Starting phenix.real_space_refine on Mon Mar 18 04:58:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl0_29263/03_2024/8fl0_29263_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl0_29263/03_2024/8fl0_29263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl0_29263/03_2024/8fl0_29263.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl0_29263/03_2024/8fl0_29263.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl0_29263/03_2024/8fl0_29263_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fl0_29263/03_2024/8fl0_29263_neut_updated.pdb" } resolution = 2.91 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= 0.022 sd= 0.123 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians K 2 8.98 5 Zn 1 6.06 5 P 1683 5.49 5 Mg 22 5.21 5 S 219 5.16 5 C 46053 2.51 5 N 15344 2.21 5 O 20053 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "BA GLU 21": "OE1" <-> "OE2" Residue "BA ASP 52": "OD1" <-> "OD2" Residue "BA GLU 72": "OE1" <-> "OE2" Residue "BA ASP 107": "OD1" <-> "OD2" Residue "BA GLU 131": "OE1" <-> "OE2" Residue "BA ASP 153": "OD1" <-> "OD2" Residue "L5 GLU 14": "OE1" <-> "OE2" Residue "L5 PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L5 ASP 101": "OD1" <-> "OD2" Residue "L5 ASP 129": "OD1" <-> "OD2" Residue "L5 GLU 161": "OE1" <-> "OE2" Residue "L5 PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L7 GLU 39": "OE1" <-> "OE2" Residue "L7 ASP 100": "OD1" <-> "OD2" Residue "L7 TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L7 TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L7 GLU 162": "OE1" <-> "OE2" Residue "L7 TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L7 ASP 190": "OD1" <-> "OD2" Residue "L8 PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L8 ASP 59": "OD1" <-> "OD2" Residue "L8 GLU 96": "OE1" <-> "OE2" Residue "L8 GLU 126": "OE1" <-> "OE2" Residue "LB ASP 124": "OD1" <-> "OD2" Residue "LB GLU 147": "OE1" <-> "OE2" Residue "LC GLU 9": "OE1" <-> "OE2" Residue "LC PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC GLU 60": "OE1" <-> "OE2" Residue "LC GLU 69": "OE1" <-> "OE2" Residue "LC ASP 85": "OD1" <-> "OD2" Residue "LC ASP 99": "OD1" <-> "OD2" Residue "LC PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LE ASP 38": "OD1" <-> "OD2" Residue "LE ASP 41": "OD1" <-> "OD2" Residue "LE TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LE GLU 118": "OE1" <-> "OE2" Residue "LG ASP 59": "OD1" <-> "OD2" Residue "LG TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG GLU 124": "OE1" <-> "OE2" Residue "LL ASP 105": "OD1" <-> "OD2" Residue "LN GLU 59": "OE1" <-> "OE2" Residue "LN PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LQ GLU 84": "OE1" <-> "OE2" Residue "LT GLU 23": "OE1" <-> "OE2" Residue "LT GLU 31": "OE1" <-> "OE2" Residue "LT GLU 38": "OE1" <-> "OE2" Residue "LT GLU 40": "OE1" <-> "OE2" Residue "NB GLU 58": "OE1" <-> "OE2" Residue "NB GLU 65": "OE1" <-> "OE2" Residue "NB GLU 73": "OE1" <-> "OE2" Residue "NC PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NC GLU 195": "OE1" <-> "OE2" Residue "NC TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NC GLU 344": "OE1" <-> "OE2" Residue "NC GLU 373": "OE1" <-> "OE2" Residue "NC GLU 385": "OE1" <-> "OE2" Residue "NC GLU 399": "OE1" <-> "OE2" Residue "NC TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NC PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ND TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ND PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ND TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ND TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ND GLU 216": "OE1" <-> "OE2" Residue "NF GLU 5": "OE1" <-> "OE2" Residue "NF GLU 69": "OE1" <-> "OE2" Residue "NF GLU 118": "OE1" <-> "OE2" Residue "NF PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NF PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NF GLU 221": "OE1" <-> "OE2" Residue "NJ GLU 239": "OE1" <-> "OE2" Residue "NJ ASP 257": "OD1" <-> "OD2" Residue "NJ ASP 317": "OD1" <-> "OD2" Residue "NJ GLU 327": "OE1" <-> "OE2" Residue "NJ ASP 350": "OD1" <-> "OD2" Residue "NJ PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NZ ASP 248": "OD1" <-> "OD2" Residue "NZ ASP 260": "OD1" <-> "OD2" Residue "SA ASP 35": "OD1" <-> "OD2" Residue "SA GLU 146": "OE1" <-> "OE2" Residue "SA ASP 156": "OD1" <-> "OD2" Residue "SA ASP 179": "OD1" <-> "OD2" Residue "SA TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA ASP 288": "OD1" <-> "OD2" Residue "SA ASP 352": "OD1" <-> "OD2" Residue "SB TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SB ASP 72": "OD1" <-> "OD2" Residue "SB GLU 82": "OE1" <-> "OE2" Residue "SB GLU 238": "OE1" <-> "OE2" Residue "SC TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SC TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SC GLU 119": "OE1" <-> "OE2" Residue "SC ASP 120": "OD1" <-> "OD2" Residue "SC ASP 214": "OD1" <-> "OD2" Residue "SC TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SC GLU 241": "OE1" <-> "OE2" Residue "SC ASP 249": "OD1" <-> "OD2" Residue "SC ASP 254": "OD1" <-> "OD2" Residue "SD PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SD TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SD GLU 137": "OE1" <-> "OE2" Residue "SD GLU 152": "OE1" <-> "OE2" Residue "SD ASP 171": "OD1" <-> "OD2" Residue "SD GLU 188": "OE1" <-> "OE2" Residue "SD GLU 193": "OE1" <-> "OE2" Residue "SD GLU 237": "OE1" <-> "OE2" Residue "SG GLU 44": "OE1" <-> "OE2" Residue "SG GLU 66": "OE1" <-> "OE2" Residue "SG GLU 152": "OE1" <-> "OE2" Residue "SG ASP 171": "OD1" <-> "OD2" Residue "SK GLU 8": "OE1" <-> "OE2" Residue "SK TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SK ASP 90": "OD1" <-> "OD2" Residue "SK GLU 168": "OE1" <-> "OE2" Residue "SK GLU 191": "OE1" <-> "OE2" Residue "SQ TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SQ ASP 87": "OD1" <-> "OD2" Residue "SQ GLU 110": "OE1" <-> "OE2" Residue "SQ TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SQ ASP 172": "OD1" <-> "OD2" Residue "SQ ASP 180": "OD1" <-> "OD2" Residue "SQ GLU 185": "OE1" <-> "OE2" Residue "SR PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR ASP 73": "OD1" <-> "OD2" Residue "SR ASP 107": "OD1" <-> "OD2" Residue "SR ASP 121": "OD1" <-> "OD2" Residue "SR GLU 149": "OE1" <-> "OE2" Residue "SR TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR GLU 231": "OE1" <-> "OE2" Residue "SR GLU 270": "OE1" <-> "OE2" Residue "SR PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR GLU 434": "OE1" <-> "OE2" Residue "SR GLU 454": "OE1" <-> "OE2" Residue "ST ASP 35": "OD1" <-> "OD2" Residue "ST GLU 82": "OE1" <-> "OE2" Residue "ST GLU 135": "OE1" <-> "OE2" Residue "ST GLU 155": "OE1" <-> "OE2" Residue "SV GLU 4": "OE1" <-> "OE2" Residue "SV TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SV TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SV ARG 56": "NH1" <-> "NH2" Residue "SV GLU 97": "OE1" <-> "OE2" Residue "SV PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 83377 Number of models: 1 Model: "" Number of chains: 37 Chain: "BA" Number of atoms: 1208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1208 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 150} Chain: "L3" Number of atoms: 33367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1558, 33367 Classifications: {'RNA': 1558} Modifications used: {'rna2p_pur': 127, 'rna2p_pyr': 98, 'rna3p_pur': 700, 'rna3p_pyr': 633} Link IDs: {'rna2p': 224, 'rna3p': 1333} Chain breaks: 33 Chain: "L4" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2561 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 54, 'rna3p_pyr': 54} Link IDs: {'rna2p': 12, 'rna3p': 107} Chain: "L5" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1349 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain: "L7" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1591 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 184} Chain breaks: 1 Chain: "L8" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1111 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain: "LB" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1223 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain: "LC" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1461 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 164} Chain: "LE" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1003 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain breaks: 1 Chain: "LG" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 848 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain breaks: 1 Chain: "LL" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1002 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "LN" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2834 Classifications: {'peptide': 352} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 339} Chain breaks: 1 Chain: "LQ" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 710 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 5, 'TRANS': 84} Chain breaks: 1 Chain: "LT" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 104} Chain: "NB" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 569 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 4, 'TRANS': 62} Chain breaks: 1 Chain: "NC" Number of atoms: 3499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3499 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 24, 'TRANS': 407} Chain breaks: 1 Chain: "ND" Number of atoms: 2193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2193 Classifications: {'peptide': 270} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 257} Chain: "NF" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2038 Classifications: {'peptide': 251} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 238} Chain breaks: 1 Chain: "NJ" Number of atoms: 3662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3662 Classifications: {'peptide': 471} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 450} Chain: "NK" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 581 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain breaks: 1 Chain: "NZ" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 420 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "SA" Number of atoms: 2183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2183 Classifications: {'peptide': 274} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 258} Chain breaks: 2 Chain: "SB" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1875 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 2 Chain: "SC" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1582 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 181} Chain breaks: 2 Chain: "SD" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "SG" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1518 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "SK" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1852 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 7, 'TRANS': 236} Chain: "SQ" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1771 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 7, 'TRANS': 209} Chain: "SR" Number of atoms: 3728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3728 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 19, 'TRANS': 433} Chain breaks: 1 Chain: "ST" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1636 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 15, 'TRANS': 183} Chain: "SV" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1171 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 5, 'TRANS': 131} Chain: "L3" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Unusual residues: {' MG': 18} Classifications: {'undetermined': 18} Link IDs: {None: 17} Chain: "L5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LT" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "NC" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' K': 1, ' MG': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "SR" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' K': 1, ' MG': 1, 'GDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "SV" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 82172 SG CYSSV 6 51.143 176.886 108.378 1.00 38.54 S ATOM 82201 SG CYSSV 9 47.554 175.773 107.929 1.00 45.12 S ATOM 82385 SG CYSSV 32 50.148 173.191 108.902 1.00 40.71 S ATOM 82415 SG CYSSV 36 50.185 174.602 105.447 1.00 46.71 S Time building chain proxies: 32.87, per 1000 atoms: 0.39 Number of scatterers: 83377 At special positions: 0 Unit cell: (244.416, 233.696, 209.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 K 2 19.00 S 219 16.00 P 1683 15.00 Mg 22 11.99 O 20053 8.00 N 15344 7.00 C 46053 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: 30.49 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNSV 500 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 36 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 9 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 32 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 6 " Number of angles added : 6 11554 Ramachandran restraints generated. 5777 Oldfield, 0 Emsley, 5777 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11026 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 190 helices and 58 sheets defined 33.9% alpha, 15.0% beta 566 base pairs and 822 stacking pairs defined. Time for finding SS restraints: 34.59 Creating SS restraints... Processing helix chain 'BA' and resid 25 through 35 Proline residue: BA 30 - end of helix Proline residue: BA 34 - end of helix Processing helix chain 'BA' and resid 39 through 51 Processing helix chain 'BA' and resid 77 through 85 Processing helix chain 'BA' and resid 106 through 115 Processing helix chain 'BA' and resid 125 through 139 Processing helix chain 'BA' and resid 148 through 157 Processing helix chain 'L5' and resid 31 through 44 Processing helix chain 'L5' and resid 77 through 90 removed outlier: 3.747A pdb=" N VALL5 89 " --> pdb=" O LYSL5 85 " (cutoff:3.500A) Processing helix chain 'L5' and resid 139 through 143 Processing helix chain 'L5' and resid 159 through 170 Processing helix chain 'L7' and resid 16 through 28 Processing helix chain 'L7' and resid 38 through 40 No H-bonds generated for 'chain 'L7' and resid 38 through 40' Processing helix chain 'L7' and resid 47 through 59 Processing helix chain 'L7' and resid 76 through 86 Processing helix chain 'L7' and resid 93 through 100 Processing helix chain 'L7' and resid 112 through 114 No H-bonds generated for 'chain 'L7' and resid 112 through 114' Processing helix chain 'L7' and resid 121 through 123 No H-bonds generated for 'chain 'L7' and resid 121 through 123' Processing helix chain 'L7' and resid 125 through 128 No H-bonds generated for 'chain 'L7' and resid 125 through 128' Processing helix chain 'L7' and resid 138 through 145 Processing helix chain 'L7' and resid 150 through 184 Processing helix chain 'L7' and resid 186 through 198 removed outlier: 5.139A pdb=" N LYSL7 191 " --> pdb=" O LYSL7 187 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N TYRL7 192 " --> pdb=" O LYSL7 188 " (cutoff:3.500A) Processing helix chain 'L8' and resid 70 through 80 Processing helix chain 'L8' and resid 82 through 88 Processing helix chain 'L8' and resid 90 through 102 Processing helix chain 'L8' and resid 106 through 135 Processing helix chain 'LB' and resid 23 through 38 Processing helix chain 'LB' and resid 43 through 51 Processing helix chain 'LB' and resid 63 through 71 Processing helix chain 'LB' and resid 107 through 115 Processing helix chain 'LB' and resid 123 through 129 Processing helix chain 'LB' and resid 147 through 151 removed outlier: 3.570A pdb=" N HISLB 151 " --> pdb=" O GLULB 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'LB' and resid 147 through 151' Processing helix chain 'LC' and resid 37 through 51 Processing helix chain 'LC' and resid 102 through 117 Processing helix chain 'LC' and resid 140 through 145 removed outlier: 4.517A pdb=" N PHELC 145 " --> pdb=" O ALALC 141 " (cutoff:3.500A) Processing helix chain 'LE' and resid 103 through 120 Processing helix chain 'LE' and resid 156 through 159 No H-bonds generated for 'chain 'LE' and resid 156 through 159' Processing helix chain 'LG' and resid 123 through 128 Processing helix chain 'LG' and resid 130 through 134 Processing helix chain 'LL' and resid 3 through 10 Processing helix chain 'LL' and resid 86 through 98 Processing helix chain 'LL' and resid 104 through 121 removed outlier: 5.101A pdb=" N METLL 108 " --> pdb=" O ASPLL 105 " (cutoff:3.500A) Processing helix chain 'LN' and resid 14 through 16 No H-bonds generated for 'chain 'LN' and resid 14 through 16' Processing helix chain 'LN' and resid 112 through 117 removed outlier: 3.888A pdb=" N ARGLN 117 " --> pdb=" O GLULN 113 " (cutoff:3.500A) Processing helix chain 'LN' and resid 131 through 138 removed outlier: 4.017A pdb=" N LYSLN 135 " --> pdb=" O THRLN 131 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYSLN 136 " --> pdb=" O LYSLN 132 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TRPLN 137 " --> pdb=" O TYRLN 133 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLNLN 138 " --> pdb=" O CYSLN 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'LN' and resid 131 through 138' Processing helix chain 'LN' and resid 140 through 156 Processing helix chain 'LN' and resid 190 through 199 Processing helix chain 'LN' and resid 207 through 210 No H-bonds generated for 'chain 'LN' and resid 207 through 210' Processing helix chain 'LN' and resid 382 through 389 Processing helix chain 'LN' and resid 393 through 402 Processing helix chain 'LQ' and resid 58 through 60 No H-bonds generated for 'chain 'LQ' and resid 58 through 60' Processing helix chain 'LQ' and resid 82 through 91 removed outlier: 4.207A pdb=" N VALLQ 87 " --> pdb=" O LYSLQ 83 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LEULQ 88 " --> pdb=" O GLULQ 84 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEULQ 89 " --> pdb=" O LEULQ 85 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N METLQ 90 " --> pdb=" O GLULQ 86 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N CYSLQ 91 " --> pdb=" O VALLQ 87 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 105 through 118 Processing helix chain 'LT' and resid 36 through 42 removed outlier: 3.884A pdb=" N GLULT 40 " --> pdb=" O ASPLT 37 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHELT 41 " --> pdb=" O GLULT 38 " (cutoff:3.500A) Processing helix chain 'LT' and resid 94 through 96 No H-bonds generated for 'chain 'LT' and resid 94 through 96' Processing helix chain 'NB' and resid 15 through 35 Processing helix chain 'NB' and resid 57 through 76 removed outlier: 3.620A pdb=" N GLUNB 72 " --> pdb=" O LYSNB 68 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLUNB 73 " --> pdb=" O GLNNB 69 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEUNB 74 " --> pdb=" O ARGNB 70 " (cutoff:3.500A) Processing helix chain 'NC' and resid 35 through 44 Processing helix chain 'NC' and resid 78 through 81 Processing helix chain 'NC' and resid 89 through 98 Processing helix chain 'NC' and resid 134 through 137 No H-bonds generated for 'chain 'NC' and resid 134 through 137' Processing helix chain 'NC' and resid 140 through 143 No H-bonds generated for 'chain 'NC' and resid 140 through 143' Processing helix chain 'NC' and resid 160 through 173 Processing helix chain 'NC' and resid 176 through 178 No H-bonds generated for 'chain 'NC' and resid 176 through 178' Processing helix chain 'NC' and resid 196 through 199 Processing helix chain 'NC' and resid 204 through 216 removed outlier: 3.651A pdb=" N LYSNC 212 " --> pdb=" O GLYNC 208 " (cutoff:3.500A) Processing helix chain 'NC' and resid 229 through 232 No H-bonds generated for 'chain 'NC' and resid 229 through 232' Processing helix chain 'NC' and resid 235 through 243 Processing helix chain 'NC' and resid 257 through 259 No H-bonds generated for 'chain 'NC' and resid 257 through 259' Processing helix chain 'NC' and resid 262 through 275 removed outlier: 3.680A pdb=" N GLNNC 274 " --> pdb=" O ALANC 270 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ASPNC 275 " --> pdb=" O VALNC 271 " (cutoff:3.500A) Processing helix chain 'NC' and resid 291 through 304 removed outlier: 3.909A pdb=" N GLNNC 300 " --> pdb=" O GLNNC 296 " (cutoff:3.500A) Processing helix chain 'NC' and resid 323 through 331 Processing helix chain 'NC' and resid 373 through 378 Processing helix chain 'NC' and resid 384 through 386 No H-bonds generated for 'chain 'NC' and resid 384 through 386' Processing helix chain 'NC' and resid 390 through 400 removed outlier: 3.850A pdb=" N GLYNC 395 " --> pdb=" O ASPNC 392 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEUNC 398 " --> pdb=" O GLYNC 395 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARGNC 400 " --> pdb=" O VALNC 397 " (cutoff:3.500A) Processing helix chain 'NC' and resid 403 through 410 Processing helix chain 'NC' and resid 418 through 429 Processing helix chain 'NC' and resid 434 through 436 No H-bonds generated for 'chain 'NC' and resid 434 through 436' Processing helix chain 'NC' and resid 440 through 452 Processing helix chain 'ND' and resid 13 through 22 Processing helix chain 'ND' and resid 43 through 56 Processing helix chain 'ND' and resid 76 through 85 Processing helix chain 'ND' and resid 148 through 152 removed outlier: 3.665A pdb=" N VALND 152 " --> pdb=" O ASPND 149 " (cutoff:3.500A) Processing helix chain 'ND' and resid 154 through 167 Processing helix chain 'ND' and resid 233 through 240 Processing helix chain 'NF' and resid 6 through 14 Processing helix chain 'NF' and resid 20 through 41 removed outlier: 4.695A pdb=" N ALANF 32 " --> pdb=" O GLUNF 28 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N HISNF 33 " --> pdb=" O SERNF 29 " (cutoff:3.500A) Processing helix chain 'NF' and resid 44 through 71 Processing helix chain 'NF' and resid 106 through 109 No H-bonds generated for 'chain 'NF' and resid 106 through 109' Processing helix chain 'NF' and resid 129 through 132 No H-bonds generated for 'chain 'NF' and resid 129 through 132' Processing helix chain 'NF' and resid 165 through 167 No H-bonds generated for 'chain 'NF' and resid 165 through 167' Processing helix chain 'NF' and resid 206 through 211 Processing helix chain 'NF' and resid 248 through 251 No H-bonds generated for 'chain 'NF' and resid 248 through 251' Processing helix chain 'NJ' and resid 41 through 52 removed outlier: 3.812A pdb=" N LEUNJ 46 " --> pdb=" O ASPNJ 42 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VALNJ 47 " --> pdb=" O ARGNJ 43 " (cutoff:3.500A) Processing helix chain 'NJ' and resid 73 through 79 removed outlier: 4.232A pdb=" N SERNJ 79 " --> pdb=" O LYSNJ 75 " (cutoff:3.500A) Processing helix chain 'NJ' and resid 298 through 303 Processing helix chain 'NJ' and resid 308 through 310 No H-bonds generated for 'chain 'NJ' and resid 308 through 310' Processing helix chain 'NJ' and resid 322 through 337 removed outlier: 3.603A pdb=" N VALNJ 336 " --> pdb=" O ARGNJ 332 " (cutoff:3.500A) Processing helix chain 'NK' and resid 8 through 34 Proline residue: NK 23 - end of helix Processing helix chain 'NK' and resid 99 through 111 Processing helix chain 'NZ' and resid 254 through 258 Processing helix chain 'NZ' and resid 261 through 263 No H-bonds generated for 'chain 'NZ' and resid 261 through 263' Processing helix chain 'NZ' and resid 267 through 281 removed outlier: 3.529A pdb=" N ARGNZ 277 " --> pdb=" O GLUNZ 273 " (cutoff:3.500A) Processing helix chain 'SA' and resid 26 through 29 Processing helix chain 'SA' and resid 34 through 45 Processing helix chain 'SA' and resid 117 through 132 Processing helix chain 'SA' and resid 134 through 139 Processing helix chain 'SA' and resid 156 through 160 Processing helix chain 'SA' and resid 164 through 173 Processing helix chain 'SA' and resid 177 through 185 Processing helix chain 'SA' and resid 217 through 222 Processing helix chain 'SA' and resid 237 through 240 No H-bonds generated for 'chain 'SA' and resid 237 through 240' Processing helix chain 'SA' and resid 254 through 264 removed outlier: 4.764A pdb=" N ASPSA 261 " --> pdb=" O PHESA 257 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLUSA 262 " --> pdb=" O ARGSA 258 " (cutoff:3.500A) Processing helix chain 'SA' and resid 289 through 293 Processing helix chain 'SA' and resid 296 through 301 removed outlier: 3.831A pdb=" N ALASA 301 " --> pdb=" O GLUSA 297 " (cutoff:3.500A) Processing helix chain 'SA' and resid 322 through 328 Processing helix chain 'SA' and resid 330 through 360 removed outlier: 3.534A pdb=" N LYSSA 333 " --> pdb=" O PROSA 330 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASNSA 338 " --> pdb=" O METSA 335 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLNSA 343 " --> pdb=" O ILESA 340 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEUSA 349 " --> pdb=" O ASNSA 346 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VALSA 351 " --> pdb=" O LYSSA 348 " (cutoff:3.500A) Processing helix chain 'SB' and resid 21 through 25 Processing helix chain 'SB' and resid 30 through 37 removed outlier: 3.888A pdb=" N ARGSB 35 " --> pdb=" O TYRSB 31 " (cutoff:3.500A) Processing helix chain 'SB' and resid 80 through 85 Proline residue: SB 84 - end of helix Processing helix chain 'SB' and resid 95 through 113 Processing helix chain 'SB' and resid 158 through 169 Processing helix chain 'SB' and resid 177 through 179 No H-bonds generated for 'chain 'SB' and resid 177 through 179' Processing helix chain 'SB' and resid 192 through 199 Processing helix chain 'SB' and resid 202 through 214 Processing helix chain 'SB' and resid 216 through 222 Processing helix chain 'SB' and resid 224 through 227 No H-bonds generated for 'chain 'SB' and resid 224 through 227' Processing helix chain 'SB' and resid 234 through 249 removed outlier: 4.073A pdb=" N GLUSB 237 " --> pdb=" O ASPSB 234 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYSSB 241 " --> pdb=" O GLUSB 238 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYSSB 242 " --> pdb=" O METSB 239 " (cutoff:3.500A) Processing helix chain 'SC' and resid 59 through 65 Processing helix chain 'SC' and resid 133 through 135 No H-bonds generated for 'chain 'SC' and resid 133 through 135' Processing helix chain 'SC' and resid 179 through 182 No H-bonds generated for 'chain 'SC' and resid 179 through 182' Processing helix chain 'SC' and resid 191 through 193 No H-bonds generated for 'chain 'SC' and resid 191 through 193' Processing helix chain 'SC' and resid 214 through 217 No H-bonds generated for 'chain 'SC' and resid 214 through 217' Processing helix chain 'SC' and resid 244 through 263 removed outlier: 3.905A pdb=" N GLNSC 256 " --> pdb=" O ALASC 252 " (cutoff:3.500A) Proline residue: SC 259 - end of helix Processing helix chain 'SC' and resid 267 through 272 Processing helix chain 'SD' and resid 25 through 77 removed outlier: 3.611A pdb=" N ILESD 69 " --> pdb=" O TYRSD 65 " (cutoff:3.500A) Processing helix chain 'SD' and resid 103 through 111 Processing helix chain 'SD' and resid 127 through 135 removed outlier: 3.512A pdb=" N METSD 132 " --> pdb=" O ALASD 128 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILESD 135 " --> pdb=" O ASNSD 131 " (cutoff:3.500A) Processing helix chain 'SD' and resid 137 through 139 No H-bonds generated for 'chain 'SD' and resid 137 through 139' Processing helix chain 'SD' and resid 147 through 157 Processing helix chain 'SD' and resid 172 through 182 removed outlier: 3.586A pdb=" N SERSD 178 " --> pdb=" O LEUSD 174 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LYSSD 181 " --> pdb=" O ARGSD 177 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N TYRSD 182 " --> pdb=" O SERSD 178 " (cutoff:3.500A) Processing helix chain 'SD' and resid 187 through 195 Processing helix chain 'SD' and resid 201 through 207 Processing helix chain 'SD' and resid 240 through 247 removed outlier: 3.566A pdb=" N ARGSD 246 " --> pdb=" O ARGSD 242 " (cutoff:3.500A) Processing helix chain 'SG' and resid 64 through 85 removed outlier: 4.123A pdb=" N THRSG 69 " --> pdb=" O LYSSG 65 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VALSG 70 " --> pdb=" O GLUSG 66 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARGSG 71 " --> pdb=" O LEUSG 67 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THRSG 72 " --> pdb=" O ALASG 68 " (cutoff:3.500A) Processing helix chain 'SG' and resid 151 through 164 Processing helix chain 'SK' and resid 13 through 16 No H-bonds generated for 'chain 'SK' and resid 13 through 16' Processing helix chain 'SK' and resid 33 through 42 removed outlier: 3.623A pdb=" N PHESK 38 " --> pdb=" O PHESK 34 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLUSK 41 " --> pdb=" O VALSK 37 " (cutoff:3.500A) Processing helix chain 'SK' and resid 78 through 87 Processing helix chain 'SK' and resid 104 through 107 No H-bonds generated for 'chain 'SK' and resid 104 through 107' Processing helix chain 'SK' and resid 123 through 133 Processing helix chain 'SK' and resid 148 through 151 No H-bonds generated for 'chain 'SK' and resid 148 through 151' Processing helix chain 'SK' and resid 167 through 177 Processing helix chain 'SK' and resid 193 through 196 No H-bonds generated for 'chain 'SK' and resid 193 through 196' Processing helix chain 'SK' and resid 212 through 221 Processing helix chain 'SK' and resid 232 through 235 No H-bonds generated for 'chain 'SK' and resid 232 through 235' Processing helix chain 'SK' and resid 237 through 243 Processing helix chain 'SQ' and resid 22 through 36 removed outlier: 3.555A pdb=" N ASPSQ 35 " --> pdb=" O ARGSQ 31 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 51 through 59 removed outlier: 3.523A pdb=" N LYSSQ 54 " --> pdb=" O SERSQ 51 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 70 through 77 Processing helix chain 'SQ' and resid 89 through 95 removed outlier: 3.831A pdb=" N ARGSQ 95 " --> pdb=" O GLNSQ 91 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 109 through 118 Processing helix chain 'SQ' and resid 147 through 155 Proline residue: SQ 151 - end of helix Processing helix chain 'SQ' and resid 184 through 193 Processing helix chain 'SR' and resid 15 through 28 removed outlier: 3.535A pdb=" N LYSSR 25 " --> pdb=" O LEUSR 21 " (cutoff:3.500A) Processing helix chain 'SR' and resid 40 through 68 removed outlier: 3.658A pdb=" N LYSSR 50 " --> pdb=" O PHESR 46 " (cutoff:3.500A) Processing helix chain 'SR' and resid 77 through 87 Processing helix chain 'SR' and resid 89 through 119 removed outlier: 3.778A pdb=" N LYSSR 118 " --> pdb=" O VALSR 114 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYRSR 119 " --> pdb=" O ARGSR 115 " (cutoff:3.500A) Processing helix chain 'SR' and resid 123 through 159 removed outlier: 3.567A pdb=" N ARGSR 143 " --> pdb=" O THRSR 139 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLNSR 144 " --> pdb=" O VALSR 140 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYSSR 145 " --> pdb=" O ILESR 141 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N GLNSR 146 " --> pdb=" O LYSSR 142 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N SERSR 147 " --> pdb=" O ARGSR 143 " (cutoff:3.500A) Processing helix chain 'SR' and resid 181 through 188 removed outlier: 3.652A pdb=" N ASNSR 186 " --> pdb=" O SERSR 182 " (cutoff:3.500A) Processing helix chain 'SR' and resid 235 through 246 removed outlier: 3.996A pdb=" N ALASR 240 " --> pdb=" O ILESR 236 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILESR 241 " --> pdb=" O GLUSR 237 " (cutoff:3.500A) Processing helix chain 'SR' and resid 265 through 274 removed outlier: 3.845A pdb=" N PHESR 272 " --> pdb=" O GLNSR 268 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLNSR 273 " --> pdb=" O LEUSR 269 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASNSR 274 " --> pdb=" O GLUSR 270 " (cutoff:3.500A) Processing helix chain 'SR' and resid 301 through 313 removed outlier: 3.662A pdb=" N ILESR 306 " --> pdb=" O ASPSR 302 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHESR 307 " --> pdb=" O ASPSR 303 " (cutoff:3.500A) Processing helix chain 'SR' and resid 328 through 349 Processing helix chain 'SR' and resid 352 through 360 removed outlier: 3.830A pdb=" N VALSR 356 " --> pdb=" O LYSSR 352 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEUSR 357 " --> pdb=" O VALSR 353 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ASNSR 358 " --> pdb=" O ASNSR 354 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ARGSR 359 " --> pdb=" O GLUSR 355 " (cutoff:3.500A) Processing helix chain 'SR' and resid 398 through 404 Processing helix chain 'SR' and resid 413 through 416 removed outlier: 3.680A pdb=" N TYRSR 416 " --> pdb=" O LEUSR 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 413 through 416' Processing helix chain 'SR' and resid 423 through 425 No H-bonds generated for 'chain 'SR' and resid 423 through 425' Processing helix chain 'SR' and resid 438 through 441 No H-bonds generated for 'chain 'SR' and resid 438 through 441' Processing helix chain 'SR' and resid 446 through 462 Processing helix chain 'ST' and resid 6 through 24 Processing helix chain 'ST' and resid 36 through 38 No H-bonds generated for 'chain 'ST' and resid 36 through 38' Processing helix chain 'ST' and resid 48 through 53 Processing helix chain 'ST' and resid 58 through 78 removed outlier: 3.583A pdb=" N LEUST 71 " --> pdb=" O ASPST 67 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLNST 75 " --> pdb=" O LEUST 71 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLNST 78 " --> pdb=" O ASNST 74 " (cutoff:3.500A) Processing helix chain 'ST' and resid 113 through 121 Processing helix chain 'ST' and resid 170 through 198 Processing helix chain 'SV' and resid 34 through 42 Processing helix chain 'SV' and resid 53 through 58 Processing helix chain 'SV' and resid 68 through 71 Processing helix chain 'SV' and resid 83 through 129 removed outlier: 3.538A pdb=" N ARGSV 111 " --> pdb=" O PHESV 107 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYSSV 114 " --> pdb=" O ASNSV 110 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASNSV 115 " --> pdb=" O ARGSV 111 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LYSSV 116 " --> pdb=" O LEUSV 112 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLUSV 117 " --> pdb=" O LYSSV 113 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYSSV 128 " --> pdb=" O ILESV 124 " (cutoff:3.500A) Processing helix chain 'SV' and resid 131 through 134 No H-bonds generated for 'chain 'SV' and resid 131 through 134' Processing sheet with id= A, first strand: chain 'BA' and resid 11 through 17 removed outlier: 4.120A pdb=" N THRBA 59 " --> pdb=" O VALBA 74 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'L5' and resid 105 through 109 removed outlier: 3.876A pdb=" N LYSL5 19 " --> pdb=" O VALL5 133 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N GLYL5 135 " --> pdb=" O ILEL5 17 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ILEL5 17 " --> pdb=" O GLYL5 135 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N SERL5 51 " --> pdb=" O ILEL5 68 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VALL5 70 " --> pdb=" O VALL5 49 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VALL5 49 " --> pdb=" O VALL5 70 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'L7' and resid 6 through 10 removed outlier: 6.823A pdb=" N LYSL7 32 " --> pdb=" O LEUL7 7 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N LEUL7 9 " --> pdb=" O LYSL7 32 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VALL7 34 " --> pdb=" O LEUL7 9 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'L7' and resid 42 through 44 Processing sheet with id= E, first strand: chain 'L8' and resid 55 through 57 removed outlier: 6.820A pdb=" N LEUL8 37 " --> pdb=" O VALL8 28 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N VALL8 30 " --> pdb=" O ARGL8 35 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ARGL8 35 " --> pdb=" O VALL8 30 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'LB' and resid 136 through 139 removed outlier: 6.203A pdb=" N THRLB 79 " --> pdb=" O VALLB 137 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEULB 139 " --> pdb=" O THRLB 79 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VALLB 81 " --> pdb=" O LEULB 139 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LYSLB 119 " --> pdb=" O VALLB 100 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ALALB 102 " --> pdb=" O LYSLB 119 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEULB 121 " --> pdb=" O ALALB 102 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'LC' and resid 27 through 34 removed outlier: 6.849A pdb=" N ARGLC 15 " --> pdb=" O ILELC 61 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ILELC 61 " --> pdb=" O ARGLC 15 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'LC' and resid 90 through 99 removed outlier: 4.305A pdb=" N ASNLC 77 " --> pdb=" O ILELC 132 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ARGLC 83 " --> pdb=" O ILELC 126 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ILELC 126 " --> pdb=" O ARGLC 83 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ASPLC 85 " --> pdb=" O ILELC 124 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILELC 124 " --> pdb=" O ASPLC 85 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'LE' and resid 96 through 98 removed outlier: 6.949A pdb=" N THRLE 61 " --> pdb=" O ASNLE 77 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ASNLE 77 " --> pdb=" O THRLE 61 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLYLE 73 " --> pdb=" O TYRLE 65 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N VALLE 67 " --> pdb=" O ALALE 71 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ALALE 71 " --> pdb=" O VALLE 67 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'LG' and resid 25 through 27 removed outlier: 6.885A pdb=" N METLG 62 " --> pdb=" O ILELG 40 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VALLG 42 " --> pdb=" O METLG 60 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N METLG 60 " --> pdb=" O VALLG 42 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALALG 102 " --> pdb=" O ILELG 82 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'LL' and resid 17 through 20 Processing sheet with id= L, first strand: chain 'LL' and resid 49 through 53 Processing sheet with id= M, first strand: chain 'LN' and resid 276 through 279 removed outlier: 5.275A pdb=" N VALLN 222 " --> pdb=" O VALLN 344 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VALLN 344 " --> pdb=" O VALLN 222 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILELN 78 " --> pdb=" O ALALN 51 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N METLN 53 " --> pdb=" O VALLN 76 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VALLN 76 " --> pdb=" O METLN 53 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N HISLN 55 " --> pdb=" O GLULN 74 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLULN 74 " --> pdb=" O HISLN 55 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VALLN 57 " --> pdb=" O VALLN 72 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VALLN 72 " --> pdb=" O VALLN 57 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYSLN 286 " --> pdb=" O METLN 332 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYSLN 334 " --> pdb=" O ILELN 284 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILELN 284 " --> pdb=" O LYSLN 334 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'LN' and resid 180 through 185 removed outlier: 4.884A pdb=" N ILELN 160 " --> pdb=" O VALLN 185 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VALLN 159 " --> pdb=" O TYRLN 92 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N HISLN 165 " --> pdb=" O VALLN 86 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N VALLN 86 " --> pdb=" O HISLN 165 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYSLN 103 " --> pdb=" O GLYLN 91 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N VALLN 93 " --> pdb=" O THRLN 101 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THRLN 101 " --> pdb=" O VALLN 93 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THRLN 95 " --> pdb=" O LEULN 99 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LEULN 99 " --> pdb=" O THRLN 95 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'LN' and resid 292 through 294 removed outlier: 3.882A pdb=" N LEULN 292 " --> pdb=" O ILELN 299 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'LN' and resid 56 through 58 Processing sheet with id= Q, first strand: chain 'LQ' and resid 75 through 79 Processing sheet with id= R, first strand: chain 'LT' and resid 100 through 104 removed outlier: 6.773A pdb=" N LEULT 27 " --> pdb=" O ALALT 12 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N TYRLT 14 " --> pdb=" O THRLT 25 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N THRLT 25 " --> pdb=" O TYRLT 14 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N METLT 83 " --> pdb=" O HISLT 78 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LYSLT 87 " --> pdb=" O VALLT 74 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N VALLT 74 " --> pdb=" O LYSLT 87 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'NC' and resid 349 through 354 removed outlier: 6.665A pdb=" N ILENC 357 " --> pdb=" O LEUNC 353 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILENC 311 " --> pdb=" O PHENC 358 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILENC 360 " --> pdb=" O ILENC 311 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VALNC 313 " --> pdb=" O ILENC 360 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VALNC 219 " --> pdb=" O GLYNC 314 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILENC 316 " --> pdb=" O VALNC 219 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VALNC 221 " --> pdb=" O ILENC 316 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N HISNC 249 " --> pdb=" O VALNC 220 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N GLNNC 222 " --> pdb=" O HISNC 249 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILENC 251 " --> pdb=" O GLNNC 222 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEUNC 224 " --> pdb=" O ILENC 251 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VALNC 253 " --> pdb=" O LEUNC 224 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'ND' and resid 60 through 62 removed outlier: 6.429A pdb=" N ALAND 33 " --> pdb=" O VALND 61 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEUND 89 " --> pdb=" O METND 34 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ILEND 36 " --> pdb=" O LEUND 89 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N METND 91 " --> pdb=" O ILEND 36 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N TYRND 109 " --> pdb=" O VALND 113 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N VALND 113 " --> pdb=" O TYRND 109 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N METND 142 " --> pdb=" O LEUND 184 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N PHEND 186 " --> pdb=" O METND 142 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILEND 144 " --> pdb=" O PHEND 186 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ALAND 188 " --> pdb=" O ILEND 144 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ALAND 146 " --> pdb=" O ALAND 188 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'ND' and resid 198 through 203 Processing sheet with id= V, first strand: chain 'ND' and resid 254 through 256 Processing sheet with id= W, first strand: chain 'NF' and resid 133 through 136 removed outlier: 4.083A pdb=" N LYSNF 147 " --> pdb=" O ILENF 136 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'NF' and resid 190 through 195 removed outlier: 3.755A pdb=" N ALANF 190 " --> pdb=" O HISNF 185 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'NJ' and resid 33 through 36 removed outlier: 6.448A pdb=" N LEUNJ 88 " --> pdb=" O GLNNJ 20 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N GLNNJ 22 " --> pdb=" O LEUNJ 88 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ILENJ 90 " --> pdb=" O GLNNJ 22 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'NJ' and resid 117 through 122 removed outlier: 6.502A pdb=" N GLYNJ 132 " --> pdb=" O ILENJ 118 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VALNJ 120 " --> pdb=" O ALANJ 130 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALANJ 130 " --> pdb=" O VALNJ 120 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEUNJ 129 " --> pdb=" O TRPNJ 141 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SERNJ 133 " --> pdb=" O THRNJ 137 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THRNJ 137 " --> pdb=" O SERNJ 133 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ASPNJ 142 " --> pdb=" O PRONJ 148 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'NJ' and resid 180 through 183 Processing sheet with id= AB, first strand: chain 'NJ' and resid 202 through 207 removed outlier: 6.827A pdb=" N SERNJ 222 " --> pdb=" O THRNJ 203 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEUNJ 205 " --> pdb=" O ALANJ 220 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALANJ 220 " --> pdb=" O LEUNJ 205 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N TRPNJ 207 " --> pdb=" O TYRNJ 218 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N TYRNJ 218 " --> pdb=" O TRPNJ 207 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ASPNJ 232 " --> pdb=" O CYSNJ 238 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N CYSNJ 238 " --> pdb=" O ASPNJ 232 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'NJ' and resid 249 through 254 removed outlier: 6.836A pdb=" N ALANJ 263 " --> pdb=" O THRNJ 250 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LEUNJ 252 " --> pdb=" O TYRNJ 261 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N TYRNJ 261 " --> pdb=" O LEUNJ 252 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N TRPNJ 254 " --> pdb=" O LEUNJ 259 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEUNJ 259 " --> pdb=" O TRPNJ 254 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N THRNJ 268 " --> pdb=" O SERNJ 264 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARGNJ 281 " --> pdb=" O VALNJ 271 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ARGNJ 273 " --> pdb=" O LEUNJ 279 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEUNJ 279 " --> pdb=" O ARGNJ 273 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'NJ' and resid 366 through 368 removed outlier: 3.803A pdb=" N THRNJ 366 " --> pdb=" O LEUNJ 355 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THRNJ 292 " --> pdb=" O GLYNJ 347 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'NJ' and resid 375 through 380 removed outlier: 6.840A pdb=" N ALANJ 390 " --> pdb=" O ASNNJ 376 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VALNJ 378 " --> pdb=" O ALANJ 388 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ALANJ 388 " --> pdb=" O VALNJ 378 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N PHENJ 380 " --> pdb=" O ILENJ 386 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILENJ 386 " --> pdb=" O PHENJ 380 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALANJ 408 " --> pdb=" O LEUNJ 398 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ASPNJ 400 " --> pdb=" O TYRNJ 406 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TYRNJ 406 " --> pdb=" O ASPNJ 400 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'NJ' and resid 417 through 422 removed outlier: 6.779A pdb=" N GLYNJ 432 " --> pdb=" O TYRNJ 418 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILENJ 420 " --> pdb=" O VALNJ 430 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VALNJ 430 " --> pdb=" O ILENJ 420 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N TRPNJ 422 " --> pdb=" O LEUNJ 428 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N LEUNJ 428 " --> pdb=" O TRPNJ 422 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ASPNJ 442 " --> pdb=" O LEUNJ 448 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEUNJ 448 " --> pdb=" O ASPNJ 442 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'NJ' and resid 105 through 110 removed outlier: 6.998A pdb=" N ILENJ 482 " --> pdb=" O THRNJ 107 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N SERNJ 109 " --> pdb=" O LEUNJ 480 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEUNJ 480 " --> pdb=" O SERNJ 109 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'SA' and resid 7 through 9 Processing sheet with id= AI, first strand: chain 'SA' and resid 152 through 154 removed outlier: 4.394A pdb=" N LEUSA 152 " --> pdb=" O CYSSA 250 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N CYSSA 208 " --> pdb=" O ILESA 251 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N THRSA 253 " --> pdb=" O CYSSA 208 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ILESA 210 " --> pdb=" O THRSA 253 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THRSA 228 " --> pdb=" O ILESA 209 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N TYRSA 211 " --> pdb=" O THRSA 228 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEUSA 230 " --> pdb=" O TYRSA 211 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'SB' and resid 145 through 147 removed outlier: 3.790A pdb=" N VALSB 53 " --> pdb=" O ASPSB 147 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYSSB 76 " --> pdb=" O ILESB 64 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N TYRSB 66 " --> pdb=" O ILESB 74 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ILESB 74 " --> pdb=" O TYRSB 66 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'SC' and resid 194 through 196 removed outlier: 7.021A pdb=" N LEUSC 174 " --> pdb=" O LEUSC 165 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'SD' and resid 120 through 124 Processing sheet with id= AM, first strand: chain 'SD' and resid 159 through 162 Processing sheet with id= AN, first strand: chain 'SG' and resid 5 through 11 Processing sheet with id= AO, first strand: chain 'SG' and resid 17 through 21 Processing sheet with id= AP, first strand: chain 'SG' and resid 133 through 136 removed outlier: 3.695A pdb=" N GLUSG 183 " --> pdb=" O LYSSG 91 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ARGSG 93 " --> pdb=" O VALSG 181 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N VALSG 181 " --> pdb=" O ARGSG 93 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VALSG 95 " --> pdb=" O ILESG 179 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILESG 179 " --> pdb=" O VALSG 95 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'SG' and resid 102 through 106 Processing sheet with id= AR, first strand: chain 'SK' and resid 2 through 5 removed outlier: 6.823A pdb=" N ALASK 204 " --> pdb=" O VALSK 3 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ALASK 5 " --> pdb=" O ALASK 204 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N CYSSK 206 " --> pdb=" O ALASK 5 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'SK' and resid 17 through 19 removed outlier: 7.792A pdb=" N VALSK 26 " --> pdb=" O PROSK 47 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VALSK 49 " --> pdb=" O VALSK 26 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'SK' and resid 69 through 72 removed outlier: 6.246A pdb=" N GLNSK 93 " --> pdb=" O LEUSK 70 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N VALSK 72 " --> pdb=" O GLNSK 93 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ARGSK 95 " --> pdb=" O VALSK 72 " (cutoff:3.500A) No H-bonds generated for sheet with id= AT Processing sheet with id= AU, first strand: chain 'SK' and resid 108 through 110 removed outlier: 6.206A pdb=" N GLUSK 136 " --> pdb=" O ALASK 115 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VALSK 117 " --> pdb=" O GLUSK 136 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N PHESK 138 " --> pdb=" O VALSK 117 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'SK' and resid 158 through 161 removed outlier: 7.300A pdb=" N VALSK 161 " --> pdb=" O PROSK 180 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VALSK 182 " --> pdb=" O VALSK 161 " (cutoff:3.500A) No H-bonds generated for sheet with id= AV Processing sheet with id= AW, first strand: chain 'SQ' and resid 64 through 66 removed outlier: 3.767A pdb=" N TYRSQ 206 " --> pdb=" O ILESQ 42 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N SERSQ 44 " --> pdb=" O ILESQ 204 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILESQ 204 " --> pdb=" O SERSQ 44 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'SQ' and resid 121 through 123 Processing sheet with id= AY, first strand: chain 'SQ' and resid 140 through 142 removed outlier: 4.266A pdb=" N VALSQ 167 " --> pdb=" O LEUSQ 142 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'SQ' and resid 135 through 137 removed outlier: 3.604A pdb=" N CYSSQ 176 " --> pdb=" O VALSQ 135 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEUSQ 137 " --> pdb=" O GLUSQ 174 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N GLUSQ 174 " --> pdb=" O LEUSQ 137 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'SR' and resid 170 through 172 removed outlier: 8.750A pdb=" N LEUSR 171 " --> pdb=" O ARGSR 216 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLNSR 218 " --> pdb=" O LEUSR 171 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'SR' and resid 251 through 255 removed outlier: 7.030A pdb=" N ALASR 288 " --> pdb=" O PROSR 316 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILESR 318 " --> pdb=" O ALASR 288 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'ST' and resid 33 through 35 Processing sheet with id= BD, first strand: chain 'ST' and resid 81 through 84 Processing sheet with id= BE, first strand: chain 'ST' and resid 131 through 134 Processing sheet with id= BF, first strand: chain 'SV' and resid 19 through 23 removed outlier: 3.842A pdb=" N LYSSV 27 " --> pdb=" O ARGSV 23 " (cutoff:3.500A) 1625 hydrogen bonds defined for protein. 4494 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1501 hydrogen bonds 2600 hydrogen bond angles 0 basepair planarities 566 basepair parallelities 822 stacking parallelities Total time for adding SS restraints: 69.30 Time building geometry restraints manager: 33.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 13224 1.33 - 1.45: 30951 1.45 - 1.57: 40588 1.57 - 1.69: 3329 1.69 - 1.82: 357 Bond restraints: 88449 Sorted by residual: bond pdb=" C5 GTPNC1000 " pdb=" N7 GTPNC1000 " ideal model delta sigma weight residual 1.350 1.518 -0.168 2.00e-02 2.50e+03 7.10e+01 bond pdb=" C6 GTPNC1000 " pdb=" O6 GTPNC1000 " ideal model delta sigma weight residual 1.230 1.398 -0.168 2.00e-02 2.50e+03 7.05e+01 bond pdb=" N7 GDPSR1001 " pdb=" C5 GDPSR1001 " ideal model delta sigma weight residual 1.350 1.517 -0.167 2.00e-02 2.50e+03 6.98e+01 bond pdb=" C6 GDPSR1001 " pdb=" O6 GDPSR1001 " ideal model delta sigma weight residual 1.250 1.399 -0.149 2.00e-02 2.50e+03 5.54e+01 bond pdb=" C2 GTPNC1000 " pdb=" N2 GTPNC1000 " ideal model delta sigma weight residual 1.330 1.450 -0.120 2.00e-02 2.50e+03 3.62e+01 ... (remaining 88444 not shown) Histogram of bond angle deviations from ideal: 98.59 - 106.73: 11002 106.73 - 114.88: 55870 114.88 - 123.03: 49132 123.03 - 131.17: 10933 131.17 - 139.32: 480 Bond angle restraints: 127417 Sorted by residual: angle pdb=" N ARGSC 156 " pdb=" CA ARGSC 156 " pdb=" C ARGSC 156 " ideal model delta sigma weight residual 111.36 104.44 6.92 1.09e+00 8.42e-01 4.03e+01 angle pdb=" N ASPNJ 383 " pdb=" CA ASPNJ 383 " pdb=" C ASPNJ 383 " ideal model delta sigma weight residual 110.48 101.91 8.57 1.48e+00 4.57e-01 3.35e+01 angle pdb=" CA GLYSC 155 " pdb=" C GLYSC 155 " pdb=" O GLYSC 155 " ideal model delta sigma weight residual 122.28 117.94 4.34 1.00e+00 1.00e+00 1.89e+01 angle pdb=" CA ASPNJ 383 " pdb=" C ASPNJ 383 " pdb=" N SERNJ 384 " ideal model delta sigma weight residual 115.49 120.80 -5.31 1.24e+00 6.50e-01 1.83e+01 angle pdb=" N PROLG 70 " pdb=" CA PROLG 70 " pdb=" C PROLG 70 " ideal model delta sigma weight residual 113.53 119.46 -5.93 1.39e+00 5.18e-01 1.82e+01 ... (remaining 127412 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 51958 35.98 - 71.97: 4138 71.97 - 107.95: 561 107.95 - 143.93: 10 143.93 - 179.92: 13 Dihedral angle restraints: 56680 sinusoidal: 39642 harmonic: 17038 Sorted by residual: dihedral pdb=" O4' CL34443 " pdb=" C1' CL34443 " pdb=" N1 CL34443 " pdb=" C2 CL34443 " ideal model delta sinusoidal sigma weight residual -160.00 17.49 -177.49 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' CL34476 " pdb=" C1' CL34476 " pdb=" N1 CL34476 " pdb=" C2 CL34476 " ideal model delta sinusoidal sigma weight residual 200.00 35.35 164.65 1 1.50e+01 4.44e-03 8.38e+01 dihedral pdb=" O4' UL34442 " pdb=" C1' UL34442 " pdb=" N1 UL34442 " pdb=" C2 UL34442 " ideal model delta sinusoidal sigma weight residual -160.00 0.85 -160.85 1 1.50e+01 4.44e-03 8.30e+01 ... (remaining 56677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 13935 0.052 - 0.104: 1190 0.104 - 0.157: 349 0.157 - 0.209: 7 0.209 - 0.261: 5 Chirality restraints: 15486 Sorted by residual: chirality pdb=" CA ARGSC 156 " pdb=" N ARGSC 156 " pdb=" C ARGSC 156 " pdb=" CB ARGSC 156 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" C3' AL31943 " pdb=" C4' AL31943 " pdb=" O3' AL31943 " pdb=" C2' AL31943 " both_signs ideal model delta sigma weight residual False -2.74 -2.49 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA ASPNJ 383 " pdb=" N ASPNJ 383 " pdb=" C ASPNJ 383 " pdb=" CB ASPNJ 383 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 15483 not shown) Planarity restraints: 9912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VALNJ 35 " 0.052 5.00e-02 4.00e+02 7.86e-02 9.88e+00 pdb=" N PRONJ 36 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRONJ 36 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRONJ 36 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLYSC 155 " -0.014 2.00e-02 2.50e+03 2.93e-02 8.59e+00 pdb=" C GLYSC 155 " 0.051 2.00e-02 2.50e+03 pdb=" O GLYSC 155 " -0.019 2.00e-02 2.50e+03 pdb=" N ARGSC 156 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEUSQ 158 " -0.045 5.00e-02 4.00e+02 6.79e-02 7.38e+00 pdb=" N PROSQ 159 " 0.117 5.00e-02 4.00e+02 pdb=" CA PROSQ 159 " -0.035 5.00e-02 4.00e+02 pdb=" CD PROSQ 159 " -0.038 5.00e-02 4.00e+02 ... (remaining 9909 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.57: 475 2.57 - 3.21: 72740 3.21 - 3.86: 178898 3.86 - 4.50: 249474 4.50 - 5.14: 350410 Nonbonded interactions: 851997 Sorted by model distance: nonbonded pdb=" OP2 AL31917 " pdb="MG MGL35107 " model vdw 1.930 2.170 nonbonded pdb=" OG1 THRNC 345 " pdb="MG MGNC1001 " model vdw 1.957 2.170 nonbonded pdb=" O2B GTPNC1000 " pdb="MG MGNC1001 " model vdw 1.973 2.170 nonbonded pdb=" OG1 THRSR 202 " pdb="MG MGSR1003 " model vdw 2.004 2.170 nonbonded pdb=" O2' CL34670 " pdb=" OP2 AL34672 " model vdw 2.005 2.440 ... (remaining 851992 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 23.580 Check model and map are aligned: 0.950 Set scattering table: 0.610 Process input model: 246.710 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.210 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:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 292.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 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 : 0.003 0.168 88449 Z= 0.195 Angle : 0.568 12.706 127417 Z= 0.297 Chirality : 0.035 0.261 15486 Planarity : 0.004 0.079 9912 Dihedral : 20.946 179.916 45654 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 0.95 % Favored : 99.03 % Rotamer: Outliers : 0.02 % Allowed : 0.12 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.11), residues: 5777 helix: 2.10 (0.12), residues: 1964 sheet: 0.87 (0.16), residues: 987 loop : 0.26 (0.11), residues: 2826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPNJ 201 HIS 0.007 0.001 HISSK 118 PHE 0.019 0.001 PHENC 140 TYR 0.028 0.001 TYRL5 92 ARG 0.020 0.001 ARGLC 138 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11554 Ramachandran restraints generated. 5777 Oldfield, 0 Emsley, 5777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11554 Ramachandran restraints generated. 5777 Oldfield, 0 Emsley, 5777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 920 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 919 time to evaluate : 5.212 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: LB 77 ASN cc_start: 0.7640 (t0) cc_final: 0.7321 (t0) REVERT: LC 127 MET cc_start: 0.8292 (mmm) cc_final: 0.7881 (mmt) REVERT: LQ 117 GLN cc_start: 0.8348 (mt0) cc_final: 0.7777 (mt0) REVERT: NB 70 ARG cc_start: 0.6683 (tpp80) cc_final: 0.5901 (tpm170) REVERT: NJ 337 ARG cc_start: 0.7547 (ttt180) cc_final: 0.7316 (ttt180) REVERT: SG 113 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6868 (mt-10) REVERT: SQ 47 ASN cc_start: 0.8183 (t0) cc_final: 0.7679 (t0) REVERT: SR 342 HIS cc_start: 0.8070 (t-90) cc_final: 0.7850 (t-170) outliers start: 1 outliers final: 4 residues processed: 920 average time/residue: 1.8440 time to fit residues: 2211.4326 Evaluate side-chains 563 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 559 time to evaluate : 5.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LQ residue 92 ASN Chi-restraints excluded: chain NJ residue 97 ILE Chi-restraints excluded: chain NJ residue 381 SER Chi-restraints excluded: chain ST residue 152 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 626 optimal weight: 9.9990 chunk 562 optimal weight: 0.9980 chunk 312 optimal weight: 7.9990 chunk 192 optimal weight: 0.0060 chunk 379 optimal weight: 0.4980 chunk 300 optimal weight: 1.9990 chunk 581 optimal weight: 5.9990 chunk 225 optimal weight: 3.9990 chunk 353 optimal weight: 8.9990 chunk 432 optimal weight: 0.8980 chunk 673 optimal weight: 2.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 103 ASN L5 110 GLN L7 96 GLN L8 131 GLN LB 21 GLN LC 91 HIS LE 77 ASN LE 90 ASN LE 112 ASN ** LG 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LL 6 GLN LL 30 ASN LL 41 ASN LL 100 ASN LN 42 HIS NB 28 HIS NB 69 GLN NC 96 GLN NC 296 GLN ND 229 HIS ND 271 GLN NF 3 GLN NF 33 HIS NJ 93 GLN NJ 275 HIS NJ 376 ASN NK 21 ASN SB 45 ASN SB 191 ASN SC 136 HIS SC 190 HIS SD 239 GLN SK 83 HIS ** SQ 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 39 GLN SR 91 HIS SR 108 ASN SR 157 HIS SR 209 HIS ** ST 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ST 78 GLN ST 130 ASN ST 188 ASN SV 17 HIS SV 87 ASN SV 104 GLN SV 115 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 88449 Z= 0.158 Angle : 0.506 10.647 127417 Z= 0.260 Chirality : 0.034 0.225 15486 Planarity : 0.004 0.073 9912 Dihedral : 22.373 179.835 33290 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.21 % Favored : 98.77 % Rotamer: Outliers : 1.68 % Allowed : 9.73 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.11), residues: 5777 helix: 2.16 (0.11), residues: 1962 sheet: 0.85 (0.16), residues: 999 loop : 0.30 (0.11), residues: 2816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPNJ 231 HIS 0.008 0.001 HISNJ 275 PHE 0.021 0.001 PHESR 18 TYR 0.023 0.001 TYRNJ 92 ARG 0.012 0.000 ARGNC 428 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11554 Ramachandran restraints generated. 5777 Oldfield, 0 Emsley, 5777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11554 Ramachandran restraints generated. 5777 Oldfield, 0 Emsley, 5777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 596 time to evaluate : 5.142 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: L5 131 TYR cc_start: 0.8574 (t80) cc_final: 0.8146 (t80) REVERT: LC 127 MET cc_start: 0.8461 (mmm) cc_final: 0.7881 (mmt) REVERT: LN 325 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.6331 (mt-10) REVERT: NB 70 ARG cc_start: 0.6775 (tpp80) cc_final: 0.6172 (tpm170) REVERT: NF 66 LYS cc_start: 0.8339 (ttmm) cc_final: 0.8106 (ttmm) REVERT: NJ 485 ARG cc_start: 0.6347 (OUTLIER) cc_final: 0.5464 (tmt170) REVERT: SC 245 GLN cc_start: 0.7241 (OUTLIER) cc_final: 0.6626 (tt0) REVERT: SQ 47 ASN cc_start: 0.8275 (t0) cc_final: 0.7853 (t0) REVERT: SR 342 HIS cc_start: 0.7865 (t-90) cc_final: 0.7658 (t-170) REVERT: ST 165 ASP cc_start: 0.7323 (OUTLIER) cc_final: 0.7021 (t0) outliers start: 86 outliers final: 31 residues processed: 638 average time/residue: 1.6460 time to fit residues: 1406.1019 Evaluate side-chains 565 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 530 time to evaluate : 5.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L8 residue 130 LEU Chi-restraints excluded: chain LB residue 42 THR Chi-restraints excluded: chain LE residue 68 THR Chi-restraints excluded: chain LE residue 84 ILE Chi-restraints excluded: chain LG residue 118 THR Chi-restraints excluded: chain LN residue 208 ASN Chi-restraints excluded: chain LN residue 325 GLU Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain NB residue 50 VAL Chi-restraints excluded: chain NC residue 97 GLU Chi-restraints excluded: chain NC residue 422 LEU Chi-restraints excluded: chain ND residue 242 MET Chi-restraints excluded: chain NF residue 29 SER Chi-restraints excluded: chain NF residue 97 SER Chi-restraints excluded: chain NJ residue 97 ILE Chi-restraints excluded: chain NJ residue 381 SER Chi-restraints excluded: chain NJ residue 485 ARG Chi-restraints excluded: chain NK residue 4 SER Chi-restraints excluded: chain SB residue 187 SER Chi-restraints excluded: chain SC residue 220 LYS Chi-restraints excluded: chain SC residue 245 GLN Chi-restraints excluded: chain SD residue 68 GLU Chi-restraints excluded: chain SG residue 6 SER Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain SG residue 182 SER Chi-restraints excluded: chain SQ residue 155 GLN Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 330 LYS Chi-restraints excluded: chain SR residue 401 LEU Chi-restraints excluded: chain SR residue 422 LEU Chi-restraints excluded: chain ST residue 24 ILE Chi-restraints excluded: chain ST residue 48 THR Chi-restraints excluded: chain ST residue 165 ASP Chi-restraints excluded: chain ST residue 188 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 374 optimal weight: 6.9990 chunk 209 optimal weight: 0.8980 chunk 560 optimal weight: 6.9990 chunk 458 optimal weight: 6.9990 chunk 185 optimal weight: 8.9990 chunk 675 optimal weight: 3.9990 chunk 729 optimal weight: 4.9990 chunk 601 optimal weight: 6.9990 chunk 669 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 541 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L7 96 GLN L8 131 GLN ** LB 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LE 98 HIS LE 112 ASN ** LE 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 101 ASN NF 3 GLN NF 4 ASN NF 10 HIS NJ 275 HIS SQ 113 ASN SR 35 HIS SR 39 GLN SR 56 GLN SR 263 HIS ST 22 GLN ST 74 ASN ST 188 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 88449 Z= 0.298 Angle : 0.545 9.498 127417 Z= 0.281 Chirality : 0.037 0.238 15486 Planarity : 0.005 0.052 9912 Dihedral : 22.287 179.211 33286 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.58 % Favored : 98.41 % Rotamer: Outliers : 2.32 % Allowed : 11.48 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.11), residues: 5777 helix: 1.94 (0.11), residues: 1966 sheet: 0.65 (0.16), residues: 1030 loop : 0.21 (0.11), residues: 2781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPNJ 356 HIS 0.008 0.001 HISLT 78 PHE 0.025 0.002 PHESR 18 TYR 0.025 0.002 TYRNJ 92 ARG 0.007 0.001 ARGLN 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11554 Ramachandran restraints generated. 5777 Oldfield, 0 Emsley, 5777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11554 Ramachandran restraints generated. 5777 Oldfield, 0 Emsley, 5777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 568 time to evaluate : 5.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L5 131 TYR cc_start: 0.8682 (t80) cc_final: 0.8305 (t80) REVERT: L8 78 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7264 (mp10) REVERT: LC 127 MET cc_start: 0.8507 (mmm) cc_final: 0.7925 (mmt) REVERT: LE 84 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7289 (pt) REVERT: LN 325 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6585 (mt-10) REVERT: NB 70 ARG cc_start: 0.6834 (tpp80) cc_final: 0.6284 (tpm170) REVERT: NF 66 LYS cc_start: 0.8411 (ttmm) cc_final: 0.8100 (ttmm) REVERT: NJ 485 ARG cc_start: 0.6582 (OUTLIER) cc_final: 0.5820 (tmt170) REVERT: NK 28 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7226 (mtm-85) REVERT: NZ 241 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.7773 (mttm) REVERT: SC 245 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.6863 (tt0) REVERT: SC 254 ASP cc_start: 0.7567 (m-30) cc_final: 0.7345 (m-30) REVERT: SQ 47 ASN cc_start: 0.8320 (t0) cc_final: 0.7806 (t0) REVERT: SQ 58 ASN cc_start: 0.7887 (t0) cc_final: 0.7618 (t0) REVERT: SR 307 PHE cc_start: 0.8558 (m-10) cc_final: 0.8289 (m-80) REVERT: SV 83 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7717 (ttp-170) outliers start: 119 outliers final: 41 residues processed: 634 average time/residue: 1.6452 time to fit residues: 1405.0535 Evaluate side-chains 571 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 522 time to evaluate : 5.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 73 THR Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 78 GLN Chi-restraints excluded: chain L8 residue 130 LEU Chi-restraints excluded: chain LB residue 42 THR Chi-restraints excluded: chain LC residue 19 THR Chi-restraints excluded: chain LE residue 68 THR Chi-restraints excluded: chain LE residue 84 ILE Chi-restraints excluded: chain LG residue 40 ILE Chi-restraints excluded: chain LG residue 118 THR Chi-restraints excluded: chain LL residue 78 VAL Chi-restraints excluded: chain LN residue 152 SER Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 208 ASN Chi-restraints excluded: chain LN residue 325 GLU Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain NB residue 14 THR Chi-restraints excluded: chain NB residue 50 VAL Chi-restraints excluded: chain NC residue 34 ASP Chi-restraints excluded: chain ND residue 242 MET Chi-restraints excluded: chain ND residue 269 GLN Chi-restraints excluded: chain NJ residue 97 ILE Chi-restraints excluded: chain NJ residue 330 LEU Chi-restraints excluded: chain NJ residue 381 SER Chi-restraints excluded: chain NJ residue 485 ARG Chi-restraints excluded: chain NK residue 28 ARG Chi-restraints excluded: chain NZ residue 241 LYS Chi-restraints excluded: chain SB residue 187 SER Chi-restraints excluded: chain SC residue 220 LYS Chi-restraints excluded: chain SC residue 245 GLN Chi-restraints excluded: chain SD residue 68 GLU Chi-restraints excluded: chain SD residue 71 MET Chi-restraints excluded: chain SG residue 6 SER Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain SK residue 173 LEU Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 330 LYS Chi-restraints excluded: chain SR residue 348 MET Chi-restraints excluded: chain SR residue 401 LEU Chi-restraints excluded: chain SR residue 422 LEU Chi-restraints excluded: chain ST residue 24 ILE Chi-restraints excluded: chain ST residue 48 THR Chi-restraints excluded: chain ST residue 81 THR Chi-restraints excluded: chain ST residue 152 ASP Chi-restraints excluded: chain ST residue 182 VAL Chi-restraints excluded: chain SV residue 83 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 666 optimal weight: 0.9990 chunk 507 optimal weight: 9.9990 chunk 350 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 322 optimal weight: 0.6980 chunk 453 optimal weight: 10.0000 chunk 677 optimal weight: 0.9980 chunk 717 optimal weight: 3.9990 chunk 353 optimal weight: 5.9990 chunk 642 optimal weight: 3.9990 chunk 193 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BA 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 115 GLN L7 96 GLN L8 44 GLN L8 75 GLN L8 131 GLN ** LB 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LE 112 ASN LG 101 ASN LN 301 ASN ND 102 ASN NF 3 GLN NJ 319 GLN SB 195 HIS SG 163 GLN SK 140 GLN ** SQ 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 39 GLN SR 41 HIS SR 263 HIS SR 268 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 88449 Z= 0.259 Angle : 0.516 9.661 127417 Z= 0.266 Chirality : 0.036 0.227 15486 Planarity : 0.004 0.051 9912 Dihedral : 22.266 179.890 33286 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.26 % Allowed : 12.69 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.11), residues: 5777 helix: 1.85 (0.11), residues: 1965 sheet: 0.58 (0.16), residues: 1038 loop : 0.17 (0.11), residues: 2774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRPNJ 356 HIS 0.007 0.001 HISNJ 275 PHE 0.022 0.001 PHESR 18 TYR 0.026 0.001 TYRNJ 92 ARG 0.005 0.000 ARGST 150 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11554 Ramachandran restraints generated. 5777 Oldfield, 0 Emsley, 5777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11554 Ramachandran restraints generated. 5777 Oldfield, 0 Emsley, 5777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 544 time to evaluate : 5.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L5 131 TYR cc_start: 0.8654 (t80) cc_final: 0.8270 (t80) REVERT: L8 78 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7257 (mp10) REVERT: LE 68 THR cc_start: 0.7054 (OUTLIER) cc_final: 0.6293 (p) REVERT: LE 84 ILE cc_start: 0.7536 (OUTLIER) cc_final: 0.7250 (pt) REVERT: LE 88 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7662 (mmm-85) REVERT: LN 325 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6591 (mt-10) REVERT: LQ 86 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: LT 66 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8449 (mtmm) REVERT: NB 70 ARG cc_start: 0.6839 (tpp80) cc_final: 0.6298 (tpm170) REVERT: NC 194 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.6834 (mt0) REVERT: NF 66 LYS cc_start: 0.8344 (ttmm) cc_final: 0.8072 (ttmm) REVERT: NJ 485 ARG cc_start: 0.6582 (OUTLIER) cc_final: 0.5697 (tmt170) REVERT: NZ 241 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.7716 (mtpm) REVERT: SB 51 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8142 (ttm) REVERT: SC 245 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.6822 (tt0) REVERT: SC 254 ASP cc_start: 0.7614 (m-30) cc_final: 0.7404 (m-30) REVERT: SD 74 MET cc_start: 0.8011 (mtp) cc_final: 0.7717 (ttm) REVERT: SQ 47 ASN cc_start: 0.8273 (t0) cc_final: 0.7790 (t0) REVERT: SQ 58 ASN cc_start: 0.7934 (t0) cc_final: 0.7673 (t0) REVERT: SV 83 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7553 (ttp-170) outliers start: 116 outliers final: 46 residues processed: 614 average time/residue: 1.6944 time to fit residues: 1396.9591 Evaluate side-chains 564 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 505 time to evaluate : 5.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 73 THR Chi-restraints excluded: chain L8 residue 38 VAL Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 78 GLN Chi-restraints excluded: chain L8 residue 130 LEU Chi-restraints excluded: chain LB residue 42 THR Chi-restraints excluded: chain LB residue 113 ILE Chi-restraints excluded: chain LC residue 19 THR Chi-restraints excluded: chain LE residue 68 THR Chi-restraints excluded: chain LE residue 84 ILE Chi-restraints excluded: chain LE residue 88 ARG Chi-restraints excluded: chain LG residue 118 THR Chi-restraints excluded: chain LG residue 127 ASP Chi-restraints excluded: chain LL residue 63 VAL Chi-restraints excluded: chain LN residue 152 SER Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 325 GLU Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LQ residue 86 GLU Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LT residue 66 LYS Chi-restraints excluded: chain NB residue 14 THR Chi-restraints excluded: chain NB residue 50 VAL Chi-restraints excluded: chain NB residue 75 LYS Chi-restraints excluded: chain NC residue 34 ASP Chi-restraints excluded: chain NC residue 97 GLU Chi-restraints excluded: chain NC residue 194 GLN Chi-restraints excluded: chain ND residue 28 GLU Chi-restraints excluded: chain ND residue 242 MET Chi-restraints excluded: chain ND residue 269 GLN Chi-restraints excluded: chain NF residue 97 SER Chi-restraints excluded: chain NF residue 135 VAL Chi-restraints excluded: chain NF residue 251 ASP Chi-restraints excluded: chain NJ residue 97 ILE Chi-restraints excluded: chain NJ residue 330 LEU Chi-restraints excluded: chain NJ residue 381 SER Chi-restraints excluded: chain NJ residue 485 ARG Chi-restraints excluded: chain NZ residue 241 LYS Chi-restraints excluded: chain NZ residue 247 LYS Chi-restraints excluded: chain SB residue 51 MET Chi-restraints excluded: chain SB residue 187 SER Chi-restraints excluded: chain SC residue 220 LYS Chi-restraints excluded: chain SC residue 245 GLN Chi-restraints excluded: chain SD residue 68 GLU Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain SG residue 138 GLN Chi-restraints excluded: chain SG residue 182 SER Chi-restraints excluded: chain SQ residue 15 THR Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 401 LEU Chi-restraints excluded: chain SR residue 422 LEU Chi-restraints excluded: chain ST residue 24 ILE Chi-restraints excluded: chain ST residue 48 THR Chi-restraints excluded: chain ST residue 137 SER Chi-restraints excluded: chain SV residue 82 GLN Chi-restraints excluded: chain SV residue 83 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 597 optimal weight: 2.9990 chunk 407 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 534 optimal weight: 1.9990 chunk 295 optimal weight: 8.9990 chunk 612 optimal weight: 4.9990 chunk 495 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 366 optimal weight: 3.9990 chunk 643 optimal weight: 7.9990 chunk 180 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BA 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 115 GLN L5 112 HIS L7 96 GLN L8 75 GLN L8 131 GLN ** LB 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LE 112 ASN NB 69 GLN NC 128 HIS NF 3 GLN NJ 275 HIS SG 163 GLN ** SQ 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 90 HIS SR 39 GLN SR 263 HIS ** ST 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SV 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 88449 Z= 0.377 Angle : 0.582 10.846 127417 Z= 0.298 Chirality : 0.039 0.250 15486 Planarity : 0.005 0.076 9912 Dihedral : 22.282 179.284 33286 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.83 % Allowed : 13.20 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.11), residues: 5777 helix: 1.53 (0.11), residues: 1978 sheet: 0.41 (0.16), residues: 1026 loop : -0.02 (0.11), residues: 2773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRPNJ 356 HIS 0.008 0.001 HISLN 123 PHE 0.029 0.002 PHESR 18 TYR 0.028 0.002 TYRNJ 92 ARG 0.018 0.001 ARGLB 112 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11554 Ramachandran restraints generated. 5777 Oldfield, 0 Emsley, 5777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11554 Ramachandran restraints generated. 5777 Oldfield, 0 Emsley, 5777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 523 time to evaluate : 5.250 Fit side-chains revert: symmetry clash REVERT: L5 131 TYR cc_start: 0.8721 (t80) cc_final: 0.8327 (t80) REVERT: L8 78 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7295 (mp10) REVERT: LE 52 MET cc_start: 0.7344 (OUTLIER) cc_final: 0.6905 (mmm) REVERT: LE 84 ILE cc_start: 0.7649 (OUTLIER) cc_final: 0.7175 (pt) REVERT: LE 88 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.7594 (mmm-85) REVERT: LN 325 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6594 (mt-10) REVERT: LQ 86 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: NC 194 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.6884 (mt0) REVERT: ND 118 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7593 (tt0) REVERT: NF 112 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7275 (pm20) REVERT: NJ 485 ARG cc_start: 0.6638 (OUTLIER) cc_final: 0.5786 (tmt170) REVERT: NK 28 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7114 (mtm-85) REVERT: NZ 241 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7695 (mtpm) REVERT: SA 261 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7959 (t70) REVERT: SC 245 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.7015 (tt0) REVERT: SC 254 ASP cc_start: 0.7612 (m-30) cc_final: 0.7406 (m-30) REVERT: SD 42 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8733 (tm) REVERT: SD 106 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7721 (ttt180) REVERT: SQ 47 ASN cc_start: 0.8347 (t0) cc_final: 0.7809 (t0) REVERT: SQ 58 ASN cc_start: 0.8096 (t0) cc_final: 0.7808 (t0) REVERT: ST 1 MET cc_start: 0.4353 (OUTLIER) cc_final: 0.1840 (tmt) REVERT: SV 114 LYS cc_start: 0.6739 (OUTLIER) cc_final: 0.5902 (mppt) outliers start: 145 outliers final: 56 residues processed: 615 average time/residue: 1.7265 time to fit residues: 1423.9414 Evaluate side-chains 577 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 503 time to evaluate : 5.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 105 THR Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 73 THR Chi-restraints excluded: chain L8 residue 38 VAL Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 78 GLN Chi-restraints excluded: chain L8 residue 130 LEU Chi-restraints excluded: chain LB residue 42 THR Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LC residue 19 THR Chi-restraints excluded: chain LE residue 52 MET Chi-restraints excluded: chain LE residue 68 THR Chi-restraints excluded: chain LE residue 84 ILE Chi-restraints excluded: chain LE residue 88 ARG Chi-restraints excluded: chain LG residue 22 VAL Chi-restraints excluded: chain LG residue 118 THR Chi-restraints excluded: chain LG residue 127 ASP Chi-restraints excluded: chain LL residue 61 VAL Chi-restraints excluded: chain LL residue 62 VAL Chi-restraints excluded: chain LL residue 63 VAL Chi-restraints excluded: chain LL residue 78 VAL Chi-restraints excluded: chain LN residue 152 SER Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 208 ASN Chi-restraints excluded: chain LN residue 325 GLU Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LQ residue 86 GLU Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain NB residue 14 THR Chi-restraints excluded: chain NB residue 50 VAL Chi-restraints excluded: chain NC residue 34 ASP Chi-restraints excluded: chain NC residue 194 GLN Chi-restraints excluded: chain ND residue 118 GLU Chi-restraints excluded: chain ND residue 189 LEU Chi-restraints excluded: chain ND residue 269 GLN Chi-restraints excluded: chain NF residue 112 GLU Chi-restraints excluded: chain NF residue 135 VAL Chi-restraints excluded: chain NF residue 176 LEU Chi-restraints excluded: chain NF residue 251 ASP Chi-restraints excluded: chain NJ residue 97 ILE Chi-restraints excluded: chain NJ residue 330 LEU Chi-restraints excluded: chain NJ residue 381 SER Chi-restraints excluded: chain NJ residue 383 ASP Chi-restraints excluded: chain NJ residue 485 ARG Chi-restraints excluded: chain NK residue 28 ARG Chi-restraints excluded: chain NZ residue 241 LYS Chi-restraints excluded: chain SA residue 261 ASP Chi-restraints excluded: chain SA residue 263 LEU Chi-restraints excluded: chain SB residue 187 SER Chi-restraints excluded: chain SB residue 230 SER Chi-restraints excluded: chain SC residue 220 LYS Chi-restraints excluded: chain SC residue 245 GLN Chi-restraints excluded: chain SD residue 36 LYS Chi-restraints excluded: chain SD residue 42 LEU Chi-restraints excluded: chain SD residue 68 GLU Chi-restraints excluded: chain SD residue 106 ARG Chi-restraints excluded: chain SD residue 150 VAL Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain SG residue 182 SER Chi-restraints excluded: chain SK residue 50 HIS Chi-restraints excluded: chain SK residue 169 ASP Chi-restraints excluded: chain SK residue 211 THR Chi-restraints excluded: chain SQ residue 15 THR Chi-restraints excluded: chain SR residue 330 LYS Chi-restraints excluded: chain SR residue 422 LEU Chi-restraints excluded: chain ST residue 1 MET Chi-restraints excluded: chain ST residue 19 GLU Chi-restraints excluded: chain ST residue 24 ILE Chi-restraints excluded: chain ST residue 137 SER Chi-restraints excluded: chain ST residue 152 ASP Chi-restraints excluded: chain ST residue 182 VAL Chi-restraints excluded: chain SV residue 114 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 241 optimal weight: 0.8980 chunk 645 optimal weight: 0.1980 chunk 141 optimal weight: 5.9990 chunk 421 optimal weight: 0.0040 chunk 177 optimal weight: 10.0000 chunk 717 optimal weight: 2.9990 chunk 595 optimal weight: 1.9990 chunk 332 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 237 optimal weight: 5.9990 chunk 376 optimal weight: 0.9990 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BA 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 115 GLN L7 96 GLN L8 75 GLN L8 131 GLN ** LE 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LE 112 ASN LN 301 ASN LT 55 ASN NB 69 GLN NC 128 HIS ND 75 GLN NF 3 GLN NJ 275 HIS NJ 469 GLN SG 140 GLN SG 163 GLN ** SQ 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 263 HIS ST 74 ASN ST 188 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 88449 Z= 0.134 Angle : 0.478 9.447 127417 Z= 0.245 Chirality : 0.033 0.218 15486 Planarity : 0.003 0.049 9912 Dihedral : 22.246 179.302 33286 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.77 % Allowed : 14.68 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.11), residues: 5777 helix: 1.84 (0.12), residues: 1966 sheet: 0.55 (0.16), residues: 1039 loop : 0.10 (0.11), residues: 2772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRPST 114 HIS 0.009 0.001 HISNJ 275 PHE 0.022 0.001 PHENC 421 TYR 0.029 0.001 TYRNJ 92 ARG 0.010 0.000 ARGSA 222 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11554 Ramachandran restraints generated. 5777 Oldfield, 0 Emsley, 5777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11554 Ramachandran restraints generated. 5777 Oldfield, 0 Emsley, 5777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 545 time to evaluate : 5.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L5 131 TYR cc_start: 0.8561 (t80) cc_final: 0.8203 (t80) REVERT: L8 78 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7197 (mp10) REVERT: LE 52 MET cc_start: 0.7359 (OUTLIER) cc_final: 0.6924 (mmm) REVERT: LE 68 THR cc_start: 0.6323 (m) cc_final: 0.5500 (p) REVERT: LE 84 ILE cc_start: 0.7450 (OUTLIER) cc_final: 0.6822 (pt) REVERT: LE 88 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8375 (mpp80) REVERT: LQ 86 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7127 (mp0) REVERT: LT 37 ASP cc_start: 0.8037 (p0) cc_final: 0.7639 (p0) REVERT: ND 108 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7688 (mtm) REVERT: ND 272 ASP cc_start: 0.6525 (t70) cc_final: 0.6322 (t70) REVERT: NF 66 LYS cc_start: 0.8301 (ttmm) cc_final: 0.8090 (ttmm) REVERT: NJ 485 ARG cc_start: 0.6486 (OUTLIER) cc_final: 0.5682 (tmt170) REVERT: NZ 241 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7671 (mttm) REVERT: SA 184 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.7563 (t80) REVERT: SB 51 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8140 (ttm) REVERT: SQ 47 ASN cc_start: 0.8166 (t0) cc_final: 0.7621 (t0) REVERT: ST 1 MET cc_start: 0.4254 (OUTLIER) cc_final: 0.1763 (tmt) outliers start: 91 outliers final: 36 residues processed: 606 average time/residue: 1.6334 time to fit residues: 1333.9717 Evaluate side-chains 558 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 511 time to evaluate : 5.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L5 residue 73 THR Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 78 GLN Chi-restraints excluded: chain L8 residue 130 LEU Chi-restraints excluded: chain LB residue 42 THR Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LE residue 52 MET Chi-restraints excluded: chain LE residue 84 ILE Chi-restraints excluded: chain LE residue 88 ARG Chi-restraints excluded: chain LG residue 94 VAL Chi-restraints excluded: chain LL residue 78 VAL Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 208 ASN Chi-restraints excluded: chain LQ residue 86 GLU Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain NB residue 14 THR Chi-restraints excluded: chain NB residue 26 ARG Chi-restraints excluded: chain NB residue 50 VAL Chi-restraints excluded: chain NB residue 75 LYS Chi-restraints excluded: chain NC residue 34 ASP Chi-restraints excluded: chain NC residue 97 GLU Chi-restraints excluded: chain ND residue 28 GLU Chi-restraints excluded: chain ND residue 108 MET Chi-restraints excluded: chain ND residue 189 LEU Chi-restraints excluded: chain NF residue 135 VAL Chi-restraints excluded: chain NF residue 251 ASP Chi-restraints excluded: chain NJ residue 97 ILE Chi-restraints excluded: chain NJ residue 275 HIS Chi-restraints excluded: chain NJ residue 330 LEU Chi-restraints excluded: chain NJ residue 381 SER Chi-restraints excluded: chain NJ residue 383 ASP Chi-restraints excluded: chain NJ residue 485 ARG Chi-restraints excluded: chain NZ residue 241 LYS Chi-restraints excluded: chain SA residue 184 TYR Chi-restraints excluded: chain SA residue 263 LEU Chi-restraints excluded: chain SB residue 51 MET Chi-restraints excluded: chain SB residue 187 SER Chi-restraints excluded: chain SB residue 230 SER Chi-restraints excluded: chain SC residue 220 LYS Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain SK residue 153 VAL Chi-restraints excluded: chain SR residue 330 LYS Chi-restraints excluded: chain ST residue 1 MET Chi-restraints excluded: chain ST residue 24 ILE Chi-restraints excluded: chain SV residue 108 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 692 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 409 optimal weight: 7.9990 chunk 524 optimal weight: 8.9990 chunk 406 optimal weight: 2.9990 chunk 604 optimal weight: 3.9990 chunk 400 optimal weight: 0.0040 chunk 715 optimal weight: 10.0000 chunk 447 optimal weight: 0.9990 chunk 436 optimal weight: 4.9990 chunk 330 optimal weight: 7.9990 overall best weight: 2.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BA 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 115 GLN L8 75 GLN L8 131 GLN ** LE 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LE 112 ASN NB 22 GLN NC 128 HIS NC 417 ASN ND 75 GLN ND 102 ASN NF 3 GLN NJ 275 HIS NJ 469 GLN ** NK 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 140 GLN SQ 24 GLN SR 263 HIS SV 132 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 88449 Z= 0.293 Angle : 0.529 9.737 127417 Z= 0.271 Chirality : 0.036 0.339 15486 Planarity : 0.004 0.061 9912 Dihedral : 22.192 179.112 33286 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.83 % Allowed : 15.36 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.11), residues: 5777 helix: 1.66 (0.12), residues: 1982 sheet: 0.41 (0.16), residues: 1047 loop : 0.04 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPNC 207 HIS 0.006 0.001 HISNJ 275 PHE 0.020 0.001 PHESR 18 TYR 0.028 0.002 TYRNJ 92 ARG 0.007 0.000 ARGLE 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11554 Ramachandran restraints generated. 5777 Oldfield, 0 Emsley, 5777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11554 Ramachandran restraints generated. 5777 Oldfield, 0 Emsley, 5777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 517 time to evaluate : 5.318 Fit side-chains revert: symmetry clash REVERT: BA 108 GLU cc_start: 0.7916 (pm20) cc_final: 0.7685 (pm20) REVERT: L5 131 TYR cc_start: 0.8623 (t80) cc_final: 0.8247 (t80) REVERT: L8 78 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7241 (mp10) REVERT: LE 52 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.6848 (mmm) REVERT: LE 68 THR cc_start: 0.6077 (OUTLIER) cc_final: 0.5509 (p) REVERT: LE 88 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.7445 (mmm-85) REVERT: LQ 83 LYS cc_start: 0.7794 (ttpt) cc_final: 0.7532 (pttm) REVERT: LQ 86 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7128 (mp0) REVERT: LT 37 ASP cc_start: 0.8172 (p0) cc_final: 0.7847 (p0) REVERT: NC 194 GLN cc_start: 0.7262 (OUTLIER) cc_final: 0.6851 (mt0) REVERT: NF 112 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7254 (pm20) REVERT: NJ 485 ARG cc_start: 0.6541 (OUTLIER) cc_final: 0.5723 (tmt170) REVERT: NZ 241 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7647 (mtpm) REVERT: SA 184 TYR cc_start: 0.8120 (OUTLIER) cc_final: 0.7589 (t80) REVERT: SC 245 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.7064 (tt0) REVERT: SD 63 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7979 (mt0) REVERT: SQ 47 ASN cc_start: 0.8249 (t0) cc_final: 0.7665 (t0) REVERT: ST 1 MET cc_start: 0.4336 (OUTLIER) cc_final: 0.1795 (tmt) outliers start: 94 outliers final: 40 residues processed: 581 average time/residue: 1.7027 time to fit residues: 1332.4536 Evaluate side-chains 553 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 500 time to evaluate : 5.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L5 residue 73 THR Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 78 GLN Chi-restraints excluded: chain L8 residue 130 LEU Chi-restraints excluded: chain LB residue 42 THR Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LE residue 52 MET Chi-restraints excluded: chain LE residue 68 THR Chi-restraints excluded: chain LE residue 88 ARG Chi-restraints excluded: chain LG residue 22 VAL Chi-restraints excluded: chain LG residue 94 VAL Chi-restraints excluded: chain LL residue 78 VAL Chi-restraints excluded: chain LN residue 101 THR Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 208 ASN Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LQ residue 86 GLU Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain NB residue 14 THR Chi-restraints excluded: chain NB residue 26 ARG Chi-restraints excluded: chain NB residue 50 VAL Chi-restraints excluded: chain NC residue 34 ASP Chi-restraints excluded: chain NC residue 194 GLN Chi-restraints excluded: chain ND residue 28 GLU Chi-restraints excluded: chain ND residue 189 LEU Chi-restraints excluded: chain NF residue 97 SER Chi-restraints excluded: chain NF residue 112 GLU Chi-restraints excluded: chain NF residue 135 VAL Chi-restraints excluded: chain NF residue 251 ASP Chi-restraints excluded: chain NJ residue 97 ILE Chi-restraints excluded: chain NJ residue 330 LEU Chi-restraints excluded: chain NJ residue 381 SER Chi-restraints excluded: chain NJ residue 383 ASP Chi-restraints excluded: chain NJ residue 485 ARG Chi-restraints excluded: chain NZ residue 241 LYS Chi-restraints excluded: chain SA residue 184 TYR Chi-restraints excluded: chain SA residue 263 LEU Chi-restraints excluded: chain SB residue 187 SER Chi-restraints excluded: chain SB residue 230 SER Chi-restraints excluded: chain SC residue 220 LYS Chi-restraints excluded: chain SC residue 245 GLN Chi-restraints excluded: chain SD residue 63 GLN Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SK residue 153 VAL Chi-restraints excluded: chain SR residue 330 LYS Chi-restraints excluded: chain SR residue 401 LEU Chi-restraints excluded: chain SR residue 422 LEU Chi-restraints excluded: chain ST residue 1 MET Chi-restraints excluded: chain ST residue 24 ILE Chi-restraints excluded: chain ST residue 152 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 442 optimal weight: 0.9980 chunk 285 optimal weight: 3.9990 chunk 427 optimal weight: 0.5980 chunk 215 optimal weight: 0.8980 chunk 140 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 chunk 454 optimal weight: 10.0000 chunk 487 optimal weight: 0.9990 chunk 353 optimal weight: 3.9990 chunk 66 optimal weight: 30.0000 chunk 562 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BA 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 115 GLN L8 75 GLN L8 131 GLN LC 37 HIS LE 95 HIS LE 112 ASN LL 41 ASN LN 301 ASN NB 22 GLN NC 128 HIS NF 3 GLN NJ 275 HIS NJ 469 GLN ** NK 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 140 GLN SQ 24 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 88449 Z= 0.140 Angle : 0.475 10.943 127417 Z= 0.243 Chirality : 0.033 0.338 15486 Planarity : 0.003 0.049 9912 Dihedral : 22.185 178.365 33286 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.62 % Allowed : 15.75 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.11), residues: 5777 helix: 1.80 (0.12), residues: 1975 sheet: 0.53 (0.16), residues: 1026 loop : 0.10 (0.11), residues: 2776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPST 114 HIS 0.011 0.001 HISNJ 275 PHE 0.010 0.001 PHESR 18 TYR 0.029 0.001 TYRNJ 92 ARG 0.008 0.000 ARGLE 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11554 Ramachandran restraints generated. 5777 Oldfield, 0 Emsley, 5777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11554 Ramachandran restraints generated. 5777 Oldfield, 0 Emsley, 5777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 526 time to evaluate : 5.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 108 GLU cc_start: 0.7857 (pm20) cc_final: 0.7613 (pm20) REVERT: L5 131 TYR cc_start: 0.8536 (t80) cc_final: 0.8200 (t80) REVERT: L8 78 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7246 (mp10) REVERT: LE 52 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.6916 (mmm) REVERT: LE 68 THR cc_start: 0.6218 (m) cc_final: 0.5510 (p) REVERT: LQ 83 LYS cc_start: 0.7719 (ttpt) cc_final: 0.7467 (pttm) REVERT: LQ 86 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: NJ 485 ARG cc_start: 0.6419 (OUTLIER) cc_final: 0.5633 (tmt170) REVERT: NZ 241 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7542 (mttm) REVERT: SB 51 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8158 (ttm) REVERT: SC 245 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.7001 (tt0) REVERT: SQ 47 ASN cc_start: 0.8157 (t0) cc_final: 0.7591 (t0) REVERT: ST 1 MET cc_start: 0.4298 (OUTLIER) cc_final: 0.1784 (tmt) REVERT: ST 29 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.7084 (pt0) outliers start: 83 outliers final: 41 residues processed: 584 average time/residue: 1.6795 time to fit residues: 1322.8245 Evaluate side-chains 559 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 509 time to evaluate : 5.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 105 THR Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 73 THR Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 78 GLN Chi-restraints excluded: chain L8 residue 130 LEU Chi-restraints excluded: chain LB residue 42 THR Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LC residue 19 THR Chi-restraints excluded: chain LE residue 52 MET Chi-restraints excluded: chain LL residue 62 VAL Chi-restraints excluded: chain LL residue 78 VAL Chi-restraints excluded: chain LN residue 101 THR Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 208 ASN Chi-restraints excluded: chain LQ residue 86 GLU Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain NB residue 14 THR Chi-restraints excluded: chain NB residue 26 ARG Chi-restraints excluded: chain NB residue 50 VAL Chi-restraints excluded: chain NC residue 34 ASP Chi-restraints excluded: chain ND residue 28 GLU Chi-restraints excluded: chain ND residue 189 LEU Chi-restraints excluded: chain NF residue 97 SER Chi-restraints excluded: chain NF residue 135 VAL Chi-restraints excluded: chain NF residue 251 ASP Chi-restraints excluded: chain NJ residue 97 ILE Chi-restraints excluded: chain NJ residue 247 GLN Chi-restraints excluded: chain NJ residue 330 LEU Chi-restraints excluded: chain NJ residue 381 SER Chi-restraints excluded: chain NJ residue 383 ASP Chi-restraints excluded: chain NJ residue 485 ARG Chi-restraints excluded: chain NZ residue 241 LYS Chi-restraints excluded: chain SA residue 263 LEU Chi-restraints excluded: chain SB residue 51 MET Chi-restraints excluded: chain SB residue 187 SER Chi-restraints excluded: chain SC residue 220 LYS Chi-restraints excluded: chain SC residue 245 GLN Chi-restraints excluded: chain SD residue 68 GLU Chi-restraints excluded: chain SD residue 132 MET Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SK residue 153 VAL Chi-restraints excluded: chain SK residue 173 LEU Chi-restraints excluded: chain ST residue 1 MET Chi-restraints excluded: chain ST residue 24 ILE Chi-restraints excluded: chain ST residue 29 GLU Chi-restraints excluded: chain SV residue 108 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 650 optimal weight: 10.0000 chunk 685 optimal weight: 5.9990 chunk 625 optimal weight: 0.8980 chunk 666 optimal weight: 0.0270 chunk 684 optimal weight: 1.9990 chunk 401 optimal weight: 5.9990 chunk 290 optimal weight: 8.9990 chunk 523 optimal weight: 0.9980 chunk 204 optimal weight: 4.9990 chunk 602 optimal weight: 0.0060 chunk 630 optimal weight: 1.9990 overall best weight: 0.7856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BA 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 115 GLN L5 71 HIS L8 131 GLN LE 112 ASN LL 41 ASN NB 22 GLN NF 3 GLN NJ 275 HIS ** NK 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 63 GLN SG 140 GLN ST 170 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 88449 Z= 0.136 Angle : 0.465 10.645 127417 Z= 0.238 Chirality : 0.033 0.285 15486 Planarity : 0.003 0.063 9912 Dihedral : 22.125 178.012 33286 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.35 % Allowed : 16.08 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.11), residues: 5777 helix: 1.90 (0.12), residues: 1976 sheet: 0.59 (0.16), residues: 1026 loop : 0.14 (0.11), residues: 2775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPST 114 HIS 0.010 0.001 HISNJ 275 PHE 0.013 0.001 PHESA 221 TYR 0.029 0.001 TYRNJ 92 ARG 0.023 0.000 ARGSA 222 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11554 Ramachandran restraints generated. 5777 Oldfield, 0 Emsley, 5777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11554 Ramachandran restraints generated. 5777 Oldfield, 0 Emsley, 5777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 539 time to evaluate : 5.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: BA 108 GLU cc_start: 0.7840 (pm20) cc_final: 0.7606 (pm20) REVERT: L5 131 TYR cc_start: 0.8502 (t80) cc_final: 0.8101 (t80) REVERT: L8 78 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7271 (mp10) REVERT: LE 52 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.6945 (mmm) REVERT: LQ 83 LYS cc_start: 0.7620 (ttpt) cc_final: 0.7420 (pttm) REVERT: NF 112 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7260 (pm20) REVERT: NJ 485 ARG cc_start: 0.6429 (OUTLIER) cc_final: 0.5661 (tmt170) REVERT: SB 51 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8155 (ttm) REVERT: SC 245 GLN cc_start: 0.7428 (OUTLIER) cc_final: 0.7051 (tt0) REVERT: SD 63 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7919 (mt0) REVERT: SQ 47 ASN cc_start: 0.8098 (t0) cc_final: 0.7577 (t0) REVERT: ST 1 MET cc_start: 0.4410 (OUTLIER) cc_final: 0.1907 (tmt) REVERT: ST 24 ILE cc_start: 0.6757 (OUTLIER) cc_final: 0.6553 (tp) REVERT: ST 29 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6999 (pt0) outliers start: 69 outliers final: 37 residues processed: 586 average time/residue: 1.6483 time to fit residues: 1295.5618 Evaluate side-chains 556 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 509 time to evaluate : 5.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 105 THR Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 73 THR Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 78 GLN Chi-restraints excluded: chain L8 residue 130 LEU Chi-restraints excluded: chain LB residue 42 THR Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LC residue 19 THR Chi-restraints excluded: chain LE residue 39 ILE Chi-restraints excluded: chain LE residue 52 MET Chi-restraints excluded: chain LE residue 103 ASP Chi-restraints excluded: chain LL residue 62 VAL Chi-restraints excluded: chain LL residue 78 VAL Chi-restraints excluded: chain LN residue 101 THR Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 208 ASN Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain NB residue 14 THR Chi-restraints excluded: chain NB residue 26 ARG Chi-restraints excluded: chain NB residue 50 VAL Chi-restraints excluded: chain NC residue 34 ASP Chi-restraints excluded: chain ND residue 28 GLU Chi-restraints excluded: chain NF residue 97 SER Chi-restraints excluded: chain NF residue 112 GLU Chi-restraints excluded: chain NF residue 135 VAL Chi-restraints excluded: chain NJ residue 97 ILE Chi-restraints excluded: chain NJ residue 247 GLN Chi-restraints excluded: chain NJ residue 330 LEU Chi-restraints excluded: chain NJ residue 381 SER Chi-restraints excluded: chain NJ residue 383 ASP Chi-restraints excluded: chain NJ residue 485 ARG Chi-restraints excluded: chain SA residue 263 LEU Chi-restraints excluded: chain SB residue 51 MET Chi-restraints excluded: chain SB residue 187 SER Chi-restraints excluded: chain SC residue 121 VAL Chi-restraints excluded: chain SC residue 220 LYS Chi-restraints excluded: chain SC residue 245 GLN Chi-restraints excluded: chain SD residue 63 GLN Chi-restraints excluded: chain SD residue 132 MET Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain ST residue 1 MET Chi-restraints excluded: chain ST residue 24 ILE Chi-restraints excluded: chain ST residue 29 GLU Chi-restraints excluded: chain SV residue 108 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 664 optimal weight: 5.9990 chunk 437 optimal weight: 0.4980 chunk 704 optimal weight: 0.0170 chunk 430 optimal weight: 6.9990 chunk 334 optimal weight: 5.9990 chunk 489 optimal weight: 0.9980 chunk 739 optimal weight: 8.9990 chunk 680 optimal weight: 0.7980 chunk 588 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 454 optimal weight: 5.9990 overall best weight: 1.0620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BA 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 115 GLN L7 46 ASN L8 131 GLN LE 112 ASN LL 41 ASN LN 301 ASN NB 22 GLN NC 89 GLN NC 93 GLN NJ 80 GLN NJ 275 HIS NK 82 ASN SD 63 GLN SG 106 GLN SG 140 GLN SV 110 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 88449 Z= 0.159 Angle : 0.475 14.123 127417 Z= 0.242 Chirality : 0.033 0.354 15486 Planarity : 0.004 0.070 9912 Dihedral : 22.098 178.175 33286 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.23 % Allowed : 16.59 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.11), residues: 5777 helix: 1.86 (0.12), residues: 1975 sheet: 0.57 (0.16), residues: 1037 loop : 0.16 (0.11), residues: 2765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPST 114 HIS 0.009 0.001 HISNJ 275 PHE 0.010 0.001 PHESR 18 TYR 0.028 0.001 TYRNJ 92 ARG 0.013 0.000 ARGNC 428 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11554 Ramachandran restraints generated. 5777 Oldfield, 0 Emsley, 5777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11554 Ramachandran restraints generated. 5777 Oldfield, 0 Emsley, 5777 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 519 time to evaluate : 5.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 108 GLU cc_start: 0.7840 (pm20) cc_final: 0.7613 (pm20) REVERT: L5 131 TYR cc_start: 0.8514 (t80) cc_final: 0.8167 (t80) REVERT: L8 78 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7281 (mp10) REVERT: LE 52 MET cc_start: 0.7465 (OUTLIER) cc_final: 0.6980 (mmm) REVERT: LE 68 THR cc_start: 0.6148 (m) cc_final: 0.5474 (p) REVERT: NF 112 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7272 (pm20) REVERT: NJ 485 ARG cc_start: 0.6455 (OUTLIER) cc_final: 0.5704 (tmt170) REVERT: SB 51 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8158 (ttm) REVERT: SC 245 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.7049 (tt0) REVERT: SQ 47 ASN cc_start: 0.8088 (t0) cc_final: 0.7574 (t0) REVERT: ST 1 MET cc_start: 0.4415 (OUTLIER) cc_final: 0.1913 (tmt) outliers start: 63 outliers final: 39 residues processed: 563 average time/residue: 1.6596 time to fit residues: 1258.0514 Evaluate side-chains 554 residues out of total 5130 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 508 time to evaluate : 5.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 105 THR Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 73 THR Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 78 GLN Chi-restraints excluded: chain L8 residue 130 LEU Chi-restraints excluded: chain LB residue 42 THR Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LC residue 19 THR Chi-restraints excluded: chain LE residue 39 ILE Chi-restraints excluded: chain LE residue 52 MET Chi-restraints excluded: chain LE residue 103 ASP Chi-restraints excluded: chain LL residue 52 GLU Chi-restraints excluded: chain LL residue 62 VAL Chi-restraints excluded: chain LL residue 78 VAL Chi-restraints excluded: chain LN residue 101 THR Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain NB residue 14 THR Chi-restraints excluded: chain NB residue 26 ARG Chi-restraints excluded: chain NB residue 50 VAL Chi-restraints excluded: chain NC residue 34 ASP Chi-restraints excluded: chain ND residue 28 GLU Chi-restraints excluded: chain NF residue 97 SER Chi-restraints excluded: chain NF residue 112 GLU Chi-restraints excluded: chain NF residue 135 VAL Chi-restraints excluded: chain NJ residue 247 GLN Chi-restraints excluded: chain NJ residue 330 LEU Chi-restraints excluded: chain NJ residue 381 SER Chi-restraints excluded: chain NJ residue 383 ASP Chi-restraints excluded: chain NJ residue 485 ARG Chi-restraints excluded: chain SA residue 263 LEU Chi-restraints excluded: chain SB residue 51 MET Chi-restraints excluded: chain SB residue 187 SER Chi-restraints excluded: chain SC residue 121 VAL Chi-restraints excluded: chain SC residue 220 LYS Chi-restraints excluded: chain SC residue 245 GLN Chi-restraints excluded: chain SD residue 68 GLU Chi-restraints excluded: chain SD residue 132 MET Chi-restraints excluded: chain SG residue 46 SER Chi-restraints excluded: chain SK residue 153 VAL Chi-restraints excluded: chain SR residue 168 THR Chi-restraints excluded: chain ST residue 1 MET Chi-restraints excluded: chain ST residue 20 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 742 random chunks: chunk 360 optimal weight: 0.9980 chunk 467 optimal weight: 4.9990 chunk 627 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 chunk 542 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 chunk 589 optimal weight: 1.9990 chunk 246 optimal weight: 5.9990 chunk 605 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BA 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 115 GLN L8 131 GLN ** LB 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 112 ASN LN 301 ASN ** NC 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NF 3 GLN NJ 275 HIS NJ 469 GLN SG 106 GLN SV 110 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.100195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.066488 restraints weight = 187463.697| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.69 r_work: 0.2835 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 88449 Z= 0.377 Angle : 0.581 10.714 127417 Z= 0.296 Chirality : 0.039 0.311 15486 Planarity : 0.005 0.071 9912 Dihedral : 22.137 179.845 33284 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.38 % Allowed : 16.71 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.11), residues: 5777 helix: 1.52 (0.12), residues: 1982 sheet: 0.36 (0.16), residues: 1020 loop : -0.03 (0.11), residues: 2775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPNC 207 HIS 0.012 0.001 HISNJ 275 PHE 0.020 0.002 PHESR 18 TYR 0.027 0.002 TYRNJ 92 ARG 0.010 0.001 ARGNC 428 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23275.87 seconds wall clock time: 408 minutes 12.32 seconds (24492.32 seconds total)