASP Chi-restraints excluded: chain N residue 204 VAL Chi-restraints excluded: chain N residue 226 THR Chi-restraints excluded: chain N residue 269 ASP Chi-restraints excluded: chain N residue 295 HIS Chi-restraints excluded: chain N residue 299 VAL Chi-restraints excluded: chain N residue 330 VAL Chi-restraints excluded: chain N residue 359 VAL Chi-restraints excluded: chain N residue 361 LEU Chi-restraints excluded: chain N residue 366 LEU Chi-restraints excluded: chain N residue 372 LEU Chi-restraints excluded: chain N residue 393 THR Chi-restraints excluded: chain N residue 394 THR Chi-restraints excluded: chain N residue 435 VAL Chi-restraints excluded: chain N residue 468 GLN Chi-restraints excluded: chain N residue 482 CYS Chi-restraints excluded: chain N residue 496 ASN Chi-restraints excluded: chain N residue 499 ASP Chi-restraints excluded: chain N residue 518 SER Chi-restraints excluded: chain N residue 573 GLN Chi-restraints excluded: chain N residue 640 ARG Chi-restraints excluded: chain N residue 644 THR Chi-restraints excluded: chain N residue 692 SER Chi-restraints excluded: chain N residue 709 SER Chi-restraints excluded: chain N residue 731 LEU Chi-restraints excluded: chain N residue 737 VAL Chi-restraints excluded: chain N residue 744 GLU Chi-restraints excluded: chain N residue 758 LEU Chi-restraints excluded: chain N residue 761 ASP Chi-restraints excluded: chain N residue 825 ASP Chi-restraints excluded: chain N residue 865 ASP Chi-restraints excluded: chain N residue 883 LEU Chi-restraints excluded: chain N residue 899 MET Chi-restraints excluded: chain N residue 907 LEU Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 95 LEU Chi-restraints excluded: chain O residue 129 MET Chi-restraints excluded: chain O residue 170 SER Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain P residue 2 LYS Chi-restraints excluded: chain P residue 18 GLN Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain P residue 53 VAL Chi-restraints excluded: chain P residue 57 SER Chi-restraints excluded: chain Q residue 50 ASP Chi-restraints excluded: chain Q residue 64 ASP Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 145 THR Chi-restraints excluded: chain Q residue 180 LEU Chi-restraints excluded: chain R residue 2 VAL Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 49 VAL Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain R residue 79 ILE Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 105 ASP Chi-restraints excluded: chain R residue 160 ASP Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 223 ASP Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 272 VAL Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 458 ASP Chi-restraints excluded: chain R residue 481 THR Chi-restraints excluded: chain R residue 488 ILE Chi-restraints excluded: chain R residue 495 VAL Chi-restraints excluded: chain T residue 4 LEU Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain T residue 64 THR Chi-restraints excluded: chain T residue 73 CYS Chi-restraints excluded: chain T residue 102 VAL Chi-restraints excluded: chain U residue 3 ASN Chi-restraints excluded: chain U residue 10 ASN Chi-restraints excluded: chain U residue 21 VAL Chi-restraints excluded: chain U residue 22 ASP Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 63 MET Chi-restraints excluded: chain U residue 72 SER Chi-restraints excluded: chain U residue 97 VAL Chi-restraints excluded: chain U residue 102 THR Chi-restraints excluded: chain U residue 105 ASN Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain U residue 119 VAL Chi-restraints excluded: chain X residue 5 THR Chi-restraints excluded: chain X residue 14 VAL Chi-restraints excluded: chain X residue 31 THR Chi-restraints excluded: chain X residue 50 THR Chi-restraints excluded: chain X residue 74 ILE Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain X residue 87 ILE Chi-restraints excluded: chain X residue 120 VAL Chi-restraints excluded: chain X residue 127 THR Chi-restraints excluded: chain X residue 137 SER Chi-restraints excluded: chain X residue 182 VAL Chi-restraints excluded: chain X residue 210 CYS Chi-restraints excluded: chain X residue 222 ASP Chi-restraints excluded: chain X residue 223 THR Chi-restraints excluded: chain X residue 236 VAL Chi-restraints excluded: chain X residue 264 HIS Chi-restraints excluded: chain X residue 268 HIS Chi-restraints excluded: chain X residue 269 VAL Chi-restraints excluded: chain X residue 345 ASP Chi-restraints excluded: chain X residue 390 ASP Chi-restraints excluded: chain X residue 396 SER Chi-restraints excluded: chain X residue 398 VAL Chi-restraints excluded: chain X residue 400 ARG Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 407 SER Chi-restraints excluded: chain X residue 411 LEU Chi-restraints excluded: chain X residue 415 ASP Chi-restraints excluded: chain X residue 450 SER Chi-restraints excluded: chain X residue 460 VAL Chi-restraints excluded: chain X residue 466 VAL Chi-restraints excluded: chain X residue 470 SER Chi-restraints excluded: chain X residue 503 SER Chi-restraints excluded: chain X residue 517 TYR Chi-restraints excluded: chain X residue 518 ASN Chi-restraints excluded: chain F residue 13 SER Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 30 CYS Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 216 THR Chi-restraints excluded: chain F residue 233 MET Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 275 GLN Chi-restraints excluded: chain F residue 309 CYS Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 395 HIS Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 482 HIS Chi-restraints excluded: chain F residue 495 VAL Chi-restraints excluded: chain F residue 496 VAL Chi-restraints excluded: chain F residue 531 GLN Chi-restraints excluded: chain F residue 544 VAL Chi-restraints excluded: chain F residue 550 THR Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 70 TYR Chi-restraints excluded: chain S residue 96 THR Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 157 VAL Chi-restraints excluded: chain S residue 159 SER Chi-restraints excluded: chain S residue 164 HIS Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain S residue 183 THR Chi-restraints excluded: chain S residue 188 THR Chi-restraints excluded: chain S residue 210 VAL Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 232 VAL Chi-restraints excluded: chain S residue 241 VAL Chi-restraints excluded: chain S residue 249 ILE Chi-restraints excluded: chain S residue 250 THR Chi-restraints excluded: chain S residue 263 SER Chi-restraints excluded: chain S residue 270 GLN Chi-restraints excluded: chain S residue 333 ILE Chi-restraints excluded: chain S residue 350 SER Chi-restraints excluded: chain S residue 382 TYR Chi-restraints excluded: chain S residue 392 ARG Chi-restraints excluded: chain S residue 449 VAL Chi-restraints excluded: chain S residue 486 SER Chi-restraints excluded: chain S residue 495 VAL Chi-restraints excluded: chain S residue 496 VAL Chi-restraints excluded: chain S residue 544 VAL Chi-restraints excluded: chain S residue 549 THR Chi-restraints excluded: chain S residue 554 HIS Chi-restraints excluded: chain S residue 572 ILE Chi-restraints excluded: chain S residue 575 ILE Chi-restraints excluded: chain S residue 582 TYR Chi-restraints excluded: chain S residue 588 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 419 optimal weight: 20.0000 chunk 562 optimal weight: 0.1980 chunk 161 optimal weight: 30.0000 chunk 487 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 529 optimal weight: 0.2980 chunk 221 optimal weight: 1.9990 chunk 543 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 573 GLN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 158 ASN N 497 ASN Q 158 GLN ** R 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 82 HIS ** X 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 455 HIS ** X 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.131352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.082230 restraints weight = 196256.496| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 4.09 r_work: 0.2991 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 55993 Z= 0.164 Angle : 0.582 13.483 76636 Z= 0.297 Chirality : 0.041 0.244 8770 Planarity : 0.004 0.062 9378 Dihedral : 11.951 169.568 9156 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.13 % Favored : 93.85 % Rotamer: Outliers : 4.55 % Allowed : 25.39 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.71 % Cis-general : 0.41 % Twisted Proline : 0.71 % Twisted General : 0.02 % 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: -0.91 (0.10), residues: 6610 helix: 1.01 (0.11), residues: 2307 sheet: -0.98 (0.17), residues: 886 loop : -1.69 (0.10), residues: 3417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP Q 182 HIS 0.017 0.001 HIS A 572 PHE 0.029 0.001 PHE B 49 TYR 0.042 0.001 TYR B 71 ARG 0.014 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12478.59 seconds wall clock time: 221 minutes 27.33 seconds (13287.33 seconds total)