Starting phenix.real_space_refine on Tue Mar 19 10:55:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkw_29259/03_2024/8fkw_29259_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkw_29259/03_2024/8fkw_29259.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkw_29259/03_2024/8fkw_29259.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkw_29259/03_2024/8fkw_29259.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkw_29259/03_2024/8fkw_29259_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkw_29259/03_2024/8fkw_29259_neut_updated.pdb" } resolution = 2.5 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= 0.035 sd= 0.174 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 1 8.98 5 Zn 2 6.06 5 P 2504 5.49 5 Mg 59 5.21 5 S 358 5.16 5 C 78526 2.51 5 N 25858 2.21 5 O 32475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "BA GLU 72": "OE1" <-> "OE2" Residue "BA ASP 107": "OD1" <-> "OD2" Residue "L6 GLU 108": "OE1" <-> "OE2" Residue "L6 PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L7 TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L7 ASP 190": "OD1" <-> "OD2" Residue "L8 GLU 8": "OE1" <-> "OE2" Residue "L8 PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L8 ASP 39": "OD1" <-> "OD2" Residue "L8 ASP 59": "OD1" <-> "OD2" Residue "L8 ASP 81": "OD1" <-> "OD2" Residue "L9 GLU 9": "OE1" <-> "OE2" Residue "L9 TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA ASP 108": "OD1" <-> "OD2" Residue "LB ASP 4": "OD1" <-> "OD2" Residue "LB GLU 17": "OE1" <-> "OE2" Residue "LB ASP 89": "OD1" <-> "OD2" Residue "LB PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC ASP 85": "OD1" <-> "OD2" Residue "LC ASP 99": "OD1" <-> "OD2" Residue "LC GLU 131": "OE1" <-> "OE2" Residue "LE ASP 41": "OD1" <-> "OD2" Residue "LE TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LE ASP 103": "OD1" <-> "OD2" Residue "LE GLU 111": "OE1" <-> "OE2" Residue "LE GLU 147": "OE1" <-> "OE2" Residue "LE GLU 149": "OE1" <-> "OE2" Residue "LE GLU 152": "OE1" <-> "OE2" Residue "LG PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG GLU 99": "OE1" <-> "OE2" Residue "LG GLU 111": "OE1" <-> "OE2" Residue "LG GLU 124": "OE1" <-> "OE2" Residue "LI ASP 10": "OD1" <-> "OD2" Residue "LI TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LI ASP 114": "OD1" <-> "OD2" Residue "LL GLU 28": "OE1" <-> "OE2" Residue "LN ASP 61": "OD1" <-> "OD2" Residue "LN TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN GLU 279": "OE1" <-> "OE2" Residue "LN ASP 308": "OD1" <-> "OD2" Residue "LN ASP 311": "OD1" <-> "OD2" Residue "LN ASP 364": "OD1" <-> "OD2" Residue "LQ ASP 42": "OD1" <-> "OD2" Residue "LQ GLU 84": "OE1" <-> "OE2" Residue "LQ TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS ASP 8": "OD1" <-> "OD2" Residue "LS ASP 22": "OD1" <-> "OD2" Residue "LS GLU 27": "OE1" <-> "OE2" Residue "LU ASP 66": "OD1" <-> "OD2" Residue "LU GLU 89": "OE1" <-> "OE2" Residue "NA TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NA TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NA TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NA ASP 487": "OD1" <-> "OD2" Residue "NA PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NB ASP 47": "OD1" <-> "OD2" Residue "NB GLU 63": "OE1" <-> "OE2" Residue "NB GLU 72": "OE1" <-> "OE2" Residue "NF TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NF GLU 8": "OE1" <-> "OE2" Residue "NF GLU 22": "OE1" <-> "OE2" Residue "NF TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NF ASP 251": "OD1" <-> "OD2" Residue "NH TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NH ASP 42": "OD1" <-> "OD2" Residue "NH TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NH ASP 87": "OD1" <-> "OD2" Residue "NH TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NH ASP 138": "OD1" <-> "OD2" Residue "NI GLU 177": "OE1" <-> "OE2" Residue "NI ASP 396": "OD1" <-> "OD2" Residue "NI TYR 763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA GLU 146": "OE1" <-> "OE2" Residue "SA GLU 155": "OE1" <-> "OE2" Residue "SA TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA ASP 352": "OD1" <-> "OD2" Residue "SC TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SC GLU 119": "OE1" <-> "OE2" Residue "SC ASP 202": "OD1" <-> "OD2" Residue "SC ASP 254": "OD1" <-> "OD2" Residue "SD TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SD GLU 52": "OE1" <-> "OE2" Residue "SD ASP 171": "OD1" <-> "OD2" Residue "SD GLU 203": "OE1" <-> "OE2" Residue "SD GLU 229": "OE1" <-> "OE2" Residue "SD ASP 232": "OD1" <-> "OD2" Residue "SD ASP 238": "OD1" <-> "OD2" Residue "SE ASP 88": "OD1" <-> "OD2" Residue "SE GLU 119": "OE1" <-> "OE2" Residue "SE GLU 210": "OE1" <-> "OE2" Residue "SE ASP 211": "OD1" <-> "OD2" Residue "SG ASP 11": "OD1" <-> "OD2" Residue "SG GLU 44": "OE1" <-> "OE2" Residue "SG TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SG GLU 147": "OE1" <-> "OE2" Residue "SG ASP 150": "OD1" <-> "OD2" Residue "SG TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SH PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SH ASP 184": "OD1" <-> "OD2" Residue "SI ASP 74": "OD1" <-> "OD2" Residue "SI GLU 245": "OE1" <-> "OE2" Residue "SJ PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SJ PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SJ PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SK GLU 32": "OE1" <-> "OE2" Residue "SL TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SL PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SL ASP 94": "OD1" <-> "OD2" Residue "SM TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM ASP 33": "OD1" <-> "OD2" Residue "SM PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM ASP 210": "OD1" <-> "OD2" Residue "SM PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM GLU 429": "OE1" <-> "OE2" Residue "SM TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SN ASP 100": "OD1" <-> "OD2" Residue "SN ASP 144": "OD1" <-> "OD2" Residue "SO ASP 169": "OD1" <-> "OD2" Residue "SO TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SO ASP 212": "OD1" <-> "OD2" Residue "SO PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SQ ASP 83": "OD1" <-> "OD2" Residue "SQ ASP 87": "OD1" <-> "OD2" Residue "SQ GLU 114": "OE1" <-> "OE2" Residue "SQ PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SQ ASP 209": "OD1" <-> "OD2" Residue "SR TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR ASP 107": "OD1" <-> "OD2" Residue "SR ASP 121": "OD1" <-> "OD2" Residue "SR TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR GLU 301": "OE1" <-> "OE2" Residue "SR GLU 325": "OE1" <-> "OE2" Residue "SR PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR ASP 412": "OD1" <-> "OD2" Residue "SR TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR ASP 443": "OD1" <-> "OD2" Residue "SS ASP 153": "OD1" <-> "OD2" Residue "SS PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SS PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SS PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SS PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SU PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SV ASP 66": "OD1" <-> "OD2" Residue "SV GLU 70": "OE1" <-> "OE2" Residue "SV PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SV GLU 72": "OE1" <-> "OE2" Residue "SV GLU 77": "OE1" <-> "OE2" Residue "SV ASP 91": "OD1" <-> "OD2" Residue "SV GLU 98": "OE1" <-> "OE2" Residue "SW PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW GLU 262": "OE1" <-> "OE2" Residue "SW PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW ASP 333": "OD1" <-> "OD2" Residue "SW PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SY GLU 265": "OE1" <-> "OE2" Residue "SY PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SY TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SY PHE 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SY PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SZ TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SZ ASP 96": "OD1" <-> "OD2" Residue "SZ ASP 114": "OD1" <-> "OD2" Residue "SZ ASP 117": "OD1" <-> "OD2" Residue "SZ ASP 129": "OD1" <-> "OD2" Residue "SZ GLU 137": "OE1" <-> "OE2" Residue "SZ ASP 143": "OD1" <-> "OD2" Residue "SZ GLU 162": "OE1" <-> "OE2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 139783 Number of models: 1 Model: "" Number of chains: 65 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: "BB" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1057 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 192} Link IDs: {'PTRANS': 8, 'TRANS': 204} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 686 Unresolved non-hydrogen angles: 858 Unresolved non-hydrogen dihedrals: 573 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 11, 'TYR:plan': 6, 'ASN:plan1': 11, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 7, 'GLU:plan': 10, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 320 Chain: "L1" Number of atoms: 3234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 3234 Classifications: {'RNA': 152} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 12, 'rna3p_pur': 60, 'rna3p_pyr': 65} Link IDs: {'rna2p': 26, 'rna3p': 125} Chain breaks: 1 Chain: "L2" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1468 Classifications: {'RNA': 69} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 6, 'rna3p_pur': 21, 'rna3p_pyr': 31} Link IDs: {'rna2p': 16, 'rna3p': 52} Chain breaks: 3 Chain: "L3" Number of atoms: 48813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2277, 48813 Classifications: {'RNA': 2277} Modifications used: {'rna2p_pur': 216, 'rna2p_pyr': 132, 'rna3p_pur': 1030, 'rna3p_pyr': 899} Link IDs: {'rna2p': 348, 'rna3p': 1928} Chain breaks: 42 Chain: "L6" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 998 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 110} Chain: "L7" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1634 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 189} 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: "L9" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1546 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 176} Chain breaks: 1 Chain: "LA" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1106 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 6, 'TRANS': 131} Chain breaks: 1 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: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 926 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain breaks: 2 Chain: "LG" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 127} Chain: "LH" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 813 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 7, 'TRANS': 125} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 268 Unresolved non-hydrogen angles: 341 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 3, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 122 Chain: "LI" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1115 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "LK" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 642 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 90 Chain: "LL" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 980 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "LN" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2884 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 345} Chain breaks: 2 Chain: "LP" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 526 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 5, 'TRANS': 100} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 369 Unresolved non-hydrogen angles: 468 Unresolved non-hydrogen dihedrals: 304 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 5, 'TYR:plan': 4, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 197 Chain: "LQ" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1053 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "LS" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1015 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} 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: "LU" Number of atoms: 840 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 102, 832 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 98} Conformer: "B" Number of residues, atoms: 102, 832 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 98} bond proxies already assigned to first conformer: 834 Chain: "LW" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 612 Classifications: {'peptide': 74} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 70} Chain: "NA" Number of atoms: 3658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3658 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 22, 'TRANS': 461} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 312 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 6, 'GLU:plan': 4, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 133 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: "NF" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1783 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 207} Chain breaks: 3 Chain: "NH" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1441 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain: "NI" Number of atoms: 5137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5137 Classifications: {'peptide': 647} Link IDs: {'PTRANS': 31, 'TRANS': 615} Chain breaks: 6 Chain: "NK" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 594 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain breaks: 1 Chain: "SA" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2853 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 339} Chain: "SC" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1627 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 189} 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: "SE" Number of atoms: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1491 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 174} Chain: "SG" Number of atoms: 1526 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 190, 1518 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Conformer: "B" Number of residues, atoms: 190, 1518 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} bond proxies already assigned to first conformer: 1528 Chain: "SH" Number of atoms: 1267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1267 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 8, 'TRANS': 141} Chain: "SI" Number of atoms: 1850 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 223, 1839 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 223, 1839 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain breaks: 1 bond proxies already assigned to first conformer: 1861 Chain: "SJ" Number of atoms: 2551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2551 Classifications: {'peptide': 313} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 300} Chain breaks: 3 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: "SL" Number of atoms: 1960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1960 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 8, 'TRANS': 234} Chain: "SM" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3735 Classifications: {'peptide': 453} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 432} Chain breaks: 3 Chain: "SN" Number of atoms: 1350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1350 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 165} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 33 Chain: "SO" Number of atoms: 2460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2460 Classifications: {'peptide': 296} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 274} Chain breaks: 1 Chain: "SQ" Number of atoms: 1778 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 217, 1771 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 7, 'TRANS': 209} Conformer: "B" Number of residues, atoms: 217, 1771 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 7, 'TRANS': 209} bond proxies already assigned to first conformer: 1797 Chain: "SR" Number of atoms: 3808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3808 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 19, 'TRANS': 442} Chain: "SS" Number of atoms: 2011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2011 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 26, 'TRANS': 216} Chain breaks: 1 Chain: "ST" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 876 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 7, 'TRANS': 114} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "SU" Number of atoms: 4442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4442 Classifications: {'peptide': 562} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 540} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 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: "SW" Number of atoms: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3549 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 19, 'TRANS': 424} Chain breaks: 1 Chain: "SY" Number of atoms: 2985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2985 Classifications: {'peptide': 378} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 357} Chain: "SZ" Number of atoms: 1338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1338 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 152} Chain breaks: 1 Chain: "L1" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "L2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "L3" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Unusual residues: {' MG': 46} Classifications: {'undetermined': 46} Link IDs: {None: 45} Chain: "L9" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LQ" 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: "LW" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "NI" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "SA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} 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: "SU" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} 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 77569 SG CYSLW 19 87.460 125.036 148.069 1.00 39.09 S ATOM 77597 SG CYSLW 22 88.053 122.343 150.726 1.00 33.82 S ATOM 77688 SG CYSLW 34 90.022 125.514 150.910 1.00 38.93 S ATOM 77707 SG CYSLW 37 90.730 123.193 148.070 1.00 35.26 S ATOM A0NO2 SG CYSSV 6 55.943 181.836 235.325 1.00 37.22 S ATOM A0NOV SG CYSSV 9 52.440 180.594 234.847 1.00 37.36 S ATOM A0NTZ SG CYSSV 32 55.184 178.066 235.388 1.00 35.39 S ATOM A0NUT SG CYSSV 36 55.021 180.007 232.098 1.00 36.29 S Time building chain proxies: 55.01, per 1000 atoms: 0.39 Number of scatterers: 139783 At special positions: 0 Unit cell: (236.912, 288.368, 334.464, 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 2 29.99 K 1 19.00 S 358 16.00 P 2504 15.00 Mg 59 11.99 O 32475 8.00 N 25858 7.00 C 78526 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: 51.01 Conformation dependent library (CDL) restraints added in 13.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNLW 500 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 37 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 34 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 19 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 22 " pdb=" ZNSV 500 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 9 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 36 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 32 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 6 " Number of angles added : 12 21388 Ramachandran restraints generated. 10694 Oldfield, 0 Emsley, 10694 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 20560 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 431 helices and 81 sheets defined 52.9% alpha, 11.5% beta 812 base pairs and 1252 stacking pairs defined. Time for finding SS restraints: 81.03 Creating SS restraints... Processing helix chain 'BA' and resid 24 through 33 Proline residue: BA 30 - end of helix Processing helix chain 'BA' and resid 38 through 51 Processing helix chain 'BA' and resid 76 through 86 removed outlier: 3.532A pdb=" N LYSBA 86 " --> pdb=" O ILEBA 82 " (cutoff:3.500A) Processing helix chain 'BA' and resid 105 through 117 Processing helix chain 'BA' and resid 124 through 140 removed outlier: 3.579A pdb=" N THRBA 128 " --> pdb=" O GLUBA 124 " (cutoff:3.500A) Processing helix chain 'BA' and resid 147 through 158 Processing helix chain 'BB' and resid 6 through 25 Processing helix chain 'BB' and resid 70 through 81 Processing helix chain 'BB' and resid 86 through 97 removed outlier: 4.334A pdb=" N LYSBB 95 " --> pdb=" O LYSBB 91 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASNBB 96 " --> pdb=" O LYSBB 92 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LYSBB 97 " --> pdb=" O LEUBB 93 " (cutoff:3.500A) Processing helix chain 'BB' and resid 98 through 108 removed outlier: 4.929A pdb=" N ASPBB 108 " --> pdb=" O ALABB 104 " (cutoff:3.500A) Processing helix chain 'BB' and resid 113 through 124 removed outlier: 3.507A pdb=" N ILEBB 117 " --> pdb=" O SERBB 113 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYSBB 118 " --> pdb=" O GLUBB 114 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLNBB 119 " --> pdb=" O SERBB 115 " (cutoff:3.500A) Proline residue: BB 121 - end of helix Processing helix chain 'BB' and resid 125 through 132 Processing helix chain 'BB' and resid 143 through 154 Processing helix chain 'BB' and resid 175 through 195 removed outlier: 5.250A pdb=" N LYSBB 195 " --> pdb=" O VALBB 191 " (cutoff:3.500A) Processing helix chain 'BB' and resid 197 through 202 removed outlier: 3.903A pdb=" N VALBB 201 " --> pdb=" O ASNBB 197 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ARGBB 202 " --> pdb=" O TRPBB 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'BB' and resid 197 through 202' Processing helix chain 'L6' and resid 27 through 47 Processing helix chain 'L6' and resid 77 through 85 Processing helix chain 'L6' and resid 87 through 95 removed outlier: 4.052A pdb=" N ARGL6 92 " --> pdb=" O LYSL6 88 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THRL6 93 " --> pdb=" O LYSL6 89 " (cutoff:3.500A) Processing helix chain 'L6' and resid 106 through 124 removed outlier: 3.724A pdb=" N LEUL6 110 " --> pdb=" O SERL6 106 " (cutoff:3.500A) Processing helix chain 'L7' and resid 15 through 30 removed outlier: 3.560A pdb=" N GLYL7 30 " --> pdb=" O GLNL7 26 " (cutoff:3.500A) Processing helix chain 'L7' and resid 46 through 60 removed outlier: 3.638A pdb=" N LYSL7 60 " --> pdb=" O ALAL7 56 " (cutoff:3.500A) Processing helix chain 'L7' and resid 65 through 70 Proline residue: L7 70 - end of helix Processing helix chain 'L7' and resid 75 through 89 removed outlier: 3.506A pdb=" N LEUL7 88 " --> pdb=" O VALL7 84 " (cutoff:3.500A) Proline residue: L7 89 - end of helix Processing helix chain 'L7' and resid 92 through 103 removed outlier: 3.604A pdb=" N LEUL7 102 " --> pdb=" O ALAL7 98 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LYSL7 103 " --> pdb=" O LEUL7 99 " (cutoff:3.500A) Processing helix chain 'L7' and resid 110 through 116 removed outlier: 7.900A pdb=" N LYSL7 114 " --> pdb=" O PROL7 110 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYSL7 115 " --> pdb=" O PROL7 111 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LYSL7 116 " --> pdb=" O TYRL7 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'L7' and resid 110 through 116' Processing helix chain 'L7' and resid 124 through 129 Processing helix chain 'L7' and resid 137 through 146 Processing helix chain 'L7' and resid 150 through 190 removed outlier: 3.515A pdb=" N GLUL7 186 " --> pdb=" O GLUL7 182 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LYSL7 187 " --> pdb=" O LYSL7 183 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LYSL7 188 " --> pdb=" O ASNL7 184 " (cutoff:3.500A) Processing helix chain 'L7' and resid 191 through 200 Processing helix chain 'L8' and resid 51 through 56 removed outlier: 3.897A pdb=" N METL8 55 " --> pdb=" O PROL8 51 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N GLNL8 56 " --> pdb=" O PHEL8 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'L8' and resid 51 through 56' Processing helix chain 'L8' and resid 69 through 81 Processing helix chain 'L8' and resid 82 through 90 removed outlier: 5.625A pdb=" N ARGL8 90 " --> pdb=" O TRPL8 86 " (cutoff:3.500A) Processing helix chain 'L8' and resid 91 through 104 removed outlier: 3.883A pdb=" N METL8 104 " --> pdb=" O ARGL8 100 " (cutoff:3.500A) Processing helix chain 'L8' and resid 105 through 136 Processing helix chain 'L9' and resid 2 through 14 removed outlier: 3.871A pdb=" N TYRL9 6 " --> pdb=" O GLYL9 2 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYSL9 13 " --> pdb=" O GLUL9 9 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LYSL9 14 " --> pdb=" O LEUL9 10 " (cutoff:3.500A) Processing helix chain 'L9' and resid 16 through 34 removed outlier: 4.849A pdb=" N SERL9 34 " --> pdb=" O TYRL9 30 " (cutoff:3.500A) Processing helix chain 'L9' and resid 44 through 52 Processing helix chain 'L9' and resid 97 through 111 removed outlier: 3.783A pdb=" N GLYL9 111 " --> pdb=" O GLYL9 107 " (cutoff:3.500A) Processing helix chain 'L9' and resid 139 through 146 removed outlier: 3.888A pdb=" N ASNL9 145 " --> pdb=" O ALAL9 141 " (cutoff:3.500A) Proline residue: L9 146 - end of helix Processing helix chain 'L9' and resid 147 through 153 removed outlier: 6.168A pdb=" N ILEL9 151 " --> pdb=" O ASPL9 147 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N THRL9 152 " --> pdb=" O THRL9 148 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYSL9 153 " --> pdb=" O GLNL9 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'L9' and resid 147 through 153' Processing helix chain 'L9' and resid 158 through 163 Processing helix chain 'L9' and resid 165 through 173 removed outlier: 4.214A pdb=" N SERL9 171 " --> pdb=" O ALAL9 167 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARGL9 172 " --> pdb=" O GLYL9 168 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLYL9 173 " --> pdb=" O ARGL9 169 " (cutoff:3.500A) Processing helix chain 'L9' and resid 187 through 197 Processing helix chain 'LA' and resid 10 through 15 removed outlier: 5.376A pdb=" N CYSLA 15 " --> pdb=" O PROLA 11 " (cutoff:3.500A) Processing helix chain 'LA' and resid 25 through 37 removed outlier: 3.501A pdb=" N GLULA 31 " --> pdb=" O LYSLA 27 " (cutoff:3.500A) Processing helix chain 'LA' and resid 40 through 54 Processing helix chain 'LA' and resid 70 through 77 removed outlier: 4.102A pdb=" N LYSLA 74 " --> pdb=" O CYSLA 70 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLNLA 75 " --> pdb=" O ALALA 71 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N TRPLA 76 " --> pdb=" O GLNLA 72 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLYLA 77 " --> pdb=" O ALALA 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'LA' and resid 70 through 77' Processing helix chain 'LA' and resid 84 through 106 removed outlier: 3.600A pdb=" N HISLA 93 " --> pdb=" O GLULA 89 " (cutoff:3.500A) Processing helix chain 'LB' and resid 22 through 39 Processing helix chain 'LB' and resid 41 through 54 removed outlier: 4.191A pdb=" N GLNLB 45 " --> pdb=" O SERLB 41 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHELB 52 " --> pdb=" O LEULB 48 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N METLB 53 " --> pdb=" O LYSLB 49 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N SERLB 54 " --> pdb=" O ARGLB 50 " (cutoff:3.500A) Processing helix chain 'LB' and resid 62 through 72 removed outlier: 3.532A pdb=" N LYSLB 69 " --> pdb=" O ARGLB 65 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEULB 72 " --> pdb=" O ARGLB 68 " (cutoff:3.500A) Processing helix chain 'LB' and resid 106 through 117 removed outlier: 3.506A pdb=" N GLYLB 117 " --> pdb=" O ILELB 113 " (cutoff:3.500A) Processing helix chain 'LB' and resid 122 through 130 Processing helix chain 'LB' and resid 146 through 152 removed outlier: 4.352A pdb=" N ARGLB 150 " --> pdb=" O ARGLB 146 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HISLB 151 " --> pdb=" O GLULB 147 " (cutoff:3.500A) Processing helix chain 'LB' and resid 7 through 12 removed outlier: 3.602A pdb=" N ASPLB 10 " --> pdb=" O HISLB 7 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ARGLB 11 " --> pdb=" O ASNLB 8 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LYSLB 12 " --> pdb=" O LYSLB 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'LB' and resid 7 through 12' Processing helix chain 'LC' and resid 36 through 52 Processing helix chain 'LC' and resid 101 through 117 Processing helix chain 'LC' and resid 120 through 125 removed outlier: 5.369A pdb=" N GLNLC 125 " --> pdb=" O ALALC 121 " (cutoff:3.500A) Processing helix chain 'LC' and resid 139 through 147 removed outlier: 4.531A pdb=" N PHELC 145 " --> pdb=" O ALALC 141 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N HISLC 146 " --> pdb=" O VALLC 142 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ASPLC 147 " --> pdb=" O LYSLC 143 " (cutoff:3.500A) Processing helix chain 'LC' and resid 161 through 166 Proline residue: LC 165 - end of helix No H-bonds generated for 'chain 'LC' and resid 161 through 166' Processing helix chain 'LE' and resid 92 through 97 removed outlier: 3.816A pdb=" N ILELE 96 " --> pdb=" O ARGLE 92 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LYSLE 97 " --> pdb=" O ILELE 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'LE' and resid 92 through 97' Processing helix chain 'LE' and resid 100 through 121 removed outlier: 3.793A pdb=" N SERLE 104 " --> pdb=" O LYSLE 100 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHELE 105 " --> pdb=" O SERLE 101 " (cutoff:3.500A) Processing helix chain 'LG' and resid 122 through 130 Proline residue: LG 130 - end of helix Processing helix chain 'LG' and resid 131 through 137 removed outlier: 5.534A pdb=" N GLYLG 137 " --> pdb=" O ALALG 133 " (cutoff:3.500A) Processing helix chain 'LH' and resid 14 through 30 Processing helix chain 'LH' and resid 72 through 78 removed outlier: 3.718A pdb=" N ILELH 77 " --> pdb=" O HISLH 73 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N LYSLH 78 " --> pdb=" O TYRLH 74 " (cutoff:3.500A) Processing helix chain 'LH' and resid 83 through 93 removed outlier: 3.550A pdb=" N ILELH 90 " --> pdb=" O ALALH 86 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLULH 91 " --> pdb=" O METLH 87 " (cutoff:3.500A) Processing helix chain 'LH' and resid 105 through 118 Processing helix chain 'LH' and resid 145 through 154 Processing helix chain 'LI' and resid 10 through 21 Processing helix chain 'LI' and resid 22 through 31 removed outlier: 3.895A pdb=" N LYSLI 28 " --> pdb=" O HISLI 24 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N SERLI 31 " --> pdb=" O ARGLI 27 " (cutoff:3.500A) Processing helix chain 'LI' and resid 35 through 43 Processing helix chain 'LI' and resid 100 through 105 removed outlier: 4.021A pdb=" N VALLI 104 " --> pdb=" O HISLI 100 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VALLI 105 " --> pdb=" O PROLI 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'LI' and resid 100 through 105' Processing helix chain 'LI' and resid 112 through 134 removed outlier: 3.623A pdb=" N ARGLI 121 " --> pdb=" O LYSLI 117 " (cutoff:3.500A) Processing helix chain 'LK' and resid 6 through 12 removed outlier: 3.996A pdb=" N LYSLK 10 " --> pdb=" O ARGLK 6 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARGLK 12 " --> pdb=" O THRLK 8 " (cutoff:3.500A) Processing helix chain 'LK' and resid 60 through 67 removed outlier: 5.550A pdb=" N GLNLK 67 " --> pdb=" O LEULK 63 " (cutoff:3.500A) Processing helix chain 'LK' and resid 74 through 83 removed outlier: 3.561A pdb=" N TRPLK 79 " --> pdb=" O LEULK 75 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N SERLK 83 " --> pdb=" O TRPLK 79 " (cutoff:3.500A) Processing helix chain 'LK' and resid 84 through 94 removed outlier: 4.841A pdb=" N LYSLK 94 " --> pdb=" O ALALK 90 " (cutoff:3.500A) Processing helix chain 'LK' and resid 102 through 107 removed outlier: 3.564A pdb=" N SERLK 106 " --> pdb=" O ASPLK 102 " (cutoff:3.500A) Processing helix chain 'LK' and resid 130 through 141 Processing helix chain 'LL' and resid 2 through 13 removed outlier: 3.563A pdb=" N VALLL 9 " --> pdb=" O LEULL 5 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ASNLL 12 " --> pdb=" O METLL 8 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N CYSLL 13 " --> pdb=" O VALLL 9 " (cutoff:3.500A) Processing helix chain 'LL' and resid 72 through 77 removed outlier: 4.647A pdb=" N TYRLL 77 " --> pdb=" O PROLL 73 " (cutoff:3.500A) Processing helix chain 'LL' and resid 85 through 101 removed outlier: 3.591A pdb=" N ASNLL 100 " --> pdb=" O METLL 96 " (cutoff:3.500A) Processing helix chain 'LL' and resid 103 through 123 removed outlier: 3.717A pdb=" N ARGLL 107 " --> pdb=" O ARGLL 103 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N METLL 108 " --> pdb=" O PROLL 104 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ALALL 109 " --> pdb=" O ASPLL 105 " (cutoff:3.500A) Proline residue: LL 123 - end of helix Processing helix chain 'LN' and resid 111 through 120 removed outlier: 3.973A pdb=" N ARGLN 117 " --> pdb=" O GLULN 113 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHELN 118 " --> pdb=" O CYSLN 114 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYRLN 119 " --> pdb=" O LYSLN 115 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N LYSLN 120 " --> pdb=" O ARGLN 116 " (cutoff:3.500A) Processing helix chain 'LN' and resid 130 through 140 removed outlier: 4.124A pdb=" N LYSLN 135 " --> pdb=" O THRLN 131 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYSLN 136 " --> pdb=" O LYSLN 132 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TRPLN 137 " --> pdb=" O TYRLN 133 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLNLN 138 " --> pdb=" O CYSLN 134 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLULN 140 " --> pdb=" O LYSLN 136 " (cutoff:3.500A) Processing helix chain 'LN' and resid 141 through 157 Processing helix chain 'LN' and resid 167 through 172 removed outlier: 3.954A pdb=" N LEULN 171 " --> pdb=" O GLNLN 167 " (cutoff:3.500A) Proline residue: LN 172 - end of helix No H-bonds generated for 'chain 'LN' and resid 167 through 172' Processing helix chain 'LN' and resid 189 through 201 Processing helix chain 'LN' and resid 206 through 211 removed outlier: 3.865A pdb=" N VALLN 210 " --> pdb=" O PROLN 206 " (cutoff:3.500A) Processing helix chain 'LN' and resid 356 through 361 removed outlier: 3.832A pdb=" N LEULN 360 " --> pdb=" O LYSLN 356 " (cutoff:3.500A) Processing helix chain 'LN' and resid 381 through 390 Processing helix chain 'LN' and resid 392 through 403 Processing helix chain 'LP' and resid 28 through 34 removed outlier: 3.893A pdb=" N ARGLP 32 " --> pdb=" O ASNLP 28 " (cutoff:3.500A) Processing helix chain 'LP' and resid 37 through 57 removed outlier: 4.745A pdb=" N ALALP 42 " --> pdb=" O PHELP 38 " (cutoff:3.500A) Proline residue: LP 43 - end of helix removed outlier: 3.578A pdb=" N LYSLP 47 " --> pdb=" O PROLP 43 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N METLP 54 " --> pdb=" O ARGLP 50 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYSLP 55 " --> pdb=" O LYSLP 51 " (cutoff:3.500A) Processing helix chain 'LP' and resid 65 through 74 Processing helix chain 'LQ' and resid 24 through 29 removed outlier: 4.912A pdb=" N VALLQ 29 " --> pdb=" O SERLQ 25 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 43 through 48 Processing helix chain 'LQ' and resid 81 through 90 removed outlier: 3.774A pdb=" N LEULQ 85 " --> pdb=" O ASNLQ 81 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLULQ 86 " --> pdb=" O VALLQ 82 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VALLQ 87 " --> pdb=" O LYSLQ 83 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEULQ 88 " --> pdb=" O GLULQ 84 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEULQ 89 " --> pdb=" O LEULQ 85 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N METLQ 90 " --> pdb=" O GLULQ 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'LQ' and resid 81 through 90' Processing helix chain 'LQ' and resid 104 through 119 removed outlier: 3.727A pdb=" N ALALQ 110 " --> pdb=" O LYSLQ 106 " (cutoff:3.500A) Processing helix chain 'LS' and resid 5 through 10 Processing helix chain 'LS' and resid 13 through 38 removed outlier: 3.513A pdb=" N LEULS 17 " --> pdb=" O LYSLS 13 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLYLS 38 " --> pdb=" O ALALS 34 " (cutoff:3.500A) Processing helix chain 'LS' and resid 40 through 74 removed outlier: 4.411A pdb=" N ARGLS 48 " --> pdb=" O LEULS 44 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VALLS 49 " --> pdb=" O SERLS 45 " (cutoff:3.500A) Processing helix chain 'LS' and resid 80 through 85 Proline residue: LS 85 - end of helix Processing helix chain 'LS' and resid 88 through 95 removed outlier: 5.693A pdb=" N LEULS 95 " --> pdb=" O METLS 91 " (cutoff:3.500A) Processing helix chain 'LS' and resid 96 through 102 Processing helix chain 'LS' and resid 104 through 115 Proline residue: LS 115 - end of helix Processing helix chain 'LT' and resid 35 through 40 removed outlier: 3.562A pdb=" N THRLT 39 " --> pdb=" O ALALT 35 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLULT 40 " --> pdb=" O ARGLT 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'LT' and resid 35 through 40' Processing helix chain 'LU' and resid 25 through 30 removed outlier: 4.012A pdb=" N ARGLU 29 " --> pdb=" O ARGLU 25 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARGLU 30 " --> pdb=" O HISLU 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'LU' and resid 25 through 30' Processing helix chain 'LU' and resid 34 through 49 removed outlier: 3.501A pdb=" N GLULU 46 " --> pdb=" O ASPLU 42 " (cutoff:3.500A) Processing helix chain 'LU' and resid 51 through 64 Processing helix chain 'LU' and resid 65 through 78 Processing helix chain 'LU' and resid 79 through 103 Processing helix chain 'LW' and resid 50 through 58 removed outlier: 3.501A pdb=" N LYSLW 54 " --> pdb=" O SERLW 50 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASNLW 57 " --> pdb=" O ALALW 53 " (cutoff:3.500A) Processing helix chain 'LW' and resid 64 through 77 removed outlier: 4.161A pdb=" N ILELW 69 " --> pdb=" O ARGLW 65 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARGLW 75 " --> pdb=" O TYRLW 71 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N HISLW 76 " --> pdb=" O ARGLW 72 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLYLW 77 " --> pdb=" O ARGLW 73 " (cutoff:3.500A) Processing helix chain 'NA' and resid 150 through 164 removed outlier: 3.739A pdb=" N VALNA 154 " --> pdb=" O THRNA 150 " (cutoff:3.500A) Processing helix chain 'NA' and resid 166 through 186 removed outlier: 3.678A pdb=" N THRNA 184 " --> pdb=" O ALANA 180 " (cutoff:3.500A) Processing helix chain 'NA' and resid 187 through 195 removed outlier: 5.411A pdb=" N LYSNA 195 " --> pdb=" O ALANA 191 " (cutoff:3.500A) Processing helix chain 'NA' and resid 200 through 214 removed outlier: 3.983A pdb=" N ARGNA 213 " --> pdb=" O THRNA 209 " (cutoff:3.500A) Processing helix chain 'NA' and resid 215 through 224 removed outlier: 3.560A pdb=" N LEUNA 222 " --> pdb=" O CYSNA 218 " (cutoff:3.500A) Processing helix chain 'NA' and resid 240 through 247 removed outlier: 4.371A pdb=" N GLYNA 244 " --> pdb=" O SERNA 240 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYSNA 245 " --> pdb=" O PRONA 241 " (cutoff:3.500A) Processing helix chain 'NA' and resid 248 through 265 removed outlier: 3.611A pdb=" N SERNA 262 " --> pdb=" O ILENA 258 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N SERNA 265 " --> pdb=" O VALNA 261 " (cutoff:3.500A) Processing helix chain 'NA' and resid 266 through 281 Processing helix chain 'NA' and resid 282 through 288 removed outlier: 3.908A pdb=" N PHENA 287 " --> pdb=" O CYSNA 283 " (cutoff:3.500A) Proline residue: NA 288 - end of helix Processing helix chain 'NA' and resid 289 through 305 removed outlier: 3.639A pdb=" N LYSNA 296 " --> pdb=" O ARGNA 292 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLYNA 305 " --> pdb=" O VALNA 301 " (cutoff:3.500A) Processing helix chain 'NA' and resid 306 through 325 Processing helix chain 'NA' and resid 328 through 346 removed outlier: 3.656A pdb=" N LYSNA 345 " --> pdb=" O VALNA 341 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N PHENA 346 " --> pdb=" O ARGNA 342 " (cutoff:3.500A) Processing helix chain 'NA' and resid 349 through 370 Proline residue: NA 353 - end of helix removed outlier: 4.187A pdb=" N GLUNA 369 " --> pdb=" O LEUNA 365 " (cutoff:3.500A) Proline residue: NA 370 - end of helix Processing helix chain 'NA' and resid 371 through 395 removed outlier: 3.658A pdb=" N GLNNA 375 " --> pdb=" O GLYNA 371 " (cutoff:3.500A) Processing helix chain 'NA' and resid 396 through 405 removed outlier: 3.699A pdb=" N VALNA 403 " --> pdb=" O THRNA 399 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASNNA 405 " --> pdb=" O GLNNA 401 " (cutoff:3.500A) Processing helix chain 'NA' and resid 406 through 422 removed outlier: 3.507A pdb=" N PHENA 413 " --> pdb=" O VALNA 409 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ALANA 422 " --> pdb=" O VALNA 418 " (cutoff:3.500A) Processing helix chain 'NA' and resid 423 through 429 removed outlier: 4.159A pdb=" N ALANA 427 " --> pdb=" O GLYNA 423 " (cutoff:3.500A) Processing helix chain 'NA' and resid 430 through 447 Proline residue: NA 434 - end of helix removed outlier: 4.516A pdb=" N ILENA 446 " --> pdb=" O CYSNA 442 " (cutoff:3.500A) Proline residue: NA 447 - end of helix Processing helix chain 'NA' and resid 448 through 470 removed outlier: 3.615A pdb=" N TYRNA 452 " --> pdb=" O THRNA 448 " (cutoff:3.500A) Proline residue: NA 453 - end of helix Processing helix chain 'NA' and resid 474 through 486 removed outlier: 4.716A pdb=" N PHENA 478 " --> pdb=" O PRONA 474 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILENA 479 " --> pdb=" O VALNA 475 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N METNA 482 " --> pdb=" O PHENA 478 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHENA 483 " --> pdb=" O ILENA 479 " (cutoff:3.500A) Processing helix chain 'NA' and resid 509 through 516 removed outlier: 3.542A pdb=" N GLNNA 514 " --> pdb=" O ASNNA 510 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LYSNA 516 " --> pdb=" O ASNNA 512 " (cutoff:3.500A) Processing helix chain 'NA' and resid 517 through 538 removed outlier: 3.535A pdb=" N GLUNA 524 " --> pdb=" O ASPNA 520 " (cutoff:3.500A) Processing helix chain 'NA' and resid 542 through 561 Proline residue: NA 549 - end of helix removed outlier: 3.523A pdb=" N ARGNA 559 " --> pdb=" O LYSNA 555 " (cutoff:3.500A) Processing helix chain 'NA' and resid 564 through 592 removed outlier: 5.871A pdb=" N SERNA 592 " --> pdb=" O ARGNA 588 " (cutoff:3.500A) Processing helix chain 'NA' and resid 597 through 612 removed outlier: 3.509A pdb=" N VALNA 601 " --> pdb=" O GLUNA 597 " (cutoff:3.500A) Processing helix chain 'NA' and resid 613 through 635 Processing helix chain 'NB' and resid 14 through 36 Processing helix chain 'NB' and resid 56 through 77 removed outlier: 3.548A pdb=" N LEUNB 71 " --> pdb=" O ARGNB 67 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLUNB 72 " --> pdb=" O LYSNB 68 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLUNB 73 " --> pdb=" O GLNNB 69 " (cutoff:3.500A) Processing helix chain 'NF' and resid 5 through 14 Processing helix chain 'NF' and resid 21 through 35 removed outlier: 4.202A pdb=" N ALANF 32 " --> pdb=" O GLUNF 28 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N HISNF 33 " --> pdb=" O SERNF 29 " (cutoff:3.500A) Processing helix chain 'NF' and resid 44 through 72 Processing helix chain 'NF' and resid 97 through 117 Processing helix chain 'NF' and resid 164 through 169 removed outlier: 3.539A pdb=" N GLUNF 168 " --> pdb=" O PRONF 164 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ARGNF 169 " --> pdb=" O PRONF 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'NF' and resid 164 through 169' Processing helix chain 'NF' and resid 173 through 178 removed outlier: 3.620A pdb=" N ARGNF 177 " --> pdb=" O PRONF 173 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N PHENF 178 " --> pdb=" O METNF 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'NF' and resid 173 through 178' Processing helix chain 'NF' and resid 205 through 212 Processing helix chain 'NF' and resid 247 through 252 Processing helix chain 'NH' and resid 5 through 20 removed outlier: 4.272A pdb=" N TYRNH 19 " --> pdb=" O LYSNH 15 " (cutoff:3.500A) Processing helix chain 'NH' and resid 22 through 30 removed outlier: 4.537A pdb=" N LEUNH 26 " --> pdb=" O GLUNH 22 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARGNH 30 " --> pdb=" O LEUNH 26 " (cutoff:3.500A) Processing helix chain 'NH' and resid 48 through 59 removed outlier: 3.600A pdb=" N ALANH 56 " --> pdb=" O METNH 52 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASNNH 57 " --> pdb=" O LYSNH 53 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILENH 58 " --> pdb=" O LEUNH 54 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N SERNH 59 " --> pdb=" O ALANH 55 " (cutoff:3.500A) Processing helix chain 'NH' and resid 82 through 93 removed outlier: 4.164A pdb=" N LEUNH 86 " --> pdb=" O HISNH 82 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASPNH 87 " --> pdb=" O VALNH 83 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N TYRNH 88 " --> pdb=" O THRNH 84 " (cutoff:3.500A) Proline residue: NH 91 - end of helix Processing helix chain 'NH' and resid 100 through 110 removed outlier: 4.140A pdb=" N GLNNH 105 " --> pdb=" O PRONH 101 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N SERNH 106 " --> pdb=" O GLYNH 102 " (cutoff:3.500A) Processing helix chain 'NH' and resid 114 through 119 removed outlier: 5.489A pdb=" N GLYNH 119 " --> pdb=" O LYSNH 115 " (cutoff:3.500A) Processing helix chain 'NH' and resid 149 through 157 removed outlier: 3.642A pdb=" N ARGNH 154 " --> pdb=" O THRNH 150 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYSNH 155 " --> pdb=" O GLNNH 151 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ASPNH 157 " --> pdb=" O CYSNH 153 " (cutoff:3.500A) Processing helix chain 'NH' and resid 168 through 175 removed outlier: 4.878A pdb=" N TYRNH 172 " --> pdb=" O ASPNH 168 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N VALNH 173 " --> pdb=" O ILENH 169 " (cutoff:3.500A) Processing helix chain 'NI' and resid 97 through 102 removed outlier: 3.835A pdb=" N GLYNI 102 " --> pdb=" O PHENI 98 " (cutoff:3.500A) Processing helix chain 'NI' and resid 104 through 115 Processing helix chain 'NI' and resid 120 through 133 Proline residue: NI 128 - end of helix Processing helix chain 'NI' and resid 145 through 159 removed outlier: 3.900A pdb=" N CYSNI 149 " --> pdb=" O GLYNI 145 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHENI 150 " --> pdb=" O LYSNI 146 " (cutoff:3.500A) Proline residue: NI 153 - end of helix Processing helix chain 'NI' and resid 175 through 191 Processing helix chain 'NI' and resid 205 through 216 removed outlier: 4.070A pdb=" N ASNNI 216 " --> pdb=" O ALANI 212 " (cutoff:3.500A) Processing helix chain 'NI' and resid 223 through 235 removed outlier: 3.648A pdb=" N HISNI 229 " --> pdb=" O GLYNI 225 " (cutoff:3.500A) Processing helix chain 'NI' and resid 248 through 256 removed outlier: 3.515A pdb=" N GLYNI 256 " --> pdb=" O LEUNI 252 " (cutoff:3.500A) Processing helix chain 'NI' and resid 257 through 269 Proline residue: NI 269 - end of helix Processing helix chain 'NI' and resid 282 through 293 Processing helix chain 'NI' and resid 301 through 307 removed outlier: 3.687A pdb=" N THRNI 305 " --> pdb=" O LEUNI 301 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYSNI 306 " --> pdb=" O ASPNI 302 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LEUNI 307 " --> pdb=" O VALNI 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'NI' and resid 301 through 307' Processing helix chain 'NI' and resid 319 through 333 removed outlier: 4.827A pdb=" N ALANI 324 " --> pdb=" O GLUNI 320 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ALANI 325 " --> pdb=" O ASPNI 321 " (cutoff:3.500A) Processing helix chain 'NI' and resid 347 through 362 removed outlier: 3.600A pdb=" N GLNNI 361 " --> pdb=" O LEUNI 357 " (cutoff:3.500A) Processing helix chain 'NI' and resid 373 through 387 Processing helix chain 'NI' and resid 395 through 403 removed outlier: 5.015A pdb=" N GLYNI 401 " --> pdb=" O LEUNI 397 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEUNI 402 " --> pdb=" O ALANI 398 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ASPNI 403 " --> pdb=" O ALANI 399 " (cutoff:3.500A) Processing helix chain 'NI' and resid 418 through 427 Processing helix chain 'NI' and resid 443 through 458 Proline residue: NI 448 - end of helix Processing helix chain 'NI' and resid 472 through 478 removed outlier: 3.501A pdb=" N VALNI 476 " --> pdb=" O GLYNI 472 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLYNI 478 " --> pdb=" O ALANI 474 " (cutoff:3.500A) Processing helix chain 'NI' and resid 486 through 503 removed outlier: 3.605A pdb=" N GLUNI 491 " --> pdb=" O VALNI 487 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLYNI 494 " --> pdb=" O GLUNI 490 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LEUNI 503 " --> pdb=" O LEUNI 499 " (cutoff:3.500A) Processing helix chain 'NI' and resid 504 through 523 Processing helix chain 'NI' and resid 527 through 538 removed outlier: 5.406A pdb=" N ASPNI 538 " --> pdb=" O ALANI 534 " (cutoff:3.500A) Processing helix chain 'NI' and resid 545 through 553 removed outlier: 4.340A pdb=" N ARGNI 551 " --> pdb=" O LEUNI 547 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHENI 552 " --> pdb=" O PHENI 548 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N GLUNI 553 " --> pdb=" O SERNI 549 " (cutoff:3.500A) Processing helix chain 'NI' and resid 554 through 569 Processing helix chain 'NI' and resid 574 through 579 removed outlier: 5.064A pdb=" N ASNNI 579 " --> pdb=" O ILENI 575 " (cutoff:3.500A) Processing helix chain 'NI' and resid 584 through 598 removed outlier: 3.704A pdb=" N LYSNI 596 " --> pdb=" O ALANI 592 " (cutoff:3.500A) Processing helix chain 'NI' and resid 599 through 618 removed outlier: 3.501A pdb=" N ARGNI 603 " --> pdb=" O LYSNI 599 " (cutoff:3.500A) Proline residue: NI 618 - end of helix Processing helix chain 'NI' and resid 703 through 712 Processing helix chain 'NI' and resid 719 through 739 removed outlier: 3.831A pdb=" N THRNI 724 " --> pdb=" O ALANI 720 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARGNI 725 " --> pdb=" O GLNNI 721 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ARGNI 727 " --> pdb=" O LEUNI 723 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEUNI 730 " --> pdb=" O GLYNI 726 " (cutoff:3.500A) Processing helix chain 'NI' and resid 766 through 776 removed outlier: 4.093A pdb=" N LYSNI 770 " --> pdb=" O ASPNI 766 " (cutoff:3.500A) Processing helix chain 'NI' and resid 825 through 845 Processing helix chain 'NK' and resid 12 through 33 Proline residue: NK 23 - end of helix Processing helix chain 'NK' and resid 98 through 114 Processing helix chain 'SA' and resid 25 through 31 removed outlier: 4.435A pdb=" N LYSSA 29 " --> pdb=" O PROSA 25 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALASA 30 " --> pdb=" O ALASA 26 " (cutoff:3.500A) Proline residue: SA 31 - end of helix No H-bonds generated for 'chain 'SA' and resid 25 through 31' Processing helix chain 'SA' and resid 33 through 49 removed outlier: 3.894A pdb=" N LYSSA 46 " --> pdb=" O THRSA 42 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASNSA 47 " --> pdb=" O ASNSA 43 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ASNSA 48 " --> pdb=" O LEUSA 44 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ARGSA 49 " --> pdb=" O ARGSA 45 " (cutoff:3.500A) Processing helix chain 'SA' and resid 116 through 134 removed outlier: 3.576A pdb=" N ALASA 132 " --> pdb=" O LEUSA 128 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEUSA 133 " --> pdb=" O ALASA 129 " (cutoff:3.500A) Proline residue: SA 134 - end of helix Processing helix chain 'SA' and resid 135 through 141 removed outlier: 3.730A pdb=" N GLYSA 141 " --> pdb=" O VALSA 137 " (cutoff:3.500A) Processing helix chain 'SA' and resid 156 through 161 removed outlier: 4.173A pdb=" N GLYSA 160 " --> pdb=" O ASPSA 156 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYRSA 161 " --> pdb=" O LYSSA 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'SA' and resid 156 through 161' Processing helix chain 'SA' and resid 163 through 175 Processing helix chain 'SA' and resid 176 through 187 removed outlier: 3.765A pdb=" N ILESA 180 " --> pdb=" O ALASA 176 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLNSA 187 " --> pdb=" O VALSA 183 " (cutoff:3.500A) Processing helix chain 'SA' and resid 193 through 198 removed outlier: 3.575A pdb=" N ARGSA 197 " --> pdb=" O LYSSA 193 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASNSA 198 " --> pdb=" O GLYSA 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'SA' and resid 193 through 198' Processing helix chain 'SA' and resid 216 through 222 Processing helix chain 'SA' and resid 236 through 242 Proline residue: SA 242 - end of helix Processing helix chain 'SA' and resid 253 through 263 removed outlier: 3.666A pdb=" N LEUSA 260 " --> pdb=" O ALASA 256 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ASPSA 261 " --> pdb=" O PHESA 257 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLUSA 262 " --> pdb=" O ARGSA 258 " (cutoff:3.500A) Processing helix chain 'SA' and resid 288 through 295 Processing helix chain 'SA' and resid 296 through 303 removed outlier: 3.798A pdb=" N ALASA 301 " --> pdb=" O GLUSA 297 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ARGSA 303 " --> pdb=" O GLNSA 299 " (cutoff:3.500A) Processing helix chain 'SA' and resid 317 through 322 removed outlier: 4.544A pdb=" N LEUSA 322 " --> pdb=" O PROSA 318 " (cutoff:3.500A) Processing helix chain 'SA' and resid 323 through 329 Processing helix chain 'SA' and resid 330 through 361 removed outlier: 4.418A pdb=" N THRSA 334 " --> pdb=" O PROSA 330 " (cutoff:3.500A) Processing helix chain 'SC' and resid 58 through 64 Processing helix chain 'SC' and resid 132 through 137 removed outlier: 6.008A pdb=" N VALSC 137 " --> pdb=" O PHESC 133 " (cutoff:3.500A) Processing helix chain 'SC' and resid 190 through 195 removed outlier: 4.024A pdb=" N VALSC 194 " --> pdb=" O HISSC 190 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ILESC 195 " --> pdb=" O GLNSC 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'SC' and resid 190 through 195' Processing helix chain 'SC' and resid 213 through 218 Processing helix chain 'SC' and resid 243 through 262 removed outlier: 3.685A pdb=" N GLNSC 256 " --> pdb=" O ALASC 252 " (cutoff:3.500A) Proline residue: SC 259 - end of helix Processing helix chain 'SC' and resid 266 through 274 removed outlier: 5.274A pdb=" N VALSC 274 " --> pdb=" O TYRSC 270 " (cutoff:3.500A) Processing helix chain 'SC' and resid 282 through 287 removed outlier: 5.479A pdb=" N VALSC 287 " --> pdb=" O PROSC 283 " (cutoff:3.500A) Processing helix chain 'SD' and resid 24 through 79 removed outlier: 3.699A pdb=" N ILESD 69 " --> pdb=" O TYRSD 65 " (cutoff:3.500A) Processing helix chain 'SD' and resid 102 through 113 Processing helix chain 'SD' and resid 126 through 137 removed outlier: 3.609A pdb=" N VALSD 136 " --> pdb=" O METSD 132 " (cutoff:3.500A) Processing helix chain 'SD' and resid 146 through 156 Processing helix chain 'SD' and resid 171 through 179 removed outlier: 4.068A pdb=" N ILESD 175 " --> pdb=" O ASPSD 171 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SERSD 178 " --> pdb=" O LEUSD 174 " (cutoff:3.500A) Processing helix chain 'SD' and resid 186 through 197 removed outlier: 3.824A pdb=" N VALSD 197 " --> pdb=" O GLUSD 193 " (cutoff:3.500A) Processing helix chain 'SD' and resid 200 through 209 removed outlier: 5.181A pdb=" N TRPSD 209 " --> pdb=" O ASNSD 205 " (cutoff:3.500A) Processing helix chain 'SD' and resid 238 through 248 removed outlier: 4.810A pdb=" N ARGSD 242 " --> pdb=" O ASPSD 238 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEUSD 243 " --> pdb=" O GLNSD 239 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARGSD 246 " --> pdb=" O ARGSD 242 " (cutoff:3.500A) Processing helix chain 'SE' and resid 58 through 74 removed outlier: 3.827A pdb=" N ALASE 68 " --> pdb=" O GLNSE 64 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYSSE 72 " --> pdb=" O ALASE 68 " (cutoff:3.500A) Processing helix chain 'SE' and resid 77 through 86 removed outlier: 4.651A pdb=" N PHESE 83 " --> pdb=" O ALASE 79 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N THRSE 84 " --> pdb=" O ILESE 80 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLNSE 85 " --> pdb=" O ASNSE 81 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ALASE 86 " --> pdb=" O GLNSE 82 " (cutoff:3.500A) Processing helix chain 'SE' and resid 88 through 103 removed outlier: 3.658A pdb=" N LYSSE 101 " --> pdb=" O LYSSE 97 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYRSE 102 " --> pdb=" O LEUSE 98 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARGSE 103 " --> pdb=" O ALASE 99 " (cutoff:3.500A) Processing helix chain 'SE' and resid 106 through 124 removed outlier: 3.665A pdb=" N GLYSE 124 " --> pdb=" O LYSSE 120 " (cutoff:3.500A) Processing helix chain 'SE' and resid 139 through 150 Processing helix chain 'SE' and resid 164 through 178 removed outlier: 4.935A pdb=" N PHESE 169 " --> pdb=" O GLUSE 165 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LEUSE 170 " --> pdb=" O LEUSE 166 " (cutoff:3.500A) Proline residue: SE 171 - end of helix Processing helix chain 'SE' and resid 186 through 195 removed outlier: 3.557A pdb=" N LEUSE 190 " --> pdb=" O GLYSE 186 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEUSE 193 " --> pdb=" O ARGSE 189 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VALSE 194 " --> pdb=" O LEUSE 190 " (cutoff:3.500A) Processing helix chain 'SE' and resid 208 through 231 removed outlier: 4.686A pdb=" N GLYSE 213 " --> pdb=" O SERSE 209 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ALASE 214 " --> pdb=" O GLUSE 210 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASPSE 228 " --> pdb=" O THRSE 224 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ARGSE 229 " --> pdb=" O ASNSE 225 " (cutoff:3.500A) Processing helix chain 'SE' and resid 232 through 237 removed outlier: 4.084A pdb=" N HISSE 236 " --> pdb=" O GLUSE 232 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N TRPSE 237 " --> pdb=" O ILESE 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'SE' and resid 232 through 237' Processing helix chain 'SG' and resid 63 through 86 removed outlier: 3.544A pdb=" N ALASG 68 " --> pdb=" O ARGSG 64 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THRSG 69 " --> pdb=" O LYSSG 65 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VALSG 70 " --> pdb=" O GLUSG 66 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ARGSG 71 " --> pdb=" O LEUSG 67 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THRSG 72 " --> pdb=" O ALASG 68 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYSSG 74 " --> pdb=" O VALSG 70 " (cutoff:3.500A) Processing helix chain 'SG' and resid 150 through 166 removed outlier: 4.072A pdb=" N THRSG 166 " --> pdb=" O GLNSG 162 " (cutoff:3.500A) Processing helix chain 'SG' and resid 171 through 176 removed outlier: 4.755A pdb=" N LEUSG 176 " --> pdb=" O ILESG 172 " (cutoff:3.500A) Processing helix chain 'SH' and resid 57 through 69 removed outlier: 3.761A pdb=" N GLNSH 67 " --> pdb=" O SERSH 63 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHESH 68 " --> pdb=" O TYRSH 64 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLYSH 69 " --> pdb=" O PHESH 65 " (cutoff:3.500A) Processing helix chain 'SH' and resid 95 through 107 Processing helix chain 'SH' and resid 122 through 127 removed outlier: 5.682A pdb=" N HISSH 127 " --> pdb=" O PROSH 123 " (cutoff:3.500A) Processing helix chain 'SH' and resid 143 through 151 Processing helix chain 'SH' and resid 154 through 180 Processing helix chain 'SI' and resid 34 through 46 Processing helix chain 'SI' and resid 60 through 84 removed outlier: 3.593A pdb=" N PHESI 64 " --> pdb=" O ARGSI 60 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLUSI 82 " --> pdb=" O LEUSI 78 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VALSI 83 " --> pdb=" O ARGSI 79 " (cutoff:3.500A) Processing helix chain 'SI' and resid 109 through 120 Processing helix chain 'SI' and resid 133 through 144 Processing helix chain 'SI' and resid 153 through 164 Processing helix chain 'SI' and resid 178 through 186 removed outlier: 3.528A pdb=" N ILESI 182 " --> pdb=" O ASPSI 178 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N HISSI 185 " --> pdb=" O VALSI 181 " (cutoff:3.500A) Processing helix chain 'SI' and resid 193 through 204 Proline residue: SI 204 - end of helix Processing helix chain 'SI' and resid 207 through 216 removed outlier: 5.088A pdb=" N CYSSI 216 " --> pdb=" O SERSI 212 " (cutoff:3.500A) Processing helix chain 'SI' and resid 225 through 230 removed outlier: 4.078A pdb=" N ASNSI 229 " --> pdb=" O HISSI 225 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ARGSI 230 " --> pdb=" O ALASI 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'SI' and resid 225 through 230' Processing helix chain 'SI' and resid 231 through 238 Processing helix chain 'SI' and resid 245 through 255 removed outlier: 4.381A pdb=" N GLNSI 249 " --> pdb=" O GLUSI 245 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEUSI 250 " --> pdb=" O ARGSI 246 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 13 through 23 Processing helix chain 'SJ' and resid 26 through 40 removed outlier: 4.967A pdb=" N PHESJ 30 " --> pdb=" O SERSJ 26 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LYSSJ 31 " --> pdb=" O ARGSJ 27 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEUSJ 32 " --> pdb=" O SERSJ 28 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARGSJ 38 " --> pdb=" O GLNSJ 34 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 56 through 66 Processing helix chain 'SJ' and resid 95 through 107 removed outlier: 4.087A pdb=" N ARGSJ 99 " --> pdb=" O THRSJ 95 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 132 through 148 removed outlier: 3.546A pdb=" N ASPSJ 146 " --> pdb=" O ARGSJ 142 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHESJ 147 " --> pdb=" O LEUSJ 143 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 163 through 175 Processing helix chain 'SJ' and resid 183 through 188 removed outlier: 3.766A pdb=" N ARGSJ 187 " --> pdb=" O PROSJ 183 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N HISSJ 188 " --> pdb=" O GLNSJ 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'SJ' and resid 183 through 188' Processing helix chain 'SJ' and resid 207 through 213 removed outlier: 4.366A pdb=" N PHESJ 211 " --> pdb=" O ASPSJ 207 " (cutoff:3.500A) Proline residue: SJ 213 - end of helix Processing helix chain 'SJ' and resid 519 through 532 removed outlier: 4.350A pdb=" N LYSSJ 532 " --> pdb=" O LEUSJ 528 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 540 through 561 removed outlier: 3.638A pdb=" N GLUSJ 544 " --> pdb=" O ASPSJ 540 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SERSJ 549 " --> pdb=" O ALASJ 545 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 664 through 677 Processing helix chain 'SJ' and resid 678 through 690 removed outlier: 4.122A pdb=" N PHESJ 689 " --> pdb=" O ILESJ 685 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ASNSJ 690 " --> pdb=" O ASPSJ 686 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 702 through 713 removed outlier: 3.637A pdb=" N GLNSJ 711 " --> pdb=" O GLNSJ 707 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 720 through 731 removed outlier: 3.551A pdb=" N GLUSJ 725 " --> pdb=" O LYSSJ 721 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARGSJ 730 " --> pdb=" O HISSJ 726 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TRPSJ 731 " --> pdb=" O TYRSJ 727 " (cutoff:3.500A) Processing helix chain 'SK' and resid 12 through 17 removed outlier: 3.814A pdb=" N PHESK 16 " --> pdb=" O GLUSK 12 " (cutoff:3.500A) Processing helix chain 'SK' and resid 32 through 42 removed outlier: 3.612A pdb=" N PHESK 38 " --> pdb=" O PHESK 34 " (cutoff:3.500A) Processing helix chain 'SK' and resid 58 through 63 removed outlier: 4.000A pdb=" N METSK 62 " --> pdb=" O ILESK 58 " (cutoff:3.500A) Processing helix chain 'SK' and resid 77 through 89 Proline residue: SK 89 - end of helix Processing helix chain 'SK' and resid 103 through 108 Processing helix chain 'SK' and resid 122 through 133 Processing helix chain 'SK' and resid 147 through 152 Processing helix chain 'SK' and resid 166 through 178 Processing helix chain 'SK' and resid 192 through 197 Processing helix chain 'SK' and resid 211 through 223 removed outlier: 4.392A pdb=" N LYSSK 223 " --> pdb=" O GLUSK 219 " (cutoff:3.500A) Processing helix chain 'SK' and resid 231 through 237 removed outlier: 3.684A pdb=" N SERSK 235 " --> pdb=" O THRSK 231 " (cutoff:3.500A) Processing helix chain 'SK' and resid 238 through 244 Processing helix chain 'SL' and resid 32 through 50 Processing helix chain 'SL' and resid 106 through 122 Processing helix chain 'SL' and resid 131 through 138 Processing helix chain 'SL' and resid 141 through 153 removed outlier: 3.823A pdb=" N PHESL 152 " --> pdb=" O LEUSL 148 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ASPSL 153 " --> pdb=" O LEUSL 149 " (cutoff:3.500A) Processing helix chain 'SL' and resid 158 through 169 removed outlier: 5.060A pdb=" N ARGSL 163 " --> pdb=" O ALASL 159 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LEUSL 164 " --> pdb=" O ARGSL 160 " (cutoff:3.500A) Proline residue: SL 166 - end of helix Processing helix chain 'SL' and resid 170 through 177 removed outlier: 4.019A pdb=" N TYRSL 174 " --> pdb=" O GLYSL 170 " (cutoff:3.500A) Processing helix chain 'SL' and resid 189 through 200 Processing helix chain 'SL' and resid 222 through 240 Processing helix chain 'SL' and resid 244 through 249 removed outlier: 6.609A pdb=" N VALSL 248 " --> pdb=" O LYSSL 244 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LYSSL 249 " --> pdb=" O TRPSL 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'SL' and resid 244 through 249' Processing helix chain 'SM' and resid 13 through 18 removed outlier: 3.526A pdb=" N TYRSM 17 " --> pdb=" O SERSM 13 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ILESM 18 " --> pdb=" O ALASM 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'SM' and resid 13 through 18' Processing helix chain 'SM' and resid 19 through 28 Processing helix chain 'SM' and resid 30 through 42 Processing helix chain 'SM' and resid 50 through 56 Processing helix chain 'SM' and resid 66 through 77 removed outlier: 3.980A pdb=" N HISSM 75 " --> pdb=" O ARGSM 71 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLUSM 76 " --> pdb=" O PHESM 72 " (cutoff:3.500A) Proline residue: SM 77 - end of helix Processing helix chain 'SM' and resid 78 through 99 removed outlier: 3.575A pdb=" N LYSSM 86 " --> pdb=" O PHESM 82 " (cutoff:3.500A) Processing helix chain 'SM' and resid 100 through 111 Processing helix chain 'SM' and resid 116 through 125 Proline residue: SM 125 - end of helix Processing helix chain 'SM' and resid 126 through 135 removed outlier: 4.694A pdb=" N ASPSM 135 " --> pdb=" O LEUSM 131 " (cutoff:3.500A) Processing helix chain 'SM' and resid 136 through 148 removed outlier: 3.898A pdb=" N THRSM 146 " --> pdb=" O PHESM 142 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHESM 147 " --> pdb=" O LEUSM 143 " (cutoff:3.500A) Proline residue: SM 148 - end of helix Processing helix chain 'SM' and resid 154 through 176 Processing helix chain 'SM' and resid 216 through 243 removed outlier: 3.528A pdb=" N THRSM 229 " --> pdb=" O GLUSM 225 " (cutoff:3.500A) Processing helix chain 'SM' and resid 270 through 279 removed outlier: 3.822A pdb=" N LEUSM 279 " --> pdb=" O LYSSM 275 " (cutoff:3.500A) Processing helix chain 'SM' and resid 307 through 326 removed outlier: 3.706A pdb=" N LYSSM 322 " --> pdb=" O GLUSM 318 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYSSM 325 " --> pdb=" O GLUSM 321 " (cutoff:3.500A) Processing helix chain 'SM' and resid 339 through 351 removed outlier: 3.640A pdb=" N GLYSM 351 " --> pdb=" O ILESM 347 " (cutoff:3.500A) Processing helix chain 'SM' and resid 394 through 405 removed outlier: 4.418A pdb=" N VALSM 398 " --> pdb=" O GLNSM 394 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHESM 399 " --> pdb=" O PROSM 395 " (cutoff:3.500A) Processing helix chain 'SM' and resid 409 through 414 removed outlier: 4.422A pdb=" N TYRSM 413 " --> pdb=" O PROSM 409 " (cutoff:3.500A) Processing helix chain 'SM' and resid 436 through 448 Processing helix chain 'SM' and resid 543 through 586 Processing helix chain 'SN' and resid 19 through 30 Processing helix chain 'SN' and resid 49 through 61 Processing helix chain 'SN' and resid 65 through 70 removed outlier: 3.509A pdb=" N ARGSN 69 " --> pdb=" O GLUSN 65 " (cutoff:3.500A) Processing helix chain 'SN' and resid 100 through 127 Proline residue: SN 121 - end of helix removed outlier: 3.510A pdb=" N LEUSN 126 " --> pdb=" O ARGSN 122 " (cutoff:3.500A) Processing helix chain 'SN' and resid 143 through 177 Processing helix chain 'SN' and resid 178 through 205 Processing helix chain 'SO' and resid 71 through 86 Proline residue: SO 86 - end of helix Processing helix chain 'SO' and resid 99 through 111 removed outlier: 4.285A pdb=" N ILESO 103 " --> pdb=" O LYSSO 99 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASNSO 104 " --> pdb=" O LEUSO 100 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLUSO 105 " --> pdb=" O PHESO 101 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N METSO 109 " --> pdb=" O GLUSO 105 " (cutoff:3.500A) Processing helix chain 'SO' and resid 169 through 176 removed outlier: 4.645A pdb=" N ASPSO 173 " --> pdb=" O ASPSO 169 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLUSO 174 " --> pdb=" O PROSO 170 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEUSO 175 " --> pdb=" O ALASO 171 " (cutoff:3.500A) Proline residue: SO 176 - end of helix No H-bonds generated for 'chain 'SO' and resid 169 through 176' Processing helix chain 'SO' and resid 177 through 190 Processing helix chain 'SO' and resid 261 through 293 removed outlier: 3.938A pdb=" N HISSO 265 " --> pdb=" O SERSO 261 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYRSO 277 " --> pdb=" O THRSO 273 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLUSO 293 " --> pdb=" O LEUSO 289 " (cutoff:3.500A) Processing helix chain 'SO' and resid 337 through 353 removed outlier: 3.515A pdb=" N LYSSO 344 " --> pdb=" O GLNSO 340 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 19 through 37 removed outlier: 6.242A pdb=" N LYSSQ 23 " --> pdb=" O GLYSQ 19 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLNSQ 24 " --> pdb=" O LEUSQ 20 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASPSQ 35 " --> pdb=" O ARGSQ 31 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 50 through 61 removed outlier: 4.787A pdb=" N LYSSQ 54 " --> pdb=" O ASNSQ 50 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASPSQ 55 " --> pdb=" O SERSQ 51 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYSSQ 61 " --> pdb=" O ARGSQ 57 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 69 through 78 Processing helix chain 'SQ' and resid 88 through 97 removed outlier: 3.692A pdb=" N ARGSQ 95 " --> pdb=" O GLNSQ 91 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEUSQ 96 " --> pdb=" O VALSQ 92 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ARGSQ 97 " --> pdb=" O SERSQ 93 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 108 through 120 removed outlier: 5.242A pdb=" N THRSQ 120 " --> pdb=" O PHESQ 116 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 146 through 157 removed outlier: 4.156A pdb=" N GLUSQ 150 " --> pdb=" O PROSQ 146 " (cutoff:3.500A) Proline residue: SQ 151 - end of helix Processing helix chain 'SQ' and resid 183 through 194 Processing helix chain 'SR' and resid 14 through 29 Processing helix chain 'SR' and resid 39 through 68 removed outlier: 3.617A pdb=" N LYSSR 50 " --> pdb=" O PHESR 46 " (cutoff:3.500A) Processing helix chain 'SR' and resid 76 through 87 Processing helix chain 'SR' and resid 88 through 120 removed outlier: 3.654A pdb=" N LYSSR 118 " --> pdb=" O VALSR 114 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N TYRSR 119 " --> pdb=" O ARGSR 115 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLYSR 120 " --> pdb=" O LEUSR 116 " (cutoff:3.500A) Processing helix chain 'SR' and resid 122 through 145 removed outlier: 3.690A pdb=" N GLNSR 144 " --> pdb=" O VALSR 140 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYSSR 145 " --> pdb=" O ILESR 141 " (cutoff:3.500A) Processing helix chain 'SR' and resid 146 through 161 Processing helix chain 'SR' and resid 180 through 189 removed outlier: 3.656A pdb=" N LYSSR 187 " --> pdb=" O SERSR 183 " (cutoff:3.500A) Processing helix chain 'SR' and resid 229 through 234 removed outlier: 3.525A pdb=" N ARGSR 233 " --> pdb=" O PROSR 229 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ASNSR 234 " --> pdb=" O LEUSR 230 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 229 through 234' Processing helix chain 'SR' and resid 235 through 247 removed outlier: 4.062A pdb=" N ALASR 240 " --> pdb=" O ILESR 236 " (cutoff:3.500A) Processing helix chain 'SR' and resid 264 through 280 Proline residue: SR 277 - end of helix removed outlier: 4.491A pdb=" N ILESR 280 " --> pdb=" O ARGSR 276 " (cutoff:3.500A) Processing helix chain 'SR' and resid 295 through 300 removed outlier: 5.250A pdb=" N SERSR 300 " --> pdb=" O ILESR 296 " (cutoff:3.500A) Processing helix chain 'SR' and resid 301 through 314 removed outlier: 3.666A pdb=" N PHESR 307 " --> pdb=" O ASPSR 303 " (cutoff:3.500A) Processing helix chain 'SR' and resid 327 through 351 removed outlier: 3.585A pdb=" N GLYSR 350 " --> pdb=" O THRSR 346 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASNSR 351 " --> pdb=" O LYSSR 347 " (cutoff:3.500A) Processing helix chain 'SR' and resid 352 through 362 removed outlier: 3.977A pdb=" N VALSR 356 " --> pdb=" O LYSSR 352 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ASNSR 358 " --> pdb=" O ASNSR 354 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ARGSR 359 " --> pdb=" O GLUSR 355 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEUSR 360 " --> pdb=" O VALSR 356 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N LEUSR 362 " --> pdb=" O ASNSR 358 " (cutoff:3.500A) Processing helix chain 'SR' and resid 380 through 391 removed outlier: 3.965A pdb=" N GLUSR 389 " --> pdb=" O ARGSR 385 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THRSR 390 " --> pdb=" O LYSSR 386 " (cutoff:3.500A) Processing helix chain 'SR' and resid 397 through 406 removed outlier: 4.134A pdb=" N GLYSR 406 " --> pdb=" O GLUSR 402 " (cutoff:3.500A) Processing helix chain 'SR' and resid 412 through 418 removed outlier: 4.700A pdb=" N TYRSR 416 " --> pdb=" O ASPSR 412 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TRPSR 417 " --> pdb=" O LEUSR 413 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ASPSR 418 " --> pdb=" O GLNSR 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 412 through 418' Processing helix chain 'SR' and resid 421 through 426 removed outlier: 4.150A pdb=" N LYSSR 425 " --> pdb=" O ASNSR 421 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N HISSR 426 " --> pdb=" O LEUSR 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 421 through 426' Processing helix chain 'SR' and resid 437 through 442 removed outlier: 4.054A pdb=" N TYRSR 441 " --> pdb=" O ASNSR 437 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILESR 442 " --> pdb=" O ILESR 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 437 through 442' Processing helix chain 'SR' and resid 445 through 463 removed outlier: 3.550A pdb=" N LYSSR 449 " --> pdb=" O ALASR 445 " (cutoff:3.500A) Processing helix chain 'SS' and resid 140 through 146 removed outlier: 4.695A pdb=" N TYRSS 144 " --> pdb=" O PROSS 140 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASPSS 145 " --> pdb=" O LEUSS 141 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ASPSS 146 " --> pdb=" O GLUSS 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'SS' and resid 140 through 146' Processing helix chain 'SS' and resid 180 through 185 removed outlier: 5.589A pdb=" N VALSS 185 " --> pdb=" O TYRSS 181 " (cutoff:3.500A) Processing helix chain 'SS' and resid 197 through 210 Processing helix chain 'SS' and resid 242 through 248 removed outlier: 3.973A pdb=" N PHESS 246 " --> pdb=" O ASPSS 242 " (cutoff:3.500A) Proline residue: SS 248 - end of helix Processing helix chain 'SS' and resid 249 through 266 removed outlier: 3.583A pdb=" N LYSSS 253 " --> pdb=" O SERSS 249 " (cutoff:3.500A) Processing helix chain 'SS' and resid 323 through 334 removed outlier: 3.512A pdb=" N GLUSS 331 " --> pdb=" O ARGSS 327 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N GLUSS 334 " --> pdb=" O TRPSS 330 " (cutoff:3.500A) Processing helix chain 'SS' and resid 349 through 354 removed outlier: 3.662A pdb=" N VALSS 353 " --> pdb=" O SERSS 349 " (cutoff:3.500A) Proline residue: SS 354 - end of helix No H-bonds generated for 'chain 'SS' and resid 349 through 354' Processing helix chain 'SS' and resid 358 through 372 removed outlier: 3.752A pdb=" N TYRSS 371 " --> pdb=" O CYSSS 367 " (cutoff:3.500A) Processing helix chain 'ST' and resid 169 through 197 removed outlier: 3.548A pdb=" N LYSST 173 " --> pdb=" O ASPST 169 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ALAST 196 " --> pdb=" O ASNST 192 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N HISST 197 " --> pdb=" O LEUST 193 " (cutoff:3.500A) Processing helix chain 'ST' and resid 214 through 229 removed outlier: 4.201A pdb=" N THRST 229 " --> pdb=" O ALAST 225 " (cutoff:3.500A) Processing helix chain 'ST' and resid 260 through 277 removed outlier: 3.533A pdb=" N GLUST 264 " --> pdb=" O ASPST 260 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYSST 265 " --> pdb=" O PHEST 261 " (cutoff:3.500A) Processing helix chain 'SU' and resid 199 through 229 Proline residue: SU 229 - end of helix Processing helix chain 'SU' and resid 232 through 245 removed outlier: 4.081A pdb=" N LEUSU 243 " --> pdb=" O LEUSU 239 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N METSU 244 " --> pdb=" O ARGSU 240 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLUSU 245 " --> pdb=" O SERSU 241 " (cutoff:3.500A) Processing helix chain 'SU' and resid 251 through 270 Processing helix chain 'SU' and resid 279 through 286 removed outlier: 5.604A pdb=" N LYSSU 286 " --> pdb=" O GLUSU 282 " (cutoff:3.500A) Processing helix chain 'SU' and resid 288 through 322 Processing helix chain 'SU' and resid 333 through 353 removed outlier: 4.618A pdb=" N GLYSU 337 " --> pdb=" O LYSSU 333 " (cutoff:3.500A) Processing helix chain 'SU' and resid 358 through 372 removed outlier: 3.590A pdb=" N ILESU 362 " --> pdb=" O PHESU 358 " (cutoff:3.500A) Proline residue: SU 368 - end of helix removed outlier: 4.065A pdb=" N ASNSU 371 " --> pdb=" O VALSU 367 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASPSU 372 " --> pdb=" O PROSU 368 " (cutoff:3.500A) Processing helix chain 'SU' and resid 374 through 392 Processing helix chain 'SU' and resid 395 through 413 Processing helix chain 'SU' and resid 417 through 427 removed outlier: 4.333A pdb=" N LEUSU 421 " --> pdb=" O ARGSU 417 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THRSU 423 " --> pdb=" O GLUSU 419 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHESU 424 " --> pdb=" O METSU 420 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEUSU 425 " --> pdb=" O LEUSU 421 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N CYSSU 426 " --> pdb=" O LYSSU 422 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEUSU 427 " --> pdb=" O THRSU 423 " (cutoff:3.500A) Processing helix chain 'SU' and resid 464 through 480 removed outlier: 4.617A pdb=" N GLUSU 477 " --> pdb=" O ARGSU 473 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ALASU 478 " --> pdb=" O GLUSU 474 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLUSU 479 " --> pdb=" O LEUSU 475 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ALASU 480 " --> pdb=" O ARGSU 476 " (cutoff:3.500A) Processing helix chain 'SU' and resid 483 through 509 Processing helix chain 'SU' and resid 514 through 526 Processing helix chain 'SU' and resid 530 through 548 removed outlier: 3.682A pdb=" N GLYSU 548 " --> pdb=" O LEUSU 544 " (cutoff:3.500A) Processing helix chain 'SU' and resid 551 through 570 removed outlier: 4.202A pdb=" N GLYSU 570 " --> pdb=" O LEUSU 566 " (cutoff:3.500A) Processing helix chain 'SU' and resid 577 through 589 removed outlier: 4.959A pdb=" N PHESU 589 " --> pdb=" O TYRSU 585 " (cutoff:3.500A) Processing helix chain 'SU' and resid 596 through 611 removed outlier: 4.221A pdb=" N VALSU 600 " --> pdb=" O THRSU 596 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLUSU 601 " --> pdb=" O ASNSU 597 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILESU 602 " --> pdb=" O GLUSU 598 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLNSU 605 " --> pdb=" O GLUSU 601 " (cutoff:3.500A) Processing helix chain 'SU' and resid 614 through 619 removed outlier: 5.522A pdb=" N SERSU 619 " --> pdb=" O ARGSU 615 " (cutoff:3.500A) Processing helix chain 'SU' and resid 620 through 637 removed outlier: 3.632A pdb=" N HISSU 636 " --> pdb=" O THRSU 632 " (cutoff:3.500A) Processing helix chain 'SU' and resid 638 through 656 removed outlier: 3.532A pdb=" N HISSU 654 " --> pdb=" O ARGSU 650 " (cutoff:3.500A) Processing helix chain 'SU' and resid 659 through 665 removed outlier: 4.067A pdb=" N LEUSU 663 " --> pdb=" O THRSU 659 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N SERSU 665 " --> pdb=" O LEUSU 661 " (cutoff:3.500A) Processing helix chain 'SU' and resid 679 through 684 removed outlier: 3.903A pdb=" N CYSSU 683 " --> pdb=" O GLUSU 679 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ASNSU 684 " --> pdb=" O PROSU 680 " (cutoff:3.500A) No H-bonds generated for 'chain 'SU' and resid 679 through 684' Processing helix chain 'SU' and resid 690 through 699 removed outlier: 4.791A pdb=" N HISSU 694 " --> pdb=" O LEUSU 690 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALASU 695 " --> pdb=" O TRPSU 691 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HISSU 699 " --> pdb=" O ALASU 695 " (cutoff:3.500A) Processing helix chain 'SU' and resid 701 through 714 removed outlier: 3.566A pdb=" N GLNSU 705 " --> pdb=" O HISSU 701 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALASU 713 " --> pdb=" O ALASU 709 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLYSU 714 " --> pdb=" O HISSU 710 " (cutoff:3.500A) Processing helix chain 'SU' and resid 724 through 731 removed outlier: 5.466A pdb=" N SERSU 731 " --> pdb=" O LEUSU 727 " (cutoff:3.500A) Processing helix chain 'SU' and resid 732 through 740 removed outlier: 4.474A pdb=" N SERSU 740 " --> pdb=" O PHESU 736 " (cutoff:3.500A) Processing helix chain 'SU' and resid 769 through 786 removed outlier: 3.550A pdb=" N ALASU 784 " --> pdb=" O SERSU 780 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N GLUSU 786 " --> pdb=" O GLUSU 782 " (cutoff:3.500A) Processing helix chain 'SV' and resid 33 through 43 Processing helix chain 'SV' and resid 45 through 50 removed outlier: 3.559A pdb=" N VALSV 49 " --> pdb=" O ASNSV 45 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ARGSV 50 " --> pdb=" O PROSV 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'SV' and resid 45 through 50' Processing helix chain 'SV' and resid 52 through 60 removed outlier: 3.501A pdb=" N ARGSV 56 " --> pdb=" O THRSV 52 " (cutoff:3.500A) Processing helix chain 'SV' and resid 66 through 72 removed outlier: 4.162A pdb=" N GLUSV 70 " --> pdb=" O ASPSV 66 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N PHESV 71 " --> pdb=" O ASNSV 67 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N GLUSV 72 " --> pdb=" O SERSV 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'SV' and resid 66 through 72' Processing helix chain 'SV' and resid 82 through 135 removed outlier: 4.005A pdb=" N ASNSV 115 " --> pdb=" O ARGSV 111 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYSSV 116 " --> pdb=" O LEUSV 112 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLUSV 117 " --> pdb=" O LYSSV 113 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEUSV 118 " --> pdb=" O LYSSV 114 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYSSV 120 " --> pdb=" O LYSSV 116 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYSSV 128 " --> pdb=" O ILESV 124 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N HISSV 132 " --> pdb=" O LYSSV 128 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEUSV 133 " --> pdb=" O GLNSV 129 " (cutoff:3.500A) Processing helix chain 'SW' and resid 178 through 184 removed outlier: 3.899A pdb=" N LEUSW 182 " --> pdb=" O SERSW 178 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N CYSSW 183 " --> pdb=" O PHESW 179 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ASNSW 184 " --> pdb=" O ALASW 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'SW' and resid 178 through 184' Processing helix chain 'SW' and resid 187 through 198 Processing helix chain 'SW' and resid 203 through 216 removed outlier: 4.489A pdb=" N ARGSW 211 " --> pdb=" O HISSW 207 " (cutoff:3.500A) Proline residue: SW 212 - end of helix Processing helix chain 'SW' and resid 228 through 245 Proline residue: SW 236 - end of helix Processing helix chain 'SW' and resid 260 through 276 removed outlier: 3.585A pdb=" N GLUSW 273 " --> pdb=" O GLYSW 269 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THRSW 276 " --> pdb=" O LYSSW 272 " (cutoff:3.500A) Processing helix chain 'SW' and resid 290 through 301 Processing helix chain 'SW' and resid 308 through 318 removed outlier: 3.504A pdb=" N ASPSW 314 " --> pdb=" O GLYSW 310 " (cutoff:3.500A) Processing helix chain 'SW' and resid 334 through 342 removed outlier: 3.586A pdb=" N GLYSW 342 " --> pdb=" O ILESW 338 " (cutoff:3.500A) Processing helix chain 'SW' and resid 343 through 355 removed outlier: 3.542A pdb=" N LEUSW 353 " --> pdb=" O GLNSW 349 " (cutoff:3.500A) Proline residue: SW 355 - end of helix Processing helix chain 'SW' and resid 368 through 379 removed outlier: 3.538A pdb=" N ILESW 377 " --> pdb=" O ASPSW 373 " (cutoff:3.500A) Processing helix chain 'SW' and resid 408 through 424 removed outlier: 4.990A pdb=" N PHESW 413 " --> pdb=" O SERSW 409 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N LEUSW 414 " --> pdb=" O GLUSW 410 " (cutoff:3.500A) Processing helix chain 'SW' and resid 434 through 449 Processing helix chain 'SW' and resid 460 through 474 Processing helix chain 'SW' and resid 482 through 487 removed outlier: 3.506A pdb=" N ARGSW 487 " --> pdb=" O ASPSW 483 " (cutoff:3.500A) Processing helix chain 'SW' and resid 505 through 516 Processing helix chain 'SW' and resid 534 through 545 removed outlier: 4.601A pdb=" N LEUSW 538 " --> pdb=" O GLUSW 534 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARGSW 539 " --> pdb=" O LEUSW 535 " (cutoff:3.500A) Processing helix chain 'SW' and resid 561 through 572 Processing helix chain 'SW' and resid 573 through 593 Processing helix chain 'SW' and resid 595 through 600 Processing helix chain 'SW' and resid 605 through 614 removed outlier: 3.626A pdb=" N PHESW 613 " --> pdb=" O VALSW 609 " (cutoff:3.500A) Processing helix chain 'SY' and resid 223 through 234 removed outlier: 3.603A pdb=" N GLNSY 229 " --> pdb=" O GLYSY 225 " (cutoff:3.500A) Proline residue: SY 234 - end of helix Processing helix chain 'SY' and resid 235 through 253 removed outlier: 3.556A pdb=" N ASPSY 252 " --> pdb=" O GLYSY 248 " (cutoff:3.500A) Processing helix chain 'SY' and resid 262 through 279 removed outlier: 3.548A pdb=" N TYRSY 266 " --> pdb=" O SERSY 262 " (cutoff:3.500A) Processing helix chain 'SY' and resid 281 through 293 Proline residue: SY 293 - end of helix Processing helix chain 'SY' and resid 294 through 307 removed outlier: 4.011A pdb=" N VALSY 298 " --> pdb=" O LEUSY 294 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLUSY 299 " --> pdb=" O SERSY 295 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLUSY 305 " --> pdb=" O LEUSY 301 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VALSY 306 " --> pdb=" O GLUSY 302 " (cutoff:3.500A) Proline residue: SY 307 - end of helix Processing helix chain 'SY' and resid 320 through 332 removed outlier: 3.534A pdb=" N ASNSY 330 " --> pdb=" O GLNSY 326 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARGSY 331 " --> pdb=" O ALASY 327 " (cutoff:3.500A) Processing helix chain 'SY' and resid 358 through 364 Processing helix chain 'SY' and resid 370 through 381 Proline residue: SY 376 - end of helix Processing helix chain 'SY' and resid 396 through 407 Processing helix chain 'SY' and resid 419 through 433 removed outlier: 4.089A pdb=" N LYSSY 423 " --> pdb=" O ALASY 419 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SERSY 424 " --> pdb=" O GLUSY 420 " (cutoff:3.500A) Processing helix chain 'SY' and resid 468 through 473 Proline residue: SY 473 - end of helix Processing helix chain 'SY' and resid 480 through 503 removed outlier: 5.509A pdb=" N ASNSY 503 " --> pdb=" O ILESY 499 " (cutoff:3.500A) Processing helix chain 'SY' and resid 520 through 535 removed outlier: 4.504A pdb=" N TRPSY 526 " --> pdb=" O GLUSY 522 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N VALSY 527 " --> pdb=" O GLUSY 523 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VALSY 528 " --> pdb=" O ASNSY 524 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYSSY 534 " --> pdb=" O TYRSY 530 " (cutoff:3.500A) Processing helix chain 'SY' and resid 562 through 567 removed outlier: 4.636A pdb=" N THRSY 566 " --> pdb=" O SERSY 562 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ARGSY 567 " --> pdb=" O LEUSY 563 " (cutoff:3.500A) No H-bonds generated for 'chain 'SY' and resid 562 through 567' Processing helix chain 'SY' and resid 570 through 575 removed outlier: 3.509A pdb=" N ASNSY 575 " --> pdb=" O TYRSY 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'SY' and resid 570 through 575' Processing helix chain 'SZ' and resid 6 through 12 removed outlier: 3.791A pdb=" N ARGSZ 10 " --> pdb=" O GLYSZ 6 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N LYSSZ 12 " --> pdb=" O THRSZ 8 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 18 through 32 Proline residue: SZ 32 - end of helix Processing helix chain 'SZ' and resid 36 through 43 Processing helix chain 'SZ' and resid 48 through 57 Processing helix chain 'SZ' and resid 61 through 67 Proline residue: SZ 67 - end of helix Processing helix chain 'SZ' and resid 90 through 103 removed outlier: 4.486A pdb=" N LEUSZ 94 " --> pdb=" O LYSSZ 90 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 112 through 126 Processing helix chain 'SZ' and resid 129 through 136 Processing helix chain 'SZ' and resid 144 through 159 Processing helix chain 'SZ' and resid 160 through 178 Processing sheet with id= 1, first strand: chain 'BA' and resid 11 through 17 removed outlier: 4.118A pdb=" N THRBA 59 " --> pdb=" O VALBA 74 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'BB' and resid 50 through 53 Processing sheet with id= 3, first strand: chain 'BB' and resid 65 through 68 Processing sheet with id= 4, first strand: chain 'BB' and resid 163 through 169 removed outlier: 6.872A pdb=" N LEUBB 163 " --> pdb=" O LEUBB 38 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VALBB 32 " --> pdb=" O VALBB 169 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'L6' and resid 57 through 60 Processing sheet with id= 6, first strand: chain 'L7' and resid 6 through 10 Processing sheet with id= 7, first strand: chain 'L8' and resid 11 through 15 removed outlier: 4.484A pdb=" N ARGL8 11 " --> pdb=" O ILEL8 27 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LYSL8 23 " --> pdb=" O VALL8 15 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEUL8 37 " --> pdb=" O VALL8 28 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'L9' and resid 35 through 39 removed outlier: 6.105A pdb=" N ALAL9 35 " --> pdb=" O ARGL9 65 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILEL9 61 " --> pdb=" O ALAL9 39 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLYL9 58 " --> pdb=" O ASPL9 136 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILEL9 133 " --> pdb=" O LEUL9 116 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'L9' and resid 117 through 121 removed outlier: 3.900A pdb=" N ASNL9 117 " --> pdb=" O ILEL9 133 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N PHEL9 129 " --> pdb=" O VALL9 121 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'LA' and resid 16 through 20 removed outlier: 5.759A pdb=" N SERLA 111 " --> pdb=" O LYSLA 153 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'LA' and resid 116 through 122 Processing sheet with id= 12, first strand: chain 'LB' and resid 78 through 82 Processing sheet with id= 13, first strand: chain 'LC' and resid 27 through 33 removed outlier: 6.680A pdb=" N VALLC 13 " --> pdb=" O VALLC 62 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'LC' and resid 91 through 99 removed outlier: 4.140A pdb=" N ASNLC 77 " --> pdb=" O ILELC 132 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'LC' and resid 9 through 13 removed outlier: 4.793A pdb=" N GLULC 9 " --> pdb=" O VALLC 67 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'LE' and resid 38 through 43 removed outlier: 4.210A pdb=" N ASPLE 38 " --> pdb=" O VALLE 64 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYSLE 60 " --> pdb=" O ILELE 42 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'LG' and resid 24 through 27 removed outlier: 4.711A pdb=" N ALALG 24 " --> pdb=" O ILELG 39 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'LG' and resid 60 through 63 removed outlier: 6.833A pdb=" N ASPLG 100 " --> pdb=" O ARGLG 85 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARGLG 85 " --> pdb=" O ASPLG 100 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'LG' and resid 87 through 90 removed outlier: 4.273A pdb=" N VALLG 94 " --> pdb=" O ARGLG 90 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'LH' and resid 95 through 100 removed outlier: 3.778A pdb=" N LYSLH 134 " --> pdb=" O VALLH 100 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'LI' and resid 53 through 56 removed outlier: 4.819A pdb=" N ASPLI 53 " --> pdb=" O VALLI 70 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'LI' and resid 72 through 75 removed outlier: 3.532A pdb=" N GLNLI 72 " --> pdb=" O TYRLI 81 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'LI' and resid 86 through 89 removed outlier: 3.564A pdb=" N LYSLI 89 " --> pdb=" O THRLI 93 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THRLI 93 " --> pdb=" O LYSLI 89 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'LK' and resid 98 through 101 Processing sheet with id= 25, first strand: chain 'LL' and resid 48 through 53 removed outlier: 5.551A pdb=" N THRLL 48 " --> pdb=" O LYSLL 65 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'LN' and resid 53 through 59 removed outlier: 6.674A pdb=" N ILELN 78 " --> pdb=" O ALALN 51 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ARGLN 343 " --> pdb=" O LYSLN 50 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VALLN 344 " --> pdb=" O VALLN 222 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N VALLN 222 " --> pdb=" O VALLN 344 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N HISLN 275 " --> pdb=" O THRLN 223 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'LN' and resid 98 through 102 removed outlier: 6.803A pdb=" N GLYLN 91 " --> pdb=" O PHELN 102 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYSLN 103 " --> pdb=" O GLYLN 91 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'LN' and resid 179 through 184 removed outlier: 4.979A pdb=" N HISLN 179 " --> pdb=" O THRLN 166 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILELN 163 " --> pdb=" O VALLN 87 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLNLN 203 " --> pdb=" O VALLN 86 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'LN' and resid 286 through 289 removed outlier: 3.638A pdb=" N LYSLN 286 " --> pdb=" O METLN 332 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHELN 330 " --> pdb=" O GLYLN 288 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'LN' and resid 77 through 80 Processing sheet with id= 31, first strand: chain 'LN' and resid 88 through 93 removed outlier: 3.741A pdb=" N VALLN 159 " --> pdb=" O TYRLN 92 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'LP' and resid 61 through 64 removed outlier: 4.802A pdb=" N ASPLP 61 " --> pdb=" O LEULP 102 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VALLP 21 " --> pdb=" O ARGLP 90 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THRLP 22 " --> pdb=" O VALLP 122 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'LQ' and resid 74 through 80 No H-bonds generated for sheet with id= 33 Processing sheet with id= 34, first strand: chain 'LT' and resid 56 through 60 removed outlier: 5.807A pdb=" N THRLT 57 " --> pdb=" O PROLT 64 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THRLT 59 " --> pdb=" O GLYLT 62 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'LT' and resid 8 through 12 removed outlier: 6.030A pdb=" N LYSLT 8 " --> pdb=" O GLULT 31 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEULT 27 " --> pdb=" O ALALT 12 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ARGLT 85 " --> pdb=" O THRLT 75 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYSLT 45 " --> pdb=" O VALLT 74 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ARGLT 46 " --> pdb=" O METLT 104 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'LT' and resid 6 through 12 removed outlier: 4.658A pdb=" N HISLT 99 " --> pdb=" O PHELT 11 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'LW' and resid 15 through 18 removed outlier: 8.477A pdb=" N THRLW 15 " --> pdb=" O HISLW 28 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N HISLW 28 " --> pdb=" O THRLW 15 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N THRLW 17 " --> pdb=" O ALALW 26 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'NF' and resid 189 through 194 removed outlier: 3.785A pdb=" N ALANF 190 " --> pdb=" O HISNF 185 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASNNF 255 " --> pdb=" O THRNF 245 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N TYRNF 241 " --> pdb=" O LEUNF 259 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THRNF 218 " --> pdb=" O VALNF 244 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'NH' and resid 36 through 39 Processing sheet with id= 40, first strand: chain 'NH' and resid 95 through 99 removed outlier: 4.975A pdb=" N TYRNH 95 " --> pdb=" O GLYNH 130 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLYNH 142 " --> pdb=" O VALNH 133 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'NI' and resid 196 through 200 removed outlier: 3.835A pdb=" N VALNI 136 " --> pdb=" O THRNI 274 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'NI' and resid 310 through 317 removed outlier: 4.414A pdb=" N GLYNI 436 " --> pdb=" O GLNNI 310 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'SA' and resid 7 through 10 removed outlier: 4.923A pdb=" N LYSSA 20 " --> pdb=" O VALSA 10 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'SA' and resid 226 through 232 removed outlier: 5.358A pdb=" N PHESA 249 " --> pdb=" O GLYSA 206 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'SC' and resid 90 through 95 removed outlier: 8.653A pdb=" N ALASC 90 " --> pdb=" O LEUSC 109 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'SC' and resid 147 through 153 removed outlier: 4.382A pdb=" N THRSC 148 " --> pdb=" O PHESC 164 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYSSC 160 " --> pdb=" O ILESC 152 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'SC' and resid 173 through 176 Processing sheet with id= 48, first strand: chain 'SD' and resid 139 through 144 removed outlier: 7.390A pdb=" N TYRSD 139 " --> pdb=" O ILESD 95 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LYSSD 88 " --> pdb=" O LEUSD 125 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASNSD 119 " --> pdb=" O ARGSD 94 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N PHESD 118 " --> pdb=" O LEUSD 213 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'SE' and resid 180 through 185 Processing sheet with id= 50, first strand: chain 'SG' and resid 5 through 12 removed outlier: 4.814A pdb=" N LYSSG 53 " --> pdb=" O ILESG 12 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'SG' and resid 16 through 20 removed outlier: 3.547A pdb=" N GLYSG 32 " --> pdb=" O GLYSG 29 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'SG' and resid 102 through 106 removed outlier: 6.510A pdb=" N SERSG 110 " --> pdb=" O METSG 128 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'SG' and resid 132 through 137 removed outlier: 5.507A pdb=" N GLUSG 143 " --> pdb=" O SERSG 137 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ASPSG 142 " --> pdb=" O SERSG 94 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'SH' and resid 72 through 76 removed outlier: 3.743A pdb=" N ARGSH 73 " --> pdb=" O GLUSH 92 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VALSH 46 " --> pdb=" O METSH 121 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'SI' and resid 147 through 151 removed outlier: 4.197A pdb=" N SERSI 126 " --> pdb=" O ARGSI 101 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N PHESI 125 " --> pdb=" O LEUSI 220 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'SJ' and resid 86 through 91 removed outlier: 3.563A pdb=" N GLNSJ 91 " --> pdb=" O ASPSJ 76 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASPSJ 117 " --> pdb=" O LEUSJ 51 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYSSJ 157 " --> pdb=" O ASNSJ 116 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'SK' and resid 1 through 5 removed outlier: 3.610A pdb=" N ALASK 204 " --> pdb=" O METSK 1 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'SK' and resid 23 through 27 Processing sheet with id= 59, first strand: chain 'SK' and resid 69 through 73 Processing sheet with id= 60, first strand: chain 'SK' and resid 114 through 117 Processing sheet with id= 61, first strand: chain 'SK' and resid 158 through 161 Processing sheet with id= 62, first strand: chain 'SL' and resid 76 through 82 removed outlier: 6.512A pdb=" N LYSSL 76 " --> pdb=" O LYSSL 207 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LYSSL 207 " --> pdb=" O LYSSL 76 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEUSL 78 " --> pdb=" O ILESL 205 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'SL' and resid 127 through 130 Processing sheet with id= 64, first strand: chain 'SL' and resid 210 through 217 removed outlier: 6.192A pdb=" N SERSL 210 " --> pdb=" O LEUSL 70 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEUSL 70 " --> pdb=" O SERSL 210 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEUSL 64 " --> pdb=" O ILESL 216 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEUSL 251 " --> pdb=" O ILESL 263 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'SM' and resid 179 through 184 Processing sheet with id= 66, first strand: chain 'SM' and resid 352 through 356 Processing sheet with id= 67, first strand: chain 'SO' and resid 87 through 91 removed outlier: 4.045A pdb=" N ASPSO 91 " --> pdb=" O ILESO 64 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N SERSO 66 " --> pdb=" O ASPSO 91 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ALASO 120 " --> pdb=" O SERSO 67 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LEUSO 126 " --> pdb=" O VALSO 143 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LYSSO 140 " --> pdb=" O ILESO 241 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ALASO 228 " --> pdb=" O ILESO 223 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ASNSO 219 " --> pdb=" O ILESO 232 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHESO 217 " --> pdb=" O PROSO 234 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N PHESO 236 " --> pdb=" O ILESO 215 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILESO 215 " --> pdb=" O PHESO 236 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASPSO 203 " --> pdb=" O ILESO 222 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'SO' and resid 137 through 140 removed outlier: 3.561A pdb=" N LYSSO 242 " --> pdb=" O LYSSO 140 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'SQ' and resid 63 through 67 removed outlier: 5.158A pdb=" N GLUSQ 99 " --> pdb=" O VALSQ 45 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILESQ 42 " --> pdb=" O LYSSQ 205 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THRSQ 203 " --> pdb=" O SERSQ 44 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'SQ' and resid 135 through 139 removed outlier: 6.832A pdb=" N VALSQ 135 " --> pdb=" O VALSQ 175 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N SERSQ 171 " --> pdb=" O PROSQ 139 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'SQ' and resid 159 through 163 Processing sheet with id= 72, first strand: chain 'SQ' and resid 213 through 217 removed outlier: 3.573A pdb=" N ARGSQ 214 " --> pdb=" O ASPSQ 209 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'SQ' and resid 38 through 42 removed outlier: 8.072A pdb=" N LYSSQ 38 " --> pdb=" O SERSQ 210 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYRSQ 206 " --> pdb=" O ILESQ 42 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'SR' and resid 205 through 211 removed outlier: 5.224A pdb=" N ARGSR 169 " --> pdb=" O ARGSR 216 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEUSR 173 " --> pdb=" O VALSR 220 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N THRSR 222 " --> pdb=" O LEUSR 173 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLYSR 175 " --> pdb=" O THRSR 222 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLYSR 224 " --> pdb=" O GLYSR 175 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N CYSSR 174 " --> pdb=" O LEUSR 252 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VALSR 254 " --> pdb=" O CYSSR 174 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TYRSR 176 " --> pdb=" O VALSR 254 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ASPSR 256 " --> pdb=" O TYRSR 176 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'SV' and resid 3 through 6 removed outlier: 6.493A pdb=" N GLUSV 4 " --> pdb=" O PROSV 12 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N CYSSV 6 " --> pdb=" O SERSV 10 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'SV' and resid 18 through 22 Processing sheet with id= 77, first strand: chain 'SW' and resid 281 through 285 Processing sheet with id= 78, first strand: chain 'SW' and resid 400 through 407 Processing sheet with id= 79, first strand: chain 'SW' and resid 452 through 455 Processing sheet with id= 80, first strand: chain 'SY' and resid 334 through 337 removed outlier: 6.899A pdb=" N ASNSY 334 " --> pdb=" O TYRSY 349 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N THRSY 344 " --> pdb=" O THRSY 314 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VALSY 310 " --> pdb=" O VALSY 348 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N HISSY 365 " --> pdb=" O ASNSY 315 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'SY' and resid 436 through 442 removed outlier: 5.643A pdb=" N ASNSY 436 " --> pdb=" O GLYSY 410 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYRSY 442 " --> pdb=" O ASPSY 416 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASPSY 460 " --> pdb=" O METSY 391 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLYSY 510 " --> pdb=" O LYSSY 586 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LYSSY 583 " --> pdb=" O VALSY 540 " (cutoff:3.500A) 4161 hydrogen bonds defined for protein. 12377 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2133 hydrogen bonds 3710 hydrogen bond angles 0 basepair planarities 812 basepair parallelities 1252 stacking parallelities Total time for adding SS restraints: 136.00 Time building geometry restraints manager: 55.65 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: 26115 1.33 - 1.45: 47006 1.45 - 1.57: 68962 1.57 - 1.69: 4963 1.69 - 1.81: 576 Bond restraints: 147622 Sorted by residual: 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 7.01e+01 bond pdb=" C6 GDPSR1001 " pdb=" O6 GDPSR1001 " ideal model delta sigma weight residual 1.250 1.397 -0.147 2.00e-02 2.50e+03 5.44e+01 bond pdb=" C2 GDPSR1001 " pdb=" N2 GDPSR1001 " ideal model delta sigma weight residual 1.355 1.449 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" N1 GDPSR1001 " pdb=" C2 GDPSR1001 " ideal model delta sigma weight residual 1.337 1.404 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" N9 GDPSR1001 " pdb=" C4 GDPSR1001 " ideal model delta sigma weight residual 1.337 1.277 0.060 2.00e-02 2.50e+03 8.95e+00 ... (remaining 147617 not shown) Histogram of bond angle deviations from ideal: 98.87 - 106.98: 17024 106.98 - 115.08: 93432 115.08 - 123.18: 84882 123.18 - 131.28: 15318 131.28 - 139.38: 640 Bond angle restraints: 211296 Sorted by residual: angle pdb=" CA PROSR 378 " pdb=" N PROSR 378 " pdb=" CD PROSR 378 " ideal model delta sigma weight residual 112.00 105.37 6.63 1.40e+00 5.10e-01 2.24e+01 angle pdb=" CA PROSR 444 " pdb=" N PROSR 444 " pdb=" CD PROSR 444 " ideal model delta sigma weight residual 112.00 105.79 6.21 1.40e+00 5.10e-01 1.97e+01 angle pdb=" C ASNBB 197 " pdb=" CA ASNBB 197 " pdb=" CB ASNBB 197 " ideal model delta sigma weight residual 116.63 111.58 5.05 1.16e+00 7.43e-01 1.90e+01 angle pdb=" C8 GDPSR1001 " pdb=" N9 GDPSR1001 " pdb=" C4 GDPSR1001 " ideal model delta sigma weight residual 108.00 120.73 -12.73 3.00e+00 1.11e-01 1.80e+01 angle pdb=" CB METSW 275 " pdb=" CG METSW 275 " pdb=" SD METSW 275 " ideal model delta sigma weight residual 112.70 122.30 -9.60 3.00e+00 1.11e-01 1.02e+01 ... (remaining 211291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 87028 36.00 - 71.99: 5961 71.99 - 107.99: 809 107.99 - 143.99: 6 143.99 - 179.98: 9 Dihedral angle restraints: 93813 sinusoidal: 62143 harmonic: 31670 Sorted by residual: dihedral pdb=" O4' UL31381 " pdb=" C1' UL31381 " pdb=" N1 UL31381 " pdb=" C2 UL31381 " ideal model delta sinusoidal sigma weight residual 200.00 34.93 165.07 1 1.50e+01 4.44e-03 8.39e+01 dihedral pdb=" O4' CL2 61 " pdb=" C1' CL2 61 " pdb=" N1 CL2 61 " pdb=" C2 CL2 61 " ideal model delta sinusoidal sigma weight residual 200.00 50.64 149.36 1 1.50e+01 4.44e-03 7.94e+01 dihedral pdb=" O4' CL32091 " pdb=" C1' CL32091 " pdb=" N1 CL32091 " pdb=" C2 CL32091 " ideal model delta sinusoidal sigma weight residual -128.00 51.98 -179.98 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 93810 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 21446 0.042 - 0.084: 3063 0.084 - 0.126: 878 0.126 - 0.167: 145 0.167 - 0.209: 8 Chirality restraints: 25540 Sorted by residual: chirality pdb=" C3' AL32798 " pdb=" C4' AL32798 " pdb=" O3' AL32798 " pdb=" C2' AL32798 " both_signs ideal model delta sigma weight residual False -2.74 -2.54 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C3' GL34520 " pdb=" C4' GL34520 " pdb=" O3' GL34520 " pdb=" C2' GL34520 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.20 2.00e-01 2.50e+01 9.78e-01 chirality pdb=" C1' AL32042 " pdb=" O4' AL32042 " pdb=" C2' AL32042 " pdb=" N9 AL32042 " both_signs ideal model delta sigma weight residual False 2.46 2.26 0.20 2.00e-01 2.50e+01 9.56e-01 ... (remaining 25537 not shown) Planarity restraints: 17587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYSSO 322 " -0.077 5.00e-02 4.00e+02 1.15e-01 2.13e+01 pdb=" N PROSO 323 " 0.200 5.00e-02 4.00e+02 pdb=" CA PROSO 323 " -0.061 5.00e-02 4.00e+02 pdb=" CD PROSO 323 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASPSR 443 " 0.074 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PROSR 444 " -0.187 5.00e-02 4.00e+02 pdb=" CA PROSR 444 " 0.054 5.00e-02 4.00e+02 pdb=" CD PROSR 444 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARGLQ 33 " 0.332 9.50e-02 1.11e+02 1.50e-01 1.60e+01 pdb=" NE ARGLQ 33 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARGLQ 33 " -0.031 2.00e-02 2.50e+03 pdb=" NH1 ARGLQ 33 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARGLQ 33 " 0.021 2.00e-02 2.50e+03 ... (remaining 17584 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.58: 807 2.58 - 3.22: 124618 3.22 - 3.86: 299175 3.86 - 4.50: 416600 4.50 - 5.14: 579606 Nonbonded interactions: 1420806 Sorted by model distance: nonbonded pdb=" OP2 GL3 356 " pdb="MG MGL36008 " model vdw 1.946 2.170 nonbonded pdb=" OG1 THRBA 105 " pdb=" OE1 GLUBA 108 " model vdw 1.957 2.440 nonbonded pdb=" OP2 AL31917 " pdb="MG MGL36026 " model vdw 1.965 2.170 nonbonded pdb=" O6 GL3 356 " pdb="MG MGL36010 " model vdw 1.976 2.170 nonbonded pdb=" OP1 CL3 112 " pdb="MG MGL36006 " model vdw 1.986 2.170 ... (remaining 1420801 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 26.290 Check model and map are aligned: 1.490 Set scattering table: 0.940 Process input model: 453.170 Find NCS groups from input model: 3.780 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:15.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 507.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 0.167 147622 Z= 0.187 Angle : 0.533 12.727 211296 Z= 0.279 Chirality : 0.035 0.209 25540 Planarity : 0.004 0.150 17587 Dihedral : 19.818 179.981 73253 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 0.01 % Allowed : 0.09 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 2.03 (0.08), residues: 10694 helix: 2.27 (0.07), residues: 4767 sheet: 1.01 (0.14), residues: 1314 loop : 0.57 (0.09), residues: 4613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPL6 18 HIS 0.011 0.001 HISL6 67 PHE 0.016 0.001 PHESU 673 TYR 0.019 0.001 TYRLI 74 ARG 0.027 0.001 ARGLQ 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21388 Ramachandran restraints generated. 10694 Oldfield, 0 Emsley, 10694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21388 Ramachandran restraints generated. 10694 Oldfield, 0 Emsley, 10694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1209 residues out of total 9533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1208 time to evaluate : 9.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: LA 4 TYR cc_start: 0.8383 (m-80) cc_final: 0.8162 (m-80) REVERT: LU 46 GLU cc_start: 0.7158 (tt0) cc_final: 0.6886 (tt0) REVERT: NK 99 GLN cc_start: 0.6836 (mt0) cc_final: 0.6374 (mt0) REVERT: SC 112 MET cc_start: 0.8128 (mmm) cc_final: 0.7609 (mmt) REVERT: SU 744 MET cc_start: 0.8109 (tpp) cc_final: 0.7809 (tpp) REVERT: SW 540 TYR cc_start: 0.7952 (t80) cc_final: 0.7715 (t80) REVERT: SY 367 MET cc_start: 0.7103 (ttt) cc_final: 0.6856 (ttt) outliers start: 1 outliers final: 4 residues processed: 1209 average time/residue: 2.3294 time to fit residues: 3896.6802 Evaluate side-chains 928 residues out of total 9533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 924 time to evaluate : 8.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LI residue 37 GLU Chi-restraints excluded: chain NK residue 98 ASN Chi-restraints excluded: chain SA residue 278 ASN Chi-restraints excluded: chain SK residue 128 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1313 random chunks: chunk 1108 optimal weight: 3.9990 chunk 995 optimal weight: 8.9990 chunk 552 optimal weight: 3.9990 chunk 339 optimal weight: 3.9990 chunk 671 optimal weight: 5.9990 chunk 531 optimal weight: 0.9980 chunk 1029 optimal weight: 6.9990 chunk 398 optimal weight: 10.0000 chunk 625 optimal weight: 0.9990 chunk 765 optimal weight: 10.0000 chunk 1192 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 118 HIS L7 5 GLN L7 65 ASN L7 167 HIS L7 180 GLN L8 69 HIS LA 28 ASN LA 72 GLN LA 80 GLN LC 125 GLN LE 90 ASN LE 95 HIS LG 135 ASN LH 57 GLN LI 14 ASN LI 86 GLN LK 62 HIS LL 6 GLN ** LL 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LN 42 HIS LQ 102 ASN LS 65 GLN LT 65 ASN LU 26 HIS LW 66 HIS ** NA 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NA 376 HIS NF 33 HIS NF 104 ASN NI 333 ASN NI 454 HIS NI 588 GLN SA 60 HIS SA 278 ASN SC 190 HIS SC 256 GLN SD 24 ASN SD 80 ASN SD 131 ASN SD 248 ASN SE 94 GLN SG 140 GLN SG 162 GLN SI 71 GLN SI 166 GLN SI 219 HIS SI 225 HIS SI 249 GLN ** SJ 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SK 83 HIS SK 178 GLN SL 112 GLN SL 218 HIS SM 154 HIS SN 125 GLN ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 24 GLN ** SQ 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 50 ASN SR 5 ASN SR 35 HIS SR 91 HIS SR 157 HIS SR 209 HIS SR 239 GLN SR 246 HIS SR 274 ASN SR 342 HIS SS 200 GLN SS 238 ASN ** SS 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SS 310 HIS SS 333 GLN SS 376 GLN ST 213 GLN SU 217 HIS SU 232 ASN SU 359 HIS SU 491 HIS SU 542 HIS SU 592 HIS SU 654 HIS SU 701 HIS SV 101 GLN ** SV 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 278 HIS SW 402 GLN SY 330 ASN SY 430 HIS Total number of N/Q/H flips: 82 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 147622 Z= 0.287 Angle : 0.558 16.311 211296 Z= 0.290 Chirality : 0.038 0.238 25540 Planarity : 0.005 0.070 17587 Dihedral : 21.556 178.671 51558 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.60 % Allowed : 6.69 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.98 (0.08), residues: 10694 helix: 2.34 (0.07), residues: 4864 sheet: 0.82 (0.14), residues: 1334 loop : 0.41 (0.09), residues: 4496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRPSJ 109 HIS 0.011 0.002 HISLA 116 PHE 0.027 0.002 PHESW 233 TYR 0.031 0.002 TYRLK 61 ARG 0.012 0.001 ARGSG 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21388 Ramachandran restraints generated. 10694 Oldfield, 0 Emsley, 10694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21388 Ramachandran restraints generated. 10694 Oldfield, 0 Emsley, 10694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1129 residues out of total 9533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 985 time to evaluate : 9.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L7 173 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7564 (tp-100) REVERT: LA 4 TYR cc_start: 0.8603 (m-80) cc_final: 0.8237 (m-80) REVERT: LC 52 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7587 (tptp) REVERT: LC 108 GLN cc_start: 0.8570 (mt0) cc_final: 0.8278 (mt0) REVERT: LG 60 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8452 (ttm) REVERT: LN 4 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.7072 (mtt180) REVERT: LS 20 GLN cc_start: 0.7636 (mm-40) cc_final: 0.7337 (tm-30) REVERT: NA 494 ARG cc_start: 0.6219 (OUTLIER) cc_final: 0.4554 (mmt180) REVERT: NF 204 SER cc_start: 0.8554 (t) cc_final: 0.8313 (m) REVERT: SC 112 MET cc_start: 0.8127 (mmm) cc_final: 0.7565 (mmt) REVERT: SC 207 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7619 (mtmp) REVERT: SD 137 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6512 (tp30) REVERT: SG 147 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7771 (mt-10) REVERT: SK 1 MET cc_start: 0.5953 (OUTLIER) cc_final: 0.5497 (mpp) REVERT: SK 18 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7245 (tppt) REVERT: SM 49 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.7095 (mtmm) REVERT: SM 557 ARG cc_start: 0.7989 (mmm-85) cc_final: 0.7772 (mtm-85) REVERT: ST 157 LEU cc_start: 0.7669 (pt) cc_final: 0.7222 (pt) REVERT: SW 540 TYR cc_start: 0.7943 (t80) cc_final: 0.7674 (t80) outliers start: 144 outliers final: 51 residues processed: 1036 average time/residue: 2.2177 time to fit residues: 3225.9796 Evaluate side-chains 969 residues out of total 9533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 908 time to evaluate : 8.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 107 ASP Chi-restraints excluded: chain L6 residue 13 HIS Chi-restraints excluded: chain L7 residue 173 GLN Chi-restraints excluded: chain L7 residue 174 LEU Chi-restraints excluded: chain L8 residue 125 ASN Chi-restraints excluded: chain L9 residue 17 ASP Chi-restraints excluded: chain L9 residue 125 SER Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 18 ARG Chi-restraints excluded: chain LA residue 111 SER Chi-restraints excluded: chain LB residue 14 ARG Chi-restraints excluded: chain LC residue 52 LYS Chi-restraints excluded: chain LE residue 39 ILE Chi-restraints excluded: chain LE residue 72 VAL Chi-restraints excluded: chain LG residue 60 MET Chi-restraints excluded: chain LI residue 9 SER Chi-restraints excluded: chain LI residue 91 ASN Chi-restraints excluded: chain LK residue 15 VAL Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LN residue 4 ARG Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LS residue 33 VAL Chi-restraints excluded: chain LW residue 83 THR Chi-restraints excluded: chain NA residue 494 ARG Chi-restraints excluded: chain NH residue 61 ASP Chi-restraints excluded: chain NH residue 168 ASP Chi-restraints excluded: chain NI residue 766 ASP Chi-restraints excluded: chain NK residue 98 ASN Chi-restraints excluded: chain SC residue 207 LYS Chi-restraints excluded: chain SD residue 137 GLU Chi-restraints excluded: chain SE residue 184 ILE Chi-restraints excluded: chain SG residue 17 ASP Chi-restraints excluded: chain SG residue 48 LEU Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SK residue 1 MET Chi-restraints excluded: chain SK residue 18 LYS Chi-restraints excluded: chain SK residue 110 CYS Chi-restraints excluded: chain SK residue 237 ARG Chi-restraints excluded: chain SL residue 109 LYS Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SM residue 49 LYS Chi-restraints excluded: chain SN residue 47 VAL Chi-restraints excluded: chain SN residue 145 LEU Chi-restraints excluded: chain SQ residue 28 GLU Chi-restraints excluded: chain SQ residue 48 MET Chi-restraints excluded: chain SR residue 12 VAL Chi-restraints excluded: chain SR residue 83 MET Chi-restraints excluded: chain SR residue 310 LEU Chi-restraints excluded: chain SR residue 459 LEU Chi-restraints excluded: chain SS residue 194 LEU Chi-restraints excluded: chain SS residue 237 THR Chi-restraints excluded: chain SS residue 298 MET Chi-restraints excluded: chain SS residue 304 LYS Chi-restraints excluded: chain SS residue 349 SER Chi-restraints excluded: chain ST residue 167 LEU Chi-restraints excluded: chain ST residue 210 THR Chi-restraints excluded: chain ST residue 227 VAL Chi-restraints excluded: chain ST residue 257 LEU Chi-restraints excluded: chain SV residue 1 MET Chi-restraints excluded: chain SV residue 93 MET Chi-restraints excluded: chain SY residue 391 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1313 random chunks: chunk 662 optimal weight: 6.9990 chunk 370 optimal weight: 5.9990 chunk 992 optimal weight: 9.9990 chunk 811 optimal weight: 0.7980 chunk 328 optimal weight: 5.9990 chunk 1194 optimal weight: 1.9990 chunk 1290 optimal weight: 0.8980 chunk 1063 optimal weight: 10.0000 chunk 1184 optimal weight: 7.9990 chunk 407 optimal weight: 9.9990 chunk 958 optimal weight: 10.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 115 GLN BA 118 HIS BA 137 GLN L7 90 HIS L7 180 GLN LA 25 HIS LC 50 GLN LE 95 HIS LI 14 ASN LL 83 ASN ** LL 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LN 322 HIS LQ 102 ASN LS 30 GLN ** NA 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NA 343 ASN NB 16 HIS NF 4 ASN SA 60 HIS SD 99 ASN SD 248 ASN SG 140 GLN SG 162 GLN SI 113 GLN SI 166 GLN SI 249 GLN ** SJ 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SL 46 HIS SL 112 GLN ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SQ 50 ASN SQ 152 GLN SR 37 HIS SR 342 HIS ** SS 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SS 238 ASN SS 296 HIS SS 376 GLN SV 101 GLN SV 110 ASN ** SV 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 278 HIS SW 402 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 147622 Z= 0.308 Angle : 0.550 16.607 211296 Z= 0.285 Chirality : 0.038 0.245 25540 Planarity : 0.005 0.081 17587 Dihedral : 21.520 178.702 51551 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.85 % Allowed : 8.63 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.83 (0.08), residues: 10694 helix: 2.28 (0.07), residues: 4875 sheet: 0.68 (0.14), residues: 1312 loop : 0.26 (0.09), residues: 4507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPST 156 HIS 0.013 0.002 HISLA 25 PHE 0.023 0.002 PHESO 65 TYR 0.024 0.002 TYRLK 61 ARG 0.010 0.001 ARGSJ 558 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21388 Ramachandran restraints generated. 10694 Oldfield, 0 Emsley, 10694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21388 Ramachandran restraints generated. 10694 Oldfield, 0 Emsley, 10694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1106 residues out of total 9533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 940 time to evaluate : 9.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: LC 93 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7801 (ptm) REVERT: LG 60 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8455 (ttm) REVERT: LL 28 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7749 (pt0) REVERT: NA 494 ARG cc_start: 0.6385 (OUTLIER) cc_final: 0.4409 (mmt180) REVERT: NF 204 SER cc_start: 0.8500 (t) cc_final: 0.8293 (m) REVERT: SA 276 ASN cc_start: 0.7621 (OUTLIER) cc_final: 0.7417 (m-40) REVERT: SC 112 MET cc_start: 0.8038 (mmm) cc_final: 0.7473 (mmt) REVERT: SC 207 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7670 (mtmp) REVERT: SD 137 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6610 (tp30) REVERT: SK 18 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7262 (tppt) REVERT: SM 49 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.7089 (mtmm) REVERT: SN 100 ASP cc_start: 0.6486 (t0) cc_final: 0.6199 (t0) REVERT: SO 332 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.5225 (mtm-85) REVERT: SW 323 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7169 (ttm) REVERT: SW 540 TYR cc_start: 0.7992 (t80) cc_final: 0.7681 (t80) outliers start: 166 outliers final: 67 residues processed: 1010 average time/residue: 2.2150 time to fit residues: 3147.1562 Evaluate side-chains 974 residues out of total 9533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 896 time to evaluate : 8.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L6 residue 13 HIS Chi-restraints excluded: chain L7 residue 59 ARG Chi-restraints excluded: chain L7 residue 174 LEU Chi-restraints excluded: chain L8 residue 125 ASN Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain L9 residue 125 SER Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 18 ARG Chi-restraints excluded: chain LC residue 51 LEU Chi-restraints excluded: chain LC residue 93 MET Chi-restraints excluded: chain LG residue 60 MET Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LI residue 9 SER Chi-restraints excluded: chain LI residue 91 ASN Chi-restraints excluded: chain LK residue 15 VAL Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LU residue 77 VAL Chi-restraints excluded: chain LW residue 15 THR Chi-restraints excluded: chain LW residue 83 THR Chi-restraints excluded: chain NA residue 362 LEU Chi-restraints excluded: chain NA residue 387 HIS Chi-restraints excluded: chain NA residue 494 ARG Chi-restraints excluded: chain NA residue 495 MET Chi-restraints excluded: chain NA residue 520 ASP Chi-restraints excluded: chain NA residue 591 VAL Chi-restraints excluded: chain NF residue 70 LYS Chi-restraints excluded: chain NF residue 98 ARG Chi-restraints excluded: chain NH residue 61 ASP Chi-restraints excluded: chain NH residue 152 ASP Chi-restraints excluded: chain NI residue 479 MET Chi-restraints excluded: chain NK residue 82 ASN Chi-restraints excluded: chain SA residue 276 ASN Chi-restraints excluded: chain SA residue 351 VAL Chi-restraints excluded: chain SC residue 207 LYS Chi-restraints excluded: chain SD residue 137 GLU Chi-restraints excluded: chain SE residue 184 ILE Chi-restraints excluded: chain SG residue 48 LEU Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SH residue 190 LEU Chi-restraints excluded: chain SI residue 147 VAL Chi-restraints excluded: chain SK residue 18 LYS Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 110 CYS Chi-restraints excluded: chain SL residue 109 LYS Chi-restraints excluded: chain SL residue 197 CYS Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SM residue 49 LYS Chi-restraints excluded: chain SM residue 133 ASP Chi-restraints excluded: chain SN residue 47 VAL Chi-restraints excluded: chain SN residue 145 LEU Chi-restraints excluded: chain SO residue 101 PHE Chi-restraints excluded: chain SO residue 332 ARG Chi-restraints excluded: chain SQ residue 192 LEU Chi-restraints excluded: chain SR residue 12 VAL Chi-restraints excluded: chain SR residue 83 MET Chi-restraints excluded: chain SR residue 310 LEU Chi-restraints excluded: chain SR residue 459 LEU Chi-restraints excluded: chain SS residue 132 ILE Chi-restraints excluded: chain SS residue 194 LEU Chi-restraints excluded: chain SS residue 228 SER Chi-restraints excluded: chain SS residue 237 THR Chi-restraints excluded: chain SS residue 298 MET Chi-restraints excluded: chain SS residue 304 LYS Chi-restraints excluded: chain SS residue 349 SER Chi-restraints excluded: chain ST residue 167 LEU Chi-restraints excluded: chain ST residue 210 THR Chi-restraints excluded: chain ST residue 227 VAL Chi-restraints excluded: chain ST residue 257 LEU Chi-restraints excluded: chain SU residue 317 LYS Chi-restraints excluded: chain SU residue 606 CYS Chi-restraints excluded: chain SV residue 1 MET Chi-restraints excluded: chain SV residue 65 VAL Chi-restraints excluded: chain SV residue 93 MET Chi-restraints excluded: chain SV residue 109 MET Chi-restraints excluded: chain SW residue 323 MET Chi-restraints excluded: chain SZ residue 37 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1313 random chunks: chunk 1180 optimal weight: 3.9990 chunk 898 optimal weight: 9.9990 chunk 619 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 570 optimal weight: 10.0000 chunk 802 optimal weight: 1.9990 chunk 1198 optimal weight: 1.9990 chunk 1269 optimal weight: 2.9990 chunk 626 optimal weight: 2.9990 chunk 1136 optimal weight: 6.9990 chunk 342 optimal weight: 8.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 115 GLN BA 118 HIS L7 180 GLN ** L9 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 75 GLN LC 50 GLN LE 95 HIS LH 57 GLN LI 14 ASN ** LK 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LL 83 ASN ** LL 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 102 ASN LS 30 GLN LS 65 GLN LU 36 HIS ** NA 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NA 589 GLN NH 124 ASN NK 21 ASN SD 248 ASN SG 140 GLN SG 162 GLN SG 189 GLN SI 71 GLN SI 113 GLN ** SJ 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SK 178 GLN SL 112 GLN SN 148 GLN SR 342 HIS SS 238 ASN SS 376 GLN SV 17 HIS SV 101 GLN SV 110 ASN ** SV 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SV 132 HIS SW 278 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 147622 Z= 0.278 Angle : 0.529 17.134 211296 Z= 0.274 Chirality : 0.037 0.245 25540 Planarity : 0.004 0.063 17587 Dihedral : 21.481 179.138 51549 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.96 % Allowed : 9.80 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.75 (0.08), residues: 10694 helix: 2.25 (0.07), residues: 4884 sheet: 0.58 (0.14), residues: 1291 loop : 0.19 (0.09), residues: 4519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRPLT 6 HIS 0.016 0.001 HISSR 342 PHE 0.023 0.002 PHESW 233 TYR 0.021 0.002 TYRSQ 206 ARG 0.011 0.001 ARGSG 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21388 Ramachandran restraints generated. 10694 Oldfield, 0 Emsley, 10694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21388 Ramachandran restraints generated. 10694 Oldfield, 0 Emsley, 10694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1114 residues out of total 9533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 938 time to evaluate : 9.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L7 173 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7560 (tp-100) REVERT: LC 93 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7780 (ptm) REVERT: LC 108 GLN cc_start: 0.8597 (mt0) cc_final: 0.8280 (mt0) REVERT: LG 60 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8500 (ttm) REVERT: LK 65 ARG cc_start: 0.7584 (mtt180) cc_final: 0.7001 (mmt180) REVERT: NF 204 SER cc_start: 0.8460 (t) cc_final: 0.8244 (m) REVERT: NH 154 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.6988 (mtm110) REVERT: SC 46 ARG cc_start: 0.3435 (mtp180) cc_final: 0.3229 (mtp180) REVERT: SC 112 MET cc_start: 0.7921 (mmm) cc_final: 0.7340 (mmt) REVERT: SC 207 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7647 (mtmp) REVERT: SD 137 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6576 (tp30) REVERT: SK 1 MET cc_start: 0.6354 (OUTLIER) cc_final: 0.5854 (mpp) REVERT: SK 18 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7214 (tppt) REVERT: SK 100 ARG cc_start: 0.7397 (tmm160) cc_final: 0.7060 (tmm160) REVERT: SM 49 LYS cc_start: 0.7493 (OUTLIER) cc_final: 0.7125 (mtmm) REVERT: SM 557 ARG cc_start: 0.7925 (mtm-85) cc_final: 0.7662 (mtm180) REVERT: SM 560 ARG cc_start: 0.6964 (OUTLIER) cc_final: 0.6759 (ttp-110) REVERT: SN 100 ASP cc_start: 0.6372 (t0) cc_final: 0.6079 (t0) REVERT: SO 94 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.8015 (mtp) REVERT: SQ 47 ASN cc_start: 0.8797 (t0) cc_final: 0.8596 (t0) REVERT: ST 157 LEU cc_start: 0.7049 (pt) cc_final: 0.6671 (pt) REVERT: SW 540 TYR cc_start: 0.8067 (t80) cc_final: 0.7704 (t80) outliers start: 176 outliers final: 77 residues processed: 1028 average time/residue: 2.1874 time to fit residues: 3180.2915 Evaluate side-chains 986 residues out of total 9533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 898 time to evaluate : 9.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L6 residue 13 HIS Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L7 residue 59 ARG Chi-restraints excluded: chain L7 residue 173 GLN Chi-restraints excluded: chain L7 residue 174 LEU Chi-restraints excluded: chain L8 residue 125 ASN Chi-restraints excluded: chain L9 residue 125 SER Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 18 ARG Chi-restraints excluded: chain LC residue 70 LYS Chi-restraints excluded: chain LC residue 93 MET Chi-restraints excluded: chain LC residue 169 THR Chi-restraints excluded: chain LG residue 60 MET Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 9 SER Chi-restraints excluded: chain LI residue 91 ASN Chi-restraints excluded: chain LK residue 15 VAL Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 160 ILE Chi-restraints excluded: chain LN residue 162 VAL Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LW residue 83 THR Chi-restraints excluded: chain NA residue 487 ASP Chi-restraints excluded: chain NA residue 520 ASP Chi-restraints excluded: chain NA residue 591 VAL Chi-restraints excluded: chain NF residue 98 ARG Chi-restraints excluded: chain NH residue 12 MET Chi-restraints excluded: chain NH residue 61 ASP Chi-restraints excluded: chain NH residue 106 SER Chi-restraints excluded: chain NH residue 124 ASN Chi-restraints excluded: chain NH residue 154 ARG Chi-restraints excluded: chain NH residue 168 ASP Chi-restraints excluded: chain NI residue 479 MET Chi-restraints excluded: chain NI residue 722 ASN Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SA residue 351 VAL Chi-restraints excluded: chain SC residue 207 LYS Chi-restraints excluded: chain SD residue 137 GLU Chi-restraints excluded: chain SE residue 184 ILE Chi-restraints excluded: chain SG residue 17 ASP Chi-restraints excluded: chain SG residue 48 LEU Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SH residue 190 LEU Chi-restraints excluded: chain SK residue 1 MET Chi-restraints excluded: chain SK residue 18 LYS Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 110 CYS Chi-restraints excluded: chain SK residue 135 VAL Chi-restraints excluded: chain SL residue 146 LEU Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SM residue 49 LYS Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 133 ASP Chi-restraints excluded: chain SM residue 150 THR Chi-restraints excluded: chain SM residue 353 GLU Chi-restraints excluded: chain SM residue 560 ARG Chi-restraints excluded: chain SN residue 47 VAL Chi-restraints excluded: chain SN residue 145 LEU Chi-restraints excluded: chain SO residue 94 MET Chi-restraints excluded: chain SO residue 101 PHE Chi-restraints excluded: chain SQ residue 48 MET Chi-restraints excluded: chain SQ residue 192 LEU Chi-restraints excluded: chain SR residue 12 VAL Chi-restraints excluded: chain SR residue 83 MET Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 324 THR Chi-restraints excluded: chain SR residue 459 LEU Chi-restraints excluded: chain SS residue 132 ILE Chi-restraints excluded: chain SS residue 136 VAL Chi-restraints excluded: chain SS residue 194 LEU Chi-restraints excluded: chain SS residue 237 THR Chi-restraints excluded: chain SS residue 304 LYS Chi-restraints excluded: chain ST residue 167 LEU Chi-restraints excluded: chain ST residue 210 THR Chi-restraints excluded: chain ST residue 227 VAL Chi-restraints excluded: chain ST residue 257 LEU Chi-restraints excluded: chain SU residue 606 CYS Chi-restraints excluded: chain SV residue 1 MET Chi-restraints excluded: chain SV residue 10 SER Chi-restraints excluded: chain SV residue 65 VAL Chi-restraints excluded: chain SV residue 93 MET Chi-restraints excluded: chain SV residue 109 MET Chi-restraints excluded: chain SW residue 327 LEU Chi-restraints excluded: chain SW residue 347 LEU Chi-restraints excluded: chain SZ residue 37 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1313 random chunks: chunk 1057 optimal weight: 10.0000 chunk 720 optimal weight: 9.9990 chunk 18 optimal weight: 50.0000 chunk 944 optimal weight: 0.2980 chunk 523 optimal weight: 10.0000 chunk 1083 optimal weight: 0.8980 chunk 877 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 648 optimal weight: 4.9990 chunk 1139 optimal weight: 10.0000 chunk 320 optimal weight: 4.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 115 GLN L6 19 GLN L7 180 GLN ** L9 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 72 GLN LA 97 ASN LB 93 GLN LC 125 GLN LG 36 ASN ** LK 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LL 83 ASN LL 121 GLN LQ 102 ASN LW 57 ASN ** NA 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NI 361 GLN SD 248 ASN SE 64 GLN SG 140 GLN SG 162 GLN SI 71 GLN SI 113 GLN ** SJ 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SL 112 GLN SR 342 HIS SS 238 ASN SS 376 GLN ** ST 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SU 668 GLN SV 101 GLN SV 110 ASN ** SV 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SW 278 HIS SY 268 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 147622 Z= 0.247 Angle : 0.512 17.078 211296 Z= 0.265 Chirality : 0.036 0.241 25540 Planarity : 0.004 0.051 17587 Dihedral : 21.458 179.387 51549 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.03 % Allowed : 10.68 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.78 (0.08), residues: 10694 helix: 2.32 (0.07), residues: 4874 sheet: 0.48 (0.14), residues: 1297 loop : 0.19 (0.09), residues: 4523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPL9 120 HIS 0.007 0.001 HISLA 116 PHE 0.023 0.001 PHESW 233 TYR 0.020 0.002 TYRSR 92 ARG 0.011 0.000 ARGSG 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21388 Ramachandran restraints generated. 10694 Oldfield, 0 Emsley, 10694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21388 Ramachandran restraints generated. 10694 Oldfield, 0 Emsley, 10694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1096 residues out of total 9533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 914 time to evaluate : 8.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 142 ASN cc_start: 0.8087 (m110) cc_final: 0.7790 (m-40) REVERT: L7 173 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7565 (tp-100) REVERT: LA 18 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7341 (ttm-80) REVERT: LC 93 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7781 (ptm) REVERT: LC 108 GLN cc_start: 0.8581 (mt0) cc_final: 0.8225 (mt0) REVERT: LG 60 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8536 (ttm) REVERT: LI 115 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7729 (tpt-90) REVERT: LK 65 ARG cc_start: 0.7569 (mtt180) cc_final: 0.6836 (mmt180) REVERT: LQ 86 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7160 (mp0) REVERT: NA 494 ARG cc_start: 0.6725 (OUTLIER) cc_final: 0.4531 (mmt180) REVERT: SA 276 ASN cc_start: 0.7599 (OUTLIER) cc_final: 0.7385 (m-40) REVERT: SC 112 MET cc_start: 0.7961 (mmm) cc_final: 0.7365 (mmt) REVERT: SC 207 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7663 (mtmp) REVERT: SD 137 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6574 (tp30) REVERT: SK 100 ARG cc_start: 0.7612 (tmm160) cc_final: 0.7300 (tmm160) REVERT: SM 49 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.7097 (mtmm) REVERT: SN 100 ASP cc_start: 0.6394 (t0) cc_final: 0.6117 (t0) REVERT: SO 94 MET cc_start: 0.8210 (mtm) cc_final: 0.8000 (mtp) REVERT: SQ 7 ASP cc_start: 0.7384 (OUTLIER) cc_final: 0.7138 (m-30) REVERT: SQ 47 ASN cc_start: 0.8814 (t0) cc_final: 0.8583 (t0) REVERT: ST 157 LEU cc_start: 0.7094 (pt) cc_final: 0.6652 (pt) REVERT: SW 323 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.7285 (ttm) outliers start: 182 outliers final: 95 residues processed: 1012 average time/residue: 2.1392 time to fit residues: 3069.8376 Evaluate side-chains 1005 residues out of total 9533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 897 time to evaluate : 8.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L6 residue 13 HIS Chi-restraints excluded: chain L6 residue 15 HIS Chi-restraints excluded: chain L7 residue 59 ARG Chi-restraints excluded: chain L7 residue 173 GLN Chi-restraints excluded: chain L7 residue 174 LEU Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 125 ASN Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain L9 residue 125 SER Chi-restraints excluded: chain L9 residue 126 THR Chi-restraints excluded: chain L9 residue 155 VAL Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 18 ARG Chi-restraints excluded: chain LA residue 53 LEU Chi-restraints excluded: chain LB residue 14 ARG Chi-restraints excluded: chain LC residue 52 LYS Chi-restraints excluded: chain LC residue 93 MET Chi-restraints excluded: chain LC residue 158 VAL Chi-restraints excluded: chain LC residue 168 THR Chi-restraints excluded: chain LG residue 60 MET Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 9 SER Chi-restraints excluded: chain LI residue 91 ASN Chi-restraints excluded: chain LI residue 115 ARG Chi-restraints excluded: chain LK residue 15 VAL Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 72 LYS Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 160 ILE Chi-restraints excluded: chain LN residue 162 VAL Chi-restraints excluded: chain LN residue 306 ASP Chi-restraints excluded: chain LQ residue 86 GLU Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LW residue 15 THR Chi-restraints excluded: chain LW residue 83 THR Chi-restraints excluded: chain NA residue 362 LEU Chi-restraints excluded: chain NA residue 365 LEU Chi-restraints excluded: chain NA residue 487 ASP Chi-restraints excluded: chain NA residue 494 ARG Chi-restraints excluded: chain NA residue 591 VAL Chi-restraints excluded: chain NF residue 98 ARG Chi-restraints excluded: chain NH residue 12 MET Chi-restraints excluded: chain NH residue 34 THR Chi-restraints excluded: chain NH residue 61 ASP Chi-restraints excluded: chain NH residue 106 SER Chi-restraints excluded: chain NH residue 152 ASP Chi-restraints excluded: chain NI residue 479 MET Chi-restraints excluded: chain NI residue 722 ASN Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SA residue 276 ASN Chi-restraints excluded: chain SA residue 284 MET Chi-restraints excluded: chain SA residue 351 VAL Chi-restraints excluded: chain SC residue 207 LYS Chi-restraints excluded: chain SD residue 137 GLU Chi-restraints excluded: chain SE residue 184 ILE Chi-restraints excluded: chain SE residue 219 VAL Chi-restraints excluded: chain SG residue 17 ASP Chi-restraints excluded: chain SG residue 48 LEU Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SI residue 147 VAL Chi-restraints excluded: chain SI residue 173 THR Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 110 CYS Chi-restraints excluded: chain SK residue 135 VAL Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SM residue 19 THR Chi-restraints excluded: chain SM residue 49 LYS Chi-restraints excluded: chain SM residue 133 ASP Chi-restraints excluded: chain SM residue 150 THR Chi-restraints excluded: chain SM residue 353 GLU Chi-restraints excluded: chain SM residue 565 LEU Chi-restraints excluded: chain SN residue 145 LEU Chi-restraints excluded: chain SO residue 101 PHE Chi-restraints excluded: chain SQ residue 7 ASP Chi-restraints excluded: chain SQ residue 48 MET Chi-restraints excluded: chain SQ residue 192 LEU Chi-restraints excluded: chain SR residue 12 VAL Chi-restraints excluded: chain SR residue 83 MET Chi-restraints excluded: chain SR residue 193 VAL Chi-restraints excluded: chain SR residue 310 LEU Chi-restraints excluded: chain SR residue 324 THR Chi-restraints excluded: chain SR residue 348 MET Chi-restraints excluded: chain SR residue 459 LEU Chi-restraints excluded: chain SS residue 132 ILE Chi-restraints excluded: chain SS residue 194 LEU Chi-restraints excluded: chain SS residue 237 THR Chi-restraints excluded: chain SS residue 304 LYS Chi-restraints excluded: chain SS residue 333 GLN Chi-restraints excluded: chain SS residue 349 SER Chi-restraints excluded: chain ST residue 167 LEU Chi-restraints excluded: chain ST residue 210 THR Chi-restraints excluded: chain ST residue 227 VAL Chi-restraints excluded: chain ST residue 257 LEU Chi-restraints excluded: chain SU residue 366 ILE Chi-restraints excluded: chain SU residue 606 CYS Chi-restraints excluded: chain SU residue 662 LEU Chi-restraints excluded: chain SV residue 1 MET Chi-restraints excluded: chain SV residue 65 VAL Chi-restraints excluded: chain SV residue 93 MET Chi-restraints excluded: chain SV residue 109 MET Chi-restraints excluded: chain SW residue 323 MET Chi-restraints excluded: chain SW residue 347 LEU Chi-restraints excluded: chain SY residue 314 THR Chi-restraints excluded: chain SY residue 517 CYS Chi-restraints excluded: chain SZ residue 37 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1313 random chunks: chunk 426 optimal weight: 40.0000 chunk 1142 optimal weight: 10.0000 chunk 250 optimal weight: 6.9990 chunk 745 optimal weight: 0.3980 chunk 313 optimal weight: 7.9990 chunk 1270 optimal weight: 0.6980 chunk 1054 optimal weight: 1.9990 chunk 588 optimal weight: 0.9980 chunk 105 optimal weight: 20.0000 chunk 420 optimal weight: 5.9990 chunk 666 optimal weight: 5.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 115 GLN L7 180 GLN ** L9 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 72 GLN LA 93 HIS LA 116 HIS LC 125 GLN LG 36 ASN LI 14 ASN ** LK 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LL 83 ASN LQ 102 ASN LS 65 GLN ** NA 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** NF 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 64 GLN SG 140 GLN SG 162 GLN SG 163 GLN SI 71 GLN SI 113 GLN SJ 135 HIS ** SJ 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SL 112 GLN SR 108 ASN SR 342 HIS SR 351 ASN SS 200 GLN SS 238 ASN SS 376 GLN ** ST 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SV 101 GLN SV 110 ASN SV 115 ASN SV 129 GLN SW 207 HIS SW 278 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 147622 Z= 0.212 Angle : 0.492 17.009 211296 Z= 0.255 Chirality : 0.035 0.234 25540 Planarity : 0.004 0.050 17587 Dihedral : 21.431 179.897 51549 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.14 % Allowed : 10.88 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.85 (0.08), residues: 10694 helix: 2.40 (0.07), residues: 4867 sheet: 0.50 (0.14), residues: 1279 loop : 0.21 (0.09), residues: 4548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPL9 120 HIS 0.008 0.001 HISLA 93 PHE 0.023 0.001 PHESW 233 TYR 0.020 0.001 TYRSR 92 ARG 0.012 0.000 ARGSG 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21388 Ramachandran restraints generated. 10694 Oldfield, 0 Emsley, 10694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21388 Ramachandran restraints generated. 10694 Oldfield, 0 Emsley, 10694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1114 residues out of total 9533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 922 time to evaluate : 9.109 Fit side-chains revert: symmetry clash REVERT: BA 142 ASN cc_start: 0.8095 (m110) cc_final: 0.7810 (m-40) REVERT: L7 173 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7582 (tp-100) REVERT: LC 93 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7747 (ptm) REVERT: LC 108 GLN cc_start: 0.8549 (mt0) cc_final: 0.8154 (mt0) REVERT: LG 60 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8529 (ttm) REVERT: LI 115 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7710 (tpt-90) REVERT: LK 65 ARG cc_start: 0.7400 (mtt180) cc_final: 0.6727 (mmt180) REVERT: LQ 86 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7134 (mp0) REVERT: NA 494 ARG cc_start: 0.6947 (OUTLIER) cc_final: 0.4714 (mmt180) REVERT: NH 154 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.6953 (mtm110) REVERT: SA 276 ASN cc_start: 0.7565 (OUTLIER) cc_final: 0.7354 (m-40) REVERT: SC 112 MET cc_start: 0.8000 (mmm) cc_final: 0.7386 (mmt) REVERT: SC 207 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7672 (mtmp) REVERT: SD 137 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6553 (tp30) REVERT: SM 49 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.7097 (mtmm) REVERT: SM 557 ARG cc_start: 0.7888 (mmm-85) cc_final: 0.7441 (mtm180) REVERT: SN 100 ASP cc_start: 0.6393 (t0) cc_final: 0.6140 (t0) REVERT: SO 94 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7983 (mtp) REVERT: SQ 7 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.7156 (m-30) REVERT: SQ 47 ASN cc_start: 0.8804 (t0) cc_final: 0.8557 (t0) REVERT: ST 157 LEU cc_start: 0.7140 (pt) cc_final: 0.6748 (pt) outliers start: 192 outliers final: 108 residues processed: 1037 average time/residue: 2.1629 time to fit residues: 3198.2593 Evaluate side-chains 1010 residues out of total 9533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 889 time to evaluate : 8.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L6 residue 13 HIS Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L7 residue 59 ARG Chi-restraints excluded: chain L7 residue 173 GLN Chi-restraints excluded: chain L7 residue 174 LEU Chi-restraints excluded: chain L8 residue 125 ASN Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain L9 residue 125 SER Chi-restraints excluded: chain L9 residue 155 VAL Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 18 ARG Chi-restraints excluded: chain LB residue 14 ARG Chi-restraints excluded: chain LB residue 92 VAL Chi-restraints excluded: chain LC residue 24 THR Chi-restraints excluded: chain LC residue 70 LYS Chi-restraints excluded: chain LC residue 93 MET Chi-restraints excluded: chain LC residue 168 THR Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 60 MET Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 9 SER Chi-restraints excluded: chain LI residue 91 ASN Chi-restraints excluded: chain LI residue 115 ARG Chi-restraints excluded: chain LK residue 15 VAL Chi-restraints excluded: chain LL residue 72 LYS Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 160 ILE Chi-restraints excluded: chain LN residue 162 VAL Chi-restraints excluded: chain LN residue 306 ASP Chi-restraints excluded: chain LQ residue 86 GLU Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LW residue 15 THR Chi-restraints excluded: chain LW residue 83 THR Chi-restraints excluded: chain NA residue 362 LEU Chi-restraints excluded: chain NA residue 365 LEU Chi-restraints excluded: chain NA residue 494 ARG Chi-restraints excluded: chain NA residue 591 VAL Chi-restraints excluded: chain NF residue 98 ARG Chi-restraints excluded: chain NH residue 12 MET Chi-restraints excluded: chain NH residue 34 THR Chi-restraints excluded: chain NH residue 61 ASP Chi-restraints excluded: chain NH residue 106 SER Chi-restraints excluded: chain NH residue 154 ARG Chi-restraints excluded: chain NH residue 175 HIS Chi-restraints excluded: chain NI residue 479 MET Chi-restraints excluded: chain NI residue 722 ASN Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SA residue 276 ASN Chi-restraints excluded: chain SA residue 284 MET Chi-restraints excluded: chain SA residue 351 VAL Chi-restraints excluded: chain SC residue 189 THR Chi-restraints excluded: chain SC residue 207 LYS Chi-restraints excluded: chain SD residue 137 GLU Chi-restraints excluded: chain SE residue 91 THR Chi-restraints excluded: chain SE residue 105 GLU Chi-restraints excluded: chain SE residue 168 VAL Chi-restraints excluded: chain SE residue 184 ILE Chi-restraints excluded: chain SE residue 207 VAL Chi-restraints excluded: chain SE residue 219 VAL Chi-restraints excluded: chain SG residue 17 ASP Chi-restraints excluded: chain SG residue 48 LEU Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SH residue 155 LEU Chi-restraints excluded: chain SI residue 147 VAL Chi-restraints excluded: chain SI residue 173 THR Chi-restraints excluded: chain SK residue 44 ASP Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 110 CYS Chi-restraints excluded: chain SK residue 135 VAL Chi-restraints excluded: chain SL residue 146 LEU Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SM residue 19 THR Chi-restraints excluded: chain SM residue 49 LYS Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 133 ASP Chi-restraints excluded: chain SM residue 150 THR Chi-restraints excluded: chain SM residue 353 GLU Chi-restraints excluded: chain SM residue 441 LYS Chi-restraints excluded: chain SM residue 565 LEU Chi-restraints excluded: chain SN residue 47 VAL Chi-restraints excluded: chain SN residue 61 LYS Chi-restraints excluded: chain SN residue 145 LEU Chi-restraints excluded: chain SN residue 161 MET Chi-restraints excluded: chain SO residue 94 MET Chi-restraints excluded: chain SO residue 101 PHE Chi-restraints excluded: chain SO residue 109 MET Chi-restraints excluded: chain SQ residue 7 ASP Chi-restraints excluded: chain SQ residue 48 MET Chi-restraints excluded: chain SR residue 12 VAL Chi-restraints excluded: chain SR residue 83 MET Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 193 VAL Chi-restraints excluded: chain SR residue 207 VAL Chi-restraints excluded: chain SR residue 287 VAL Chi-restraints excluded: chain SR residue 310 LEU Chi-restraints excluded: chain SR residue 324 THR Chi-restraints excluded: chain SR residue 331 VAL Chi-restraints excluded: chain SR residue 459 LEU Chi-restraints excluded: chain SS residue 136 VAL Chi-restraints excluded: chain SS residue 237 THR Chi-restraints excluded: chain SS residue 304 LYS Chi-restraints excluded: chain SS residue 333 GLN Chi-restraints excluded: chain SS residue 349 SER Chi-restraints excluded: chain ST residue 167 LEU Chi-restraints excluded: chain ST residue 210 THR Chi-restraints excluded: chain ST residue 227 VAL Chi-restraints excluded: chain ST residue 257 LEU Chi-restraints excluded: chain SU residue 205 ILE Chi-restraints excluded: chain SU residue 366 ILE Chi-restraints excluded: chain SU residue 566 LEU Chi-restraints excluded: chain SU residue 606 CYS Chi-restraints excluded: chain SV residue 1 MET Chi-restraints excluded: chain SV residue 65 VAL Chi-restraints excluded: chain SV residue 93 MET Chi-restraints excluded: chain SV residue 109 MET Chi-restraints excluded: chain SW residue 347 LEU Chi-restraints excluded: chain SY residue 314 THR Chi-restraints excluded: chain SZ residue 37 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1313 random chunks: chunk 1224 optimal weight: 30.0000 chunk 143 optimal weight: 10.0000 chunk 723 optimal weight: 3.9990 chunk 927 optimal weight: 7.9990 chunk 718 optimal weight: 3.9990 chunk 1069 optimal weight: 0.9990 chunk 709 optimal weight: 0.2980 chunk 1265 optimal weight: 0.9980 chunk 791 optimal weight: 0.8980 chunk 771 optimal weight: 5.9990 chunk 584 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 115 GLN L7 180 GLN ** L9 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 93 HIS LA 116 HIS LC 37 HIS LG 36 ASN LH 57 GLN LI 14 ASN ** LK 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LL 83 ASN LS 65 GLN ** NA 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** NA 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NF 127 GLN SG 140 GLN SG 162 GLN SG 163 GLN SI 113 GLN SJ 135 HIS ** SJ 712 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SJ 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SK 178 GLN SL 112 GLN SM 243 ASN SR 342 HIS SS 208 GLN SS 238 ASN SS 376 GLN ** ST 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SV 101 GLN SV 110 ASN SY 268 ASN ** SY 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SZ 11 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 147622 Z= 0.167 Angle : 0.475 16.835 211296 Z= 0.246 Chirality : 0.034 0.226 25540 Planarity : 0.004 0.057 17587 Dihedral : 21.405 179.755 51549 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.66 % Allowed : 11.76 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.92 (0.08), residues: 10694 helix: 2.48 (0.07), residues: 4878 sheet: 0.53 (0.14), residues: 1285 loop : 0.22 (0.09), residues: 4531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPL9 120 HIS 0.011 0.001 HISLA 93 PHE 0.023 0.001 PHESW 233 TYR 0.021 0.001 TYRSR 92 ARG 0.014 0.000 ARGSG 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21388 Ramachandran restraints generated. 10694 Oldfield, 0 Emsley, 10694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21388 Ramachandran restraints generated. 10694 Oldfield, 0 Emsley, 10694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1063 residues out of total 9533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 914 time to evaluate : 9.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 142 ASN cc_start: 0.8088 (m110) cc_final: 0.7807 (m-40) REVERT: LC 93 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7749 (ptm) REVERT: LG 60 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8450 (ttm) REVERT: LI 115 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7673 (tpt-90) REVERT: LK 65 ARG cc_start: 0.7306 (mtt180) cc_final: 0.6673 (mmt180) REVERT: LS 13 LYS cc_start: 0.6299 (tmtm) cc_final: 0.5876 (tppp) REVERT: NA 494 ARG cc_start: 0.6839 (OUTLIER) cc_final: 0.4644 (mmt180) REVERT: SC 112 MET cc_start: 0.8025 (mmm) cc_final: 0.7439 (mmt) REVERT: SD 137 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6551 (tp30) REVERT: SG 128 MET cc_start: 0.8810 (mmp) cc_final: 0.8500 (mmp) REVERT: SL 67 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.8111 (mmm) REVERT: SM 49 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.7136 (mtmm) REVERT: SM 557 ARG cc_start: 0.7835 (mmm-85) cc_final: 0.7588 (mtm180) REVERT: SN 100 ASP cc_start: 0.6355 (t0) cc_final: 0.6068 (t0) REVERT: SO 94 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7972 (mtp) REVERT: SQ 7 ASP cc_start: 0.7321 (OUTLIER) cc_final: 0.7080 (m-30) REVERT: SQ 47 ASN cc_start: 0.8781 (t0) cc_final: 0.8559 (t0) REVERT: ST 157 LEU cc_start: 0.7278 (pt) cc_final: 0.6953 (pt) outliers start: 149 outliers final: 97 residues processed: 1007 average time/residue: 2.1514 time to fit residues: 3088.0994 Evaluate side-chains 1000 residues out of total 9533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 894 time to evaluate : 8.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L6 residue 13 HIS Chi-restraints excluded: chain L6 residue 17 ASP Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 104 MET Chi-restraints excluded: chain L8 residue 125 ASN Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain L9 residue 126 THR Chi-restraints excluded: chain L9 residue 155 VAL Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 18 ARG Chi-restraints excluded: chain LB residue 14 ARG Chi-restraints excluded: chain LB residue 42 THR Chi-restraints excluded: chain LB residue 92 VAL Chi-restraints excluded: chain LC residue 24 THR Chi-restraints excluded: chain LC residue 93 MET Chi-restraints excluded: chain LC residue 158 VAL Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 60 MET Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 91 ASN Chi-restraints excluded: chain LI residue 115 ARG Chi-restraints excluded: chain LK residue 15 VAL Chi-restraints excluded: chain LL residue 60 VAL Chi-restraints excluded: chain LN residue 57 VAL Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 160 ILE Chi-restraints excluded: chain LN residue 306 ASP Chi-restraints excluded: chain LN residue 389 MET Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LW residue 15 THR Chi-restraints excluded: chain LW residue 83 THR Chi-restraints excluded: chain NA residue 365 LEU Chi-restraints excluded: chain NA residue 487 ASP Chi-restraints excluded: chain NA residue 494 ARG Chi-restraints excluded: chain NA residue 591 VAL Chi-restraints excluded: chain NF residue 98 ARG Chi-restraints excluded: chain NH residue 12 MET Chi-restraints excluded: chain NH residue 61 ASP Chi-restraints excluded: chain NH residue 106 SER Chi-restraints excluded: chain NI residue 206 MET Chi-restraints excluded: chain NI residue 437 THR Chi-restraints excluded: chain NI residue 479 MET Chi-restraints excluded: chain NI residue 722 ASN Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SA residue 284 MET Chi-restraints excluded: chain SC residue 189 THR Chi-restraints excluded: chain SD residue 137 GLU Chi-restraints excluded: chain SE residue 184 ILE Chi-restraints excluded: chain SE residue 207 VAL Chi-restraints excluded: chain SE residue 219 VAL Chi-restraints excluded: chain SG residue 17 ASP Chi-restraints excluded: chain SG residue 48 LEU Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SH residue 97 ASP Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SI residue 147 VAL Chi-restraints excluded: chain SJ residue 729 LYS Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 110 CYS Chi-restraints excluded: chain SK residue 135 VAL Chi-restraints excluded: chain SL residue 67 MET Chi-restraints excluded: chain SL residue 146 LEU Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SM residue 19 THR Chi-restraints excluded: chain SM residue 49 LYS Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 353 GLU Chi-restraints excluded: chain SM residue 441 LYS Chi-restraints excluded: chain SM residue 565 LEU Chi-restraints excluded: chain SN residue 145 LEU Chi-restraints excluded: chain SO residue 94 MET Chi-restraints excluded: chain SQ residue 7 ASP Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 193 VAL Chi-restraints excluded: chain SR residue 207 VAL Chi-restraints excluded: chain SR residue 287 VAL Chi-restraints excluded: chain SR residue 324 THR Chi-restraints excluded: chain SR residue 348 MET Chi-restraints excluded: chain SR residue 459 LEU Chi-restraints excluded: chain SS residue 136 VAL Chi-restraints excluded: chain SS residue 197 THR Chi-restraints excluded: chain SS residue 304 LYS Chi-restraints excluded: chain SS residue 349 SER Chi-restraints excluded: chain ST residue 167 LEU Chi-restraints excluded: chain ST residue 210 THR Chi-restraints excluded: chain ST residue 228 SER Chi-restraints excluded: chain ST residue 257 LEU Chi-restraints excluded: chain SU residue 205 ILE Chi-restraints excluded: chain SU residue 366 ILE Chi-restraints excluded: chain SU residue 385 VAL Chi-restraints excluded: chain SU residue 566 LEU Chi-restraints excluded: chain SU residue 606 CYS Chi-restraints excluded: chain SU residue 678 ASP Chi-restraints excluded: chain SV residue 1 MET Chi-restraints excluded: chain SV residue 10 SER Chi-restraints excluded: chain SV residue 65 VAL Chi-restraints excluded: chain SV residue 93 MET Chi-restraints excluded: chain SV residue 109 MET Chi-restraints excluded: chain SW residue 347 LEU Chi-restraints excluded: chain SY residue 508 THR Chi-restraints excluded: chain SY residue 517 CYS Chi-restraints excluded: chain SZ residue 37 SER Chi-restraints excluded: chain SZ residue 169 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1313 random chunks: chunk 782 optimal weight: 5.9990 chunk 505 optimal weight: 40.0000 chunk 755 optimal weight: 5.9990 chunk 381 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 245 optimal weight: 10.0000 chunk 804 optimal weight: 7.9990 chunk 862 optimal weight: 4.9990 chunk 625 optimal weight: 9.9990 chunk 117 optimal weight: 7.9990 chunk 994 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 115 GLN L7 180 GLN ** L9 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L9 32 GLN LA 72 GLN LA 93 HIS ** LA 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LG 36 ASN LG 135 ASN ** LK 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 102 ASN LS 30 GLN LS 65 GLN ** NA 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SG 42 ASN SG 140 GLN SG 162 GLN SI 71 GLN SI 113 GLN SJ 135 HIS SJ 712 HIS ** SJ 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SK 178 GLN SL 112 GLN SM 209 HIS SR 342 HIS SS 208 GLN SS 238 ASN SS 376 GLN SU 232 ASN SU 355 HIS SV 101 GLN SV 110 ASN SV 115 ASN SW 184 ASN SW 402 GLN ** SY 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SY 478 ASN SZ 11 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.082 147622 Z= 0.544 Angle : 0.668 16.970 211296 Z= 0.338 Chirality : 0.045 0.278 25540 Planarity : 0.006 0.069 17587 Dihedral : 21.460 179.583 51549 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.07 % Allowed : 11.94 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.08), residues: 10694 helix: 1.98 (0.07), residues: 4859 sheet: 0.33 (0.14), residues: 1288 loop : -0.02 (0.09), residues: 4547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRPLT 6 HIS 0.015 0.002 HISNA 376 PHE 0.030 0.003 PHENA 488 TYR 0.026 0.003 TYRNA 433 ARG 0.014 0.001 ARGSJ 176 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21388 Ramachandran restraints generated. 10694 Oldfield, 0 Emsley, 10694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21388 Ramachandran restraints generated. 10694 Oldfield, 0 Emsley, 10694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1095 residues out of total 9533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 909 time to evaluate : 9.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L7 68 ARG cc_start: 0.6832 (mmp-170) cc_final: 0.6611 (mmt180) REVERT: L7 173 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7584 (tp-100) REVERT: LA 89 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.6993 (pt0) REVERT: LA 93 HIS cc_start: 0.6526 (OUTLIER) cc_final: 0.6173 (m-70) REVERT: LC 93 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7978 (ptm) REVERT: LL 28 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7420 (pt0) REVERT: NA 494 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.4791 (mmt180) REVERT: NH 154 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7062 (mtm110) REVERT: SC 112 MET cc_start: 0.7982 (mmm) cc_final: 0.7377 (mmt) REVERT: SC 207 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7643 (mtmp) REVERT: SD 137 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6674 (tp30) REVERT: SM 49 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7231 (mtmm) REVERT: SM 557 ARG cc_start: 0.7845 (mmm-85) cc_final: 0.7632 (mtm180) REVERT: SN 100 ASP cc_start: 0.6518 (t0) cc_final: 0.6300 (t0) REVERT: SQ 7 ASP cc_start: 0.7438 (OUTLIER) cc_final: 0.7201 (m-30) REVERT: ST 157 LEU cc_start: 0.7428 (pt) cc_final: 0.7087 (pt) REVERT: SW 323 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7155 (ttm) outliers start: 186 outliers final: 119 residues processed: 1021 average time/residue: 2.0851 time to fit residues: 3043.1980 Evaluate side-chains 1021 residues out of total 9533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 890 time to evaluate : 8.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L6 residue 13 HIS Chi-restraints excluded: chain L6 residue 17 ASP Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L7 residue 59 ARG Chi-restraints excluded: chain L7 residue 173 GLN Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 125 ASN Chi-restraints excluded: chain L9 residue 17 ASP Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain L9 residue 125 SER Chi-restraints excluded: chain L9 residue 126 THR Chi-restraints excluded: chain L9 residue 155 VAL Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 18 ARG Chi-restraints excluded: chain LA residue 89 GLU Chi-restraints excluded: chain LA residue 93 HIS Chi-restraints excluded: chain LB residue 14 ARG Chi-restraints excluded: chain LB residue 92 VAL Chi-restraints excluded: chain LC residue 70 LYS Chi-restraints excluded: chain LC residue 93 MET Chi-restraints excluded: chain LC residue 158 VAL Chi-restraints excluded: chain LC residue 168 THR Chi-restraints excluded: chain LC residue 169 THR Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LI residue 9 SER Chi-restraints excluded: chain LI residue 91 ASN Chi-restraints excluded: chain LK residue 15 VAL Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LN residue 57 VAL Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 160 ILE Chi-restraints excluded: chain LN residue 162 VAL Chi-restraints excluded: chain LN residue 306 ASP Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 75 THR Chi-restraints excluded: chain LW residue 15 THR Chi-restraints excluded: chain LW residue 83 THR Chi-restraints excluded: chain NA residue 365 LEU Chi-restraints excluded: chain NA residue 494 ARG Chi-restraints excluded: chain NA residue 591 VAL Chi-restraints excluded: chain NF residue 98 ARG Chi-restraints excluded: chain NH residue 12 MET Chi-restraints excluded: chain NH residue 34 THR Chi-restraints excluded: chain NH residue 61 ASP Chi-restraints excluded: chain NH residue 106 SER Chi-restraints excluded: chain NH residue 152 ASP Chi-restraints excluded: chain NH residue 154 ARG Chi-restraints excluded: chain NH residue 175 HIS Chi-restraints excluded: chain NI residue 206 MET Chi-restraints excluded: chain NI residue 437 THR Chi-restraints excluded: chain NI residue 479 MET Chi-restraints excluded: chain NI residue 722 ASN Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SA residue 319 LEU Chi-restraints excluded: chain SA residue 351 VAL Chi-restraints excluded: chain SC residue 189 THR Chi-restraints excluded: chain SC residue 207 LYS Chi-restraints excluded: chain SD residue 137 GLU Chi-restraints excluded: chain SE residue 91 THR Chi-restraints excluded: chain SE residue 184 ILE Chi-restraints excluded: chain SE residue 219 VAL Chi-restraints excluded: chain SG residue 17 ASP Chi-restraints excluded: chain SG residue 48 LEU Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SH residue 135 ASN Chi-restraints excluded: chain SH residue 155 LEU Chi-restraints excluded: chain SI residue 147 VAL Chi-restraints excluded: chain SI residue 173 THR Chi-restraints excluded: chain SK residue 44 ASP Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 110 CYS Chi-restraints excluded: chain SK residue 135 VAL Chi-restraints excluded: chain SK residue 160 LEU Chi-restraints excluded: chain SL residue 146 LEU Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SM residue 19 THR Chi-restraints excluded: chain SM residue 49 LYS Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 133 ASP Chi-restraints excluded: chain SM residue 150 THR Chi-restraints excluded: chain SM residue 353 GLU Chi-restraints excluded: chain SM residue 565 LEU Chi-restraints excluded: chain SN residue 145 LEU Chi-restraints excluded: chain SN residue 161 MET Chi-restraints excluded: chain SN residue 183 GLU Chi-restraints excluded: chain SO residue 292 LYS Chi-restraints excluded: chain SQ residue 7 ASP Chi-restraints excluded: chain SQ residue 48 MET Chi-restraints excluded: chain SQ residue 192 LEU Chi-restraints excluded: chain SR residue 12 VAL Chi-restraints excluded: chain SR residue 83 MET Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 193 VAL Chi-restraints excluded: chain SR residue 207 VAL Chi-restraints excluded: chain SR residue 287 VAL Chi-restraints excluded: chain SR residue 324 THR Chi-restraints excluded: chain SR residue 331 VAL Chi-restraints excluded: chain SR residue 348 MET Chi-restraints excluded: chain SR residue 459 LEU Chi-restraints excluded: chain SS residue 132 ILE Chi-restraints excluded: chain SS residue 136 VAL Chi-restraints excluded: chain SS residue 194 LEU Chi-restraints excluded: chain SS residue 237 THR Chi-restraints excluded: chain SS residue 304 LYS Chi-restraints excluded: chain SS residue 333 GLN Chi-restraints excluded: chain SS residue 349 SER Chi-restraints excluded: chain ST residue 167 LEU Chi-restraints excluded: chain ST residue 210 THR Chi-restraints excluded: chain ST residue 227 VAL Chi-restraints excluded: chain ST residue 257 LEU Chi-restraints excluded: chain SU residue 366 ILE Chi-restraints excluded: chain SU residue 420 MET Chi-restraints excluded: chain SU residue 566 LEU Chi-restraints excluded: chain SU residue 606 CYS Chi-restraints excluded: chain SU residue 678 ASP Chi-restraints excluded: chain SV residue 1 MET Chi-restraints excluded: chain SV residue 10 SER Chi-restraints excluded: chain SV residue 65 VAL Chi-restraints excluded: chain SV residue 93 MET Chi-restraints excluded: chain SV residue 109 MET Chi-restraints excluded: chain SW residue 323 MET Chi-restraints excluded: chain SW residue 347 LEU Chi-restraints excluded: chain SY residue 314 THR Chi-restraints excluded: chain SY residue 406 MET Chi-restraints excluded: chain SY residue 451 VAL Chi-restraints excluded: chain SY residue 508 THR Chi-restraints excluded: chain SY residue 517 CYS Chi-restraints excluded: chain SZ residue 37 SER Chi-restraints excluded: chain SZ residue 169 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1313 random chunks: chunk 1151 optimal weight: 0.9990 chunk 1212 optimal weight: 0.8980 chunk 1106 optimal weight: 0.7980 chunk 1179 optimal weight: 6.9990 chunk 709 optimal weight: 0.9990 chunk 513 optimal weight: 3.9990 chunk 926 optimal weight: 6.9990 chunk 361 optimal weight: 1.9990 chunk 1065 optimal weight: 1.9990 chunk 1115 optimal weight: 0.0770 chunk 1175 optimal weight: 7.9990 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 115 GLN L6 19 GLN L6 67 HIS L7 180 GLN ** L9 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 116 HIS LG 36 ASN LI 14 ASN LK 60 HIS LS 30 GLN LS 65 GLN ** NA 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** NA 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SE 64 GLN SG 140 GLN SG 162 GLN SG 163 GLN SI 71 GLN SI 113 GLN SJ 135 HIS ** SJ 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SK 178 GLN SL 112 GLN SR 342 HIS ** SR 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SS 208 GLN SS 238 ASN ** ST 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SU 232 ASN SV 101 GLN SV 110 ASN SW 184 ASN SW 278 HIS SY 268 ASN ** SY 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SZ 11 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 147622 Z= 0.132 Angle : 0.485 16.580 211296 Z= 0.250 Chirality : 0.033 0.227 25540 Planarity : 0.004 0.056 17587 Dihedral : 21.445 180.000 51549 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.25 % Allowed : 12.80 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.79 (0.08), residues: 10694 helix: 2.39 (0.07), residues: 4880 sheet: 0.45 (0.14), residues: 1282 loop : 0.14 (0.09), residues: 4532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPL9 120 HIS 0.022 0.001 HISLA 93 PHE 0.021 0.001 PHESW 233 TYR 0.025 0.001 TYRLK 61 ARG 0.015 0.000 ARGSG 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21388 Ramachandran restraints generated. 10694 Oldfield, 0 Emsley, 10694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21388 Ramachandran restraints generated. 10694 Oldfield, 0 Emsley, 10694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1019 residues out of total 9533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 907 time to evaluate : 9.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L7 68 ARG cc_start: 0.6639 (mmp-170) cc_final: 0.6427 (mmt180) REVERT: LC 93 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7653 (ptm) REVERT: SC 112 MET cc_start: 0.8011 (mmm) cc_final: 0.7409 (mmt) REVERT: SM 49 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.7130 (mtmm) REVERT: SN 100 ASP cc_start: 0.6395 (t0) cc_final: 0.6126 (t0) REVERT: ST 157 LEU cc_start: 0.7452 (pt) cc_final: 0.7134 (pt) outliers start: 112 outliers final: 68 residues processed: 977 average time/residue: 2.2056 time to fit residues: 3069.7750 Evaluate side-chains 955 residues out of total 9533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 885 time to evaluate : 8.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L6 residue 13 HIS Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 132 SER Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 125 ASN Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain L9 residue 125 SER Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 18 ARG Chi-restraints excluded: chain LC residue 52 LYS Chi-restraints excluded: chain LC residue 70 LYS Chi-restraints excluded: chain LC residue 93 MET Chi-restraints excluded: chain LC residue 168 THR Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LI residue 91 ASN Chi-restraints excluded: chain LK residue 15 VAL Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 160 ILE Chi-restraints excluded: chain LN residue 306 ASP Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain NA residue 365 LEU Chi-restraints excluded: chain NA residue 591 VAL Chi-restraints excluded: chain NF residue 98 ARG Chi-restraints excluded: chain NH residue 12 MET Chi-restraints excluded: chain NH residue 34 THR Chi-restraints excluded: chain NH residue 106 SER Chi-restraints excluded: chain NI residue 437 THR Chi-restraints excluded: chain NI residue 479 MET Chi-restraints excluded: chain NI residue 722 ASN Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SC residue 189 THR Chi-restraints excluded: chain SE residue 91 THR Chi-restraints excluded: chain SE residue 105 GLU Chi-restraints excluded: chain SG residue 48 LEU Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SH residue 155 LEU Chi-restraints excluded: chain SI residue 147 VAL Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 135 VAL Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SM residue 19 THR Chi-restraints excluded: chain SM residue 49 LYS Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 353 GLU Chi-restraints excluded: chain SN residue 145 LEU Chi-restraints excluded: chain SN residue 183 GLU Chi-restraints excluded: chain SQ residue 48 MET Chi-restraints excluded: chain SR residue 12 VAL Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 193 VAL Chi-restraints excluded: chain SR residue 324 THR Chi-restraints excluded: chain SR residue 459 LEU Chi-restraints excluded: chain SS residue 136 VAL Chi-restraints excluded: chain SS residue 228 SER Chi-restraints excluded: chain SS residue 349 SER Chi-restraints excluded: chain ST residue 210 THR Chi-restraints excluded: chain ST residue 228 SER Chi-restraints excluded: chain ST residue 257 LEU Chi-restraints excluded: chain SU residue 366 ILE Chi-restraints excluded: chain SU residue 606 CYS Chi-restraints excluded: chain SU residue 678 ASP Chi-restraints excluded: chain SV residue 1 MET Chi-restraints excluded: chain SV residue 65 VAL Chi-restraints excluded: chain SV residue 93 MET Chi-restraints excluded: chain SV residue 109 MET Chi-restraints excluded: chain SW residue 347 LEU Chi-restraints excluded: chain SY residue 508 THR Chi-restraints excluded: chain SZ residue 169 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1313 random chunks: chunk 774 optimal weight: 3.9990 chunk 1247 optimal weight: 10.0000 chunk 761 optimal weight: 8.9990 chunk 591 optimal weight: 6.9990 chunk 866 optimal weight: 1.9990 chunk 1308 optimal weight: 9.9990 chunk 1203 optimal weight: 10.0000 chunk 1041 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 804 optimal weight: 7.9990 chunk 638 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 115 GLN L7 180 GLN ** L9 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 72 GLN LA 93 HIS LA 116 HIS LG 36 ASN LI 14 ASN LQ 102 ASN LS 65 GLN ** NA 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** NA 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** NK 101 GLN SE 64 GLN SG 140 GLN SG 162 GLN SI 71 GLN SI 113 GLN SJ 135 HIS ** SJ 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SL 53 ASN SL 112 GLN SR 342 HIS SS 208 GLN SS 238 ASN SS 376 GLN ** ST 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SU 232 ASN SU 686 GLN SV 101 GLN SV 110 ASN SW 184 ASN ** SW 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SY 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SZ 11 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 147622 Z= 0.366 Angle : 0.571 16.915 211296 Z= 0.292 Chirality : 0.039 0.254 25540 Planarity : 0.005 0.057 17587 Dihedral : 21.402 179.957 51549 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.27 % Allowed : 12.94 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.58 (0.08), residues: 10694 helix: 2.19 (0.07), residues: 4880 sheet: 0.39 (0.14), residues: 1285 loop : 0.04 (0.09), residues: 4529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPLT 6 HIS 0.009 0.001 HISNA 376 PHE 0.021 0.002 PHESO 65 TYR 0.020 0.002 TYRSW 540 ARG 0.016 0.001 ARGSY 238 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 21388 Ramachandran restraints generated. 10694 Oldfield, 0 Emsley, 10694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 21388 Ramachandran restraints generated. 10694 Oldfield, 0 Emsley, 10694 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1013 residues out of total 9533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 899 time to evaluate : 9.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L7 68 ARG cc_start: 0.6771 (mmp-170) cc_final: 0.6557 (mmt180) REVERT: LA 18 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7674 (ttm-80) REVERT: LC 93 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7879 (ptm) REVERT: LG 60 MET cc_start: 0.8773 (ttp) cc_final: 0.8519 (ttm) REVERT: LL 28 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7360 (pt0) REVERT: NA 387 HIS cc_start: 0.7937 (OUTLIER) cc_final: 0.7613 (t70) REVERT: NA 494 ARG cc_start: 0.6969 (OUTLIER) cc_final: 0.4728 (mmt180) REVERT: SC 112 MET cc_start: 0.7997 (mmm) cc_final: 0.7425 (mmt) REVERT: SD 137 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6630 (tp30) REVERT: SM 49 LYS cc_start: 0.7563 (OUTLIER) cc_final: 0.7170 (mtmm) REVERT: SN 100 ASP cc_start: 0.6613 (t0) cc_final: 0.6380 (t0) REVERT: ST 157 LEU cc_start: 0.7515 (pt) cc_final: 0.7183 (pt) REVERT: SW 323 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7193 (ttm) outliers start: 114 outliers final: 85 residues processed: 974 average time/residue: 2.1777 time to fit residues: 3026.0370 Evaluate side-chains 982 residues out of total 9533 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 889 time to evaluate : 8.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L6 residue 13 HIS Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 132 SER Chi-restraints excluded: chain L8 residue 125 ASN Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain L9 residue 125 SER Chi-restraints excluded: chain L9 residue 126 THR Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 18 ARG Chi-restraints excluded: chain LB residue 14 ARG Chi-restraints excluded: chain LB residue 92 VAL Chi-restraints excluded: chain LC residue 52 LYS Chi-restraints excluded: chain LC residue 70 LYS Chi-restraints excluded: chain LC residue 93 MET Chi-restraints excluded: chain LC residue 158 VAL Chi-restraints excluded: chain LC residue 168 THR Chi-restraints excluded: chain LE residue 99 SER Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LI residue 9 SER Chi-restraints excluded: chain LI residue 91 ASN Chi-restraints excluded: chain LK residue 15 VAL Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LN residue 57 VAL Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 160 ILE Chi-restraints excluded: chain LN residue 162 VAL Chi-restraints excluded: chain LN residue 306 ASP Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LW residue 15 THR Chi-restraints excluded: chain NA residue 365 LEU Chi-restraints excluded: chain NA residue 387 HIS Chi-restraints excluded: chain NA residue 494 ARG Chi-restraints excluded: chain NA residue 591 VAL Chi-restraints excluded: chain NF residue 98 ARG Chi-restraints excluded: chain NH residue 12 MET Chi-restraints excluded: chain NH residue 34 THR Chi-restraints excluded: chain NH residue 61 ASP Chi-restraints excluded: chain NH residue 106 SER Chi-restraints excluded: chain NI residue 234 MET Chi-restraints excluded: chain NI residue 437 THR Chi-restraints excluded: chain NI residue 479 MET Chi-restraints excluded: chain NI residue 722 ASN Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SA residue 319 LEU Chi-restraints excluded: chain SA residue 351 VAL Chi-restraints excluded: chain SC residue 189 THR Chi-restraints excluded: chain SD residue 137 GLU Chi-restraints excluded: chain SE residue 91 THR Chi-restraints excluded: chain SE residue 105 GLU Chi-restraints excluded: chain SE residue 184 ILE Chi-restraints excluded: chain SG residue 48 LEU Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SH residue 155 LEU Chi-restraints excluded: chain SI residue 147 VAL Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 110 CYS Chi-restraints excluded: chain SK residue 135 VAL Chi-restraints excluded: chain SL residue 268 VAL Chi-restraints excluded: chain SM residue 19 THR Chi-restraints excluded: chain SM residue 49 LYS Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 133 ASP Chi-restraints excluded: chain SM residue 353 GLU Chi-restraints excluded: chain SN residue 145 LEU Chi-restraints excluded: chain SN residue 183 GLU Chi-restraints excluded: chain SQ residue 48 MET Chi-restraints excluded: chain SR residue 12 VAL Chi-restraints excluded: chain SR residue 170 THR Chi-restraints excluded: chain SR residue 193 VAL Chi-restraints excluded: chain SR residue 207 VAL Chi-restraints excluded: chain SR residue 324 THR Chi-restraints excluded: chain SR residue 348 MET Chi-restraints excluded: chain SR residue 459 LEU Chi-restraints excluded: chain SS residue 136 VAL Chi-restraints excluded: chain SS residue 194 LEU Chi-restraints excluded: chain SS residue 228 SER Chi-restraints excluded: chain SS residue 349 SER Chi-restraints excluded: chain ST residue 210 THR Chi-restraints excluded: chain ST residue 228 SER Chi-restraints excluded: chain ST residue 257 LEU Chi-restraints excluded: chain SU residue 366 ILE Chi-restraints excluded: chain SU residue 606 CYS Chi-restraints excluded: chain SU residue 678 ASP Chi-restraints excluded: chain SV residue 1 MET Chi-restraints excluded: chain SV residue 65 VAL Chi-restraints excluded: chain SV residue 93 MET Chi-restraints excluded: chain SV residue 109 MET Chi-restraints excluded: chain SW residue 323 MET Chi-restraints excluded: chain SW residue 347 LEU Chi-restraints excluded: chain SY residue 508 THR Chi-restraints excluded: chain SZ residue 169 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1313 random chunks: chunk 827 optimal weight: 0.9980 chunk 1109 optimal weight: 10.0000 chunk 319 optimal weight: 0.9990 chunk 960 optimal weight: 0.0970 chunk 153 optimal weight: 7.9990 chunk 289 optimal weight: 0.3980 chunk 1043 optimal weight: 0.9990 chunk 436 optimal weight: 0.7980 chunk 1071 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 192 optimal weight: 20.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 115 GLN L7 180 GLN ** L9 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 93 HIS LA 116 HIS LH 57 GLN LI 14 ASN LL 70 GLN LS 65 GLN ** NA 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** NA 376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SE 64 GLN SG 140 GLN SG 162 GLN SG 163 GLN SI 113 GLN SJ 135 HIS ** SJ 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SL 53 ASN SL 112 GLN SL 133 GLN SR 342 HIS ** SR 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SS 208 GLN SS 238 ASN ** ST 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SU 232 ASN SV 101 GLN SV 110 ASN SY 268 ASN ** SY 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SZ 11 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.097090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.067435 restraints weight = 340282.059| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.67 r_work: 0.3013 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 147622 Z= 0.138 Angle : 0.477 16.526 211296 Z= 0.245 Chirality : 0.033 0.218 25540 Planarity : 0.004 0.090 17587 Dihedral : 21.377 179.355 51549 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.03 % Allowed : 13.26 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 1.86 (0.08), residues: 10694 helix: 2.45 (0.07), residues: 4887 sheet: 0.48 (0.14), residues: 1268 loop : 0.16 (0.09), residues: 4539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRPNI 732 HIS 0.009 0.001 HISLA 93 PHE 0.019 0.001 PHESW 233 TYR 0.024 0.001 TYRSR 92 ARG 0.019 0.000 ARGNF 125 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 50112.16 seconds wall clock time: 867 minutes 40.89 seconds (52060.89 seconds total)