Starting phenix.real_space_refine on Tue Mar 19 15:13:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkq_29253/03_2024/8fkq_29253_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkq_29253/03_2024/8fkq_29253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkq_29253/03_2024/8fkq_29253.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkq_29253/03_2024/8fkq_29253.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkq_29253/03_2024/8fkq_29253_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fkq_29253/03_2024/8fkq_29253_neut_updated.pdb" } resolution = 2.76 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= 0.141 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1786 5.49 5 Mg 51 5.21 5 S 232 5.16 5 C 52231 2.51 5 N 17545 2.21 5 O 21958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L6 GLU 79": "OE1" <-> "OE2" Residue "L7 GLU 39": "OE1" <-> "OE2" Residue "L7 PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L7 GLU 144": "OE1" <-> "OE2" Residue "L7 TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L7 ASP 190": "OD1" <-> "OD2" Residue "L8 PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L8 ASP 32": "OD1" <-> "OD2" Residue "L8 ASP 81": "OD1" <-> "OD2" Residue "L8 GLU 96": "OE1" <-> "OE2" Residue "L9 TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L9 TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L9 PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L9 GLU 103": "OE1" <-> "OE2" Residue "L9 GLU 123": "OE1" <-> "OE2" Residue "L9 ASP 147": "OD1" <-> "OD2" Residue "LA PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA GLU 89": "OE1" <-> "OE2" Residue "LA GLU 115": "OE1" <-> "OE2" Residue "LA GLU 154": "OE1" <-> "OE2" Residue "LB GLU 17": "OE1" <-> "OE2" Residue "LB GLU 76": "OE1" <-> "OE2" Residue "LB ASP 89": "OD1" <-> "OD2" Residue "LC TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC ASP 99": "OD1" <-> "OD2" Residue "LC TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC GLU 130": "OE1" <-> "OE2" Residue "LE ASP 113": "OD1" <-> "OD2" Residue "LE GLU 137": "OE1" <-> "OE2" Residue "LG ASP 59": "OD1" <-> "OD2" Residue "LG TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG GLU 99": "OE1" <-> "OE2" Residue "LI GLU 54": "OE1" <-> "OE2" Residue "LI GLU 88": "OE1" <-> "OE2" Residue "LI ASP 114": "OD1" <-> "OD2" Residue "LI GLU 120": "OE1" <-> "OE2" Residue "LK PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LL GLU 28": "OE1" <-> "OE2" Residue "LN PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN GLU 140": "OE1" <-> "OE2" Residue "LN ASP 306": "OD1" <-> "OD2" Residue "LN ASP 308": "OD1" <-> "OD2" Residue "LN ASP 395": "OD1" <-> "OD2" Residue "LQ ASP 42": "OD1" <-> "OD2" Residue "LQ GLU 86": "OE1" <-> "OE2" Residue "LQ TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS GLU 16": "OE1" <-> "OE2" Residue "LS GLU 67": "OE1" <-> "OE2" Residue "LT GLU 40": "OE1" <-> "OE2" Residue "LU GLU 46": "OE1" <-> "OE2" Residue "LU PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LW TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NE GLU 278": "OE1" <-> "OE2" Residue "NE GLU 297": "OE1" <-> "OE2" Residue "NG GLU 143": "OE1" <-> "OE2" Residue "NG ASP 151": "OD1" <-> "OD2" Residue "NG ASP 155": "OD1" <-> "OD2" Residue "NG ASP 209": "OD1" <-> "OD2" Residue "NN ASP 72": "OD1" <-> "OD2" Residue "NN ASP 120": "OD1" <-> "OD2" Residue "NN ASP 184": "OD1" <-> "OD2" Residue "NN ASP 193": "OD1" <-> "OD2" Residue "NN GLU 288": "OE1" <-> "OE2" Residue "SA PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA GLU 145": "OE1" <-> "OE2" Residue "SA ASP 156": "OD1" <-> "OD2" Residue "SA ASP 214": "OD1" <-> "OD2" Residue "SA PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA ASP 261": "OD1" <-> "OD2" Residue "SC TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SC GLU 119": "OE1" <-> "OE2" Residue "SC ASP 214": "OD1" <-> "OD2" Residue "SC TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SD TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SD GLU 68": "OE1" <-> "OE2" Residue "SD ASP 171": "OD1" <-> "OD2" Residue "SD ASP 189": "OD1" <-> "OD2" Residue "SD GLU 229": "OE1" <-> "OE2" Residue "SD GLU 237": "OE1" <-> "OE2" Residue "SD ASP 238": "OD1" <-> "OD2" Residue "SE GLU 119": "OE1" <-> "OE2" Residue "SE ASP 162": "OD1" <-> "OD2" Residue "SE GLU 165": "OE1" <-> "OE2" Residue "SE PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SE PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SE ASP 228": "OD1" <-> "OD2" Residue "SH PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SH PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SH TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SH ASP 184": "OD1" <-> "OD2" Residue "SI GLU 62": "OE1" <-> "OE2" Residue "SI ASP 67": "OD1" <-> "OD2" Residue "SI GLU 89": "OE1" <-> "OE2" Residue "SI ASP 178": "OD1" <-> "OD2" Residue "SI ASP 196": "OD1" <-> "OD2" Residue "SI PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SI PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SJ ASP 697": "OD1" <-> "OD2" Residue "SJ GLU 698": "OE1" <-> "OE2" Residue "SJ GLU 708": "OE1" <-> "OE2" Residue "SK GLU 8": "OE1" <-> "OE2" Residue "SK ASP 90": "OD1" <-> "OD2" Residue "SK GLU 168": "OE1" <-> "OE2" Residue "SK GLU 172": "OE1" <-> "OE2" Residue "SK GLU 191": "OE1" <-> "OE2" Residue "SL GLU 34": "OE1" <-> "OE2" Residue "SL PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SL ASP 101": "OD1" <-> "OD2" Residue "SL PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SL ASP 153": "OD1" <-> "OD2" Residue "SL GLU 193": "OE1" <-> "OE2" Residue "SL GLU 243": "OE1" <-> "OE2" Residue "SL GLU 246": "OE1" <-> "OE2" Residue "SM ASP 33": "OD1" <-> "OD2" Residue "SM TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM GLU 105": "OE1" <-> "OE2" Residue "SM ASP 117": "OD1" <-> "OD2" Residue "SM TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM GLU 311": "OE1" <-> "OE2" Residue "SM GLU 353": "OE1" <-> "OE2" Residue "SN ASP 63": "OD1" <-> "OD2" Residue "SN GLU 68": "OE1" <-> "OE2" Residue "SN ASP 100": "OD1" <-> "OD2" Residue "SN ASP 135": "OD1" <-> "OD2" Residue "SO GLU 60": "OE1" <-> "OE2" Residue "SO PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SO GLU 183": "OE1" <-> "OE2" Residue "SO ASP 348": "OD1" <-> "OD2" Residue "SR ASP 369": "OD1" <-> "OD2" Residue "SR GLU 379": "OE1" <-> "OE2" Residue "SR TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR GLU 424": "OE1" <-> "OE2" Residue "SR TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR GLU 454": "OE1" <-> "OE2" Residue "SS GLU 129": "OE1" <-> "OE2" Residue "SS GLU 142": "OE1" <-> "OE2" Residue "SS ASP 146": "OD1" <-> "OD2" Residue "SS ASP 198": "OD1" <-> "OD2" Residue "SS GLU 199": "OE1" <-> "OE2" Residue "SS PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SS PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SS TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SS TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "ST GLU 237": "OE1" <-> "OE2" Residue "SV GLU 4": "OE1" <-> "OE2" Residue "SV TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SV ASP 25": "OD1" <-> "OD2" Residue "SV PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SV GLU 70": "OE1" <-> "OE2" Residue "SV ASP 91": "OD1" <-> "OD2" Residue "SV GLU 98": "OE1" <-> "OE2" Residue "SV PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SV ASP 123": "OD1" <-> "OD2" Residue "SW GLU 262": "OE1" <-> "OE2" Residue "SW TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW GLU 334": "OE1" <-> "OE2" Residue "SW PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SW GLU 581": "OE1" <-> "OE2" Residue "SW PHE 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SZ ASP 44": "OD1" <-> "OD2" Residue "SZ ASP 61": "OD1" <-> "OD2" Residue "SZ ASP 96": "OD1" <-> "OD2" Residue "SZ GLU 105": "OE1" <-> "OE2" Residue "SZ ASP 136": "OD1" <-> "OD2" Residue "SZ ASP 168": "OD1" <-> "OD2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 93805 Number of models: 1 Model: "" Number of chains: 52 Chain: "L1" Number of atoms: 3189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3189 Classifications: {'RNA': 150} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 11, 'rna3p_pur': 59, 'rna3p_pyr': 66} Link IDs: {'rna2p': 24, 'rna3p': 125} Chain breaks: 2 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: 33557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1565, 33557 Classifications: {'RNA': 1565} Modifications used: {'rna2p_pur': 159, 'rna2p_pyr': 99, 'rna3p_pur': 691, 'rna3p_pyr': 616} Link IDs: {'rna2p': 258, 'rna3p': 1306} Chain breaks: 32 Chain: "L6" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 936 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 104} Chain: "L7" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1507 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 176} Chain breaks: 1 Chain: "L8" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1111 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain: "L9" Number of atoms: 1553 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 183, 1546 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 176} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 183, 1546 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 176} Chain breaks: 1 bond proxies already assigned to first conformer: 1575 Chain: "LA" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 981 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain breaks: 2 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: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1431 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 161} Chain: "LE" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 702 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain breaks: 2 Unresolved non-hydrogen bonds: 186 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 4, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 83 Chain: "LG" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 844 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain breaks: 1 Chain: "LH" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 146 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} 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: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3044 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 13, 'TRANS': 363} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 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: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 563 Classifications: {'peptide': 69} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 65} Chain breaks: 1 Chain: "NE" Number of atoms: 1331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1331 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain breaks: 1 Chain: "NG" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 738 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 1, 'TRANS': 87} Chain: "NN" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1950 Classifications: {'peptide': 244} Link IDs: {'PCIS': 4, 'PTRANS': 9, 'TRANS': 230} Chain breaks: 2 Chain: "SA" Number of atoms: 2645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2645 Classifications: {'peptide': 329} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 311} Chain breaks: 1 Chain: "SC" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1692 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 197} Chain breaks: 2 Chain: "SD" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1755 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain: "SE" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1498 Classifications: {'peptide': 186} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 175} 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: 1661 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 199, 1650 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 189} Conformer: "B" Number of residues, atoms: 199, 1650 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 189} bond proxies already assigned to first conformer: 1672 Chain: "SJ" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 609 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "SK" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1721 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 6, 'TRANS': 219} 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: 3452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3452 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 416} Chain breaks: 4 Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 90 Chain: "SN" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1308 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 160} Chain breaks: 2 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: "SR" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 642 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 6, 'TRANS': 70} Chain breaks: 1 Chain: "SS" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1955 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 25, 'TRANS': 209} Chain breaks: 2 Chain: "ST" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 263 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} 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: 3560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3560 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 19, 'TRANS': 425} Chain breaks: 1 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Unusual residues: {' MG': 42} Classifications: {'undetermined': 42} Link IDs: {None: 41} 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: "SA" 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 58260 SG CYSLW 19 100.085 126.404 147.581 1.00 56.13 S ATOM 58288 SG CYSLW 22 100.771 123.523 149.988 1.00 52.21 S ATOM 58379 SG CYSLW 34 102.648 126.781 150.371 1.00 56.45 S ATOM 58398 SG CYSLW 37 103.434 124.637 147.405 1.00 52.97 S ATOM 87734 SG CYSSV 6 57.494 190.380 249.863 1.00 34.10 S ATOM 87763 SG CYSSV 9 54.123 188.757 249.274 1.00 38.42 S ATOM 87947 SG CYSSV 32 57.141 186.549 249.114 1.00 31.84 S ATOM 87977 SG CYSSV 36 56.601 189.013 246.390 1.00 35.61 S Time building chain proxies: 37.50, per 1000 atoms: 0.40 Number of scatterers: 93805 At special positions: 0 Unit cell: (212.256, 234.768, 319.456, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 232 16.00 P 1786 15.00 Mg 51 11.99 O 21958 8.00 N 17545 7.00 C 52231 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: 35.08 Conformation dependent library (CDL) restraints added in 8.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNLW 500 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 34 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 37 " 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 32 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 36 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 6 " Number of angles added : 12 13484 Ramachandran restraints generated. 6742 Oldfield, 0 Emsley, 6742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13016 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 258 helices and 56 sheets defined 40.6% alpha, 11.1% beta 581 base pairs and 846 stacking pairs defined. Time for finding SS restraints: 36.63 Creating SS restraints... Processing helix chain 'L6' and resid 28 through 45 Processing helix chain 'L6' and resid 78 through 84 Processing helix chain 'L6' and resid 88 through 94 removed outlier: 4.211A pdb=" N ARGL6 92 " --> pdb=" O LYSL6 88 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THRL6 93 " --> pdb=" O LYSL6 89 " (cutoff:3.500A) Processing helix chain 'L6' and resid 107 through 122 Processing helix chain 'L7' and resid 16 through 29 Processing helix chain 'L7' and resid 38 through 40 No H-bonds generated for 'chain 'L7' and resid 38 through 40' Processing helix chain 'L7' and resid 47 through 55 Processing helix chain 'L7' and resid 76 through 86 Processing helix chain 'L7' and resid 93 through 100 Processing helix chain 'L7' and resid 112 through 114 No H-bonds generated for 'chain 'L7' and resid 112 through 114' Processing helix chain 'L7' and resid 121 through 123 No H-bonds generated for 'chain 'L7' and resid 121 through 123' Processing helix chain 'L7' and resid 125 through 128 No H-bonds generated for 'chain 'L7' and resid 125 through 128' Processing helix chain 'L7' and resid 138 through 145 Processing helix chain 'L7' and resid 150 through 198 removed outlier: 3.535A pdb=" N VALL7 185 " --> pdb=" O ALAL7 181 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLUL7 186 " --> pdb=" O GLUL7 182 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LYSL7 187 " --> pdb=" O LYSL7 183 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYSL7 188 " --> pdb=" O ASNL7 184 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N LYSL7 191 " --> pdb=" O LYSL7 187 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TYRL7 192 " --> pdb=" O LYSL7 188 " (cutoff:3.500A) Processing helix chain 'L8' and resid 70 through 80 Processing helix chain 'L8' and resid 82 through 88 Processing helix chain 'L8' and resid 90 through 103 Processing helix chain 'L8' and resid 106 through 135 Processing helix chain 'L9' and resid 3 through 12 Processing helix chain 'L9' and resid 17 through 32 Processing helix chain 'L9' and resid 45 through 50 Processing helix chain 'L9' and resid 98 through 109 Processing helix chain 'L9' and resid 140 through 143 No H-bonds generated for 'chain 'L9' and resid 140 through 143' Processing helix chain 'L9' and resid 146 through 152 removed outlier: 4.513A pdb=" N TRPL9 150 " --> pdb=" O ASPL9 147 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILEL9 151 " --> pdb=" O THRL9 148 " (cutoff:3.500A) Processing helix chain 'L9' and resid 154 through 156 No H-bonds generated for 'chain 'L9' and resid 154 through 156' Processing helix chain 'L9' and resid 166 through 172 removed outlier: 4.034A pdb=" N SERL9 171 " --> pdb=" O ALAL9 167 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARGL9 172 " --> pdb=" O GLYL9 168 " (cutoff:3.500A) Processing helix chain 'L9' and resid 178 through 183 removed outlier: 3.719A pdb=" N HISL9 181 " --> pdb=" O HISL9 178 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N HISL9 182 " --> pdb=" O LYSL9 179 " (cutoff:3.500A) Processing helix chain 'L9' and resid 188 through 196 Processing helix chain 'LA' and resid 26 through 36 Processing helix chain 'LA' and resid 41 through 53 Processing helix chain 'LA' and resid 85 through 105 Processing helix chain 'LB' and resid 23 through 38 Processing helix chain 'LB' and resid 42 through 52 removed outlier: 3.541A pdb=" N PHELB 52 " --> pdb=" O LEULB 48 " (cutoff:3.500A) Processing helix chain 'LB' and resid 63 through 70 Processing helix chain 'LB' and resid 107 through 115 Processing helix chain 'LB' and resid 123 through 129 Processing helix chain 'LB' and resid 147 through 151 removed outlier: 3.605A pdb=" N HISLB 151 " --> pdb=" O GLULB 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'LB' and resid 147 through 151' Processing helix chain 'LC' and resid 37 through 51 Processing helix chain 'LC' and resid 102 through 116 Processing helix chain 'LC' and resid 140 through 145 removed outlier: 4.290A pdb=" N PHELC 145 " --> pdb=" O ALALC 141 " (cutoff:3.500A) Processing helix chain 'LE' and resid 101 through 120 removed outlier: 4.537A pdb=" N PHELE 105 " --> pdb=" O SERLE 101 " (cutoff:3.500A) Processing helix chain 'LG' and resid 70 through 72 No H-bonds generated for 'chain 'LG' and resid 70 through 72' Processing helix chain 'LG' and resid 123 through 128 Processing helix chain 'LG' and resid 130 through 135 removed outlier: 3.833A pdb=" N ASNLG 135 " --> pdb=" O ARGLG 131 " (cutoff:3.500A) Processing helix chain 'LH' and resid 15 through 30 Processing helix chain 'LI' and resid 11 through 19 Processing helix chain 'LI' and resid 23 through 29 removed outlier: 3.572A pdb=" N LYSLI 28 " --> pdb=" O HISLI 24 " (cutoff:3.500A) Processing helix chain 'LI' and resid 36 through 42 Processing helix chain 'LI' and resid 75 through 77 No H-bonds generated for 'chain 'LI' and resid 75 through 77' Processing helix chain 'LI' and resid 101 through 103 No H-bonds generated for 'chain 'LI' and resid 101 through 103' Processing helix chain 'LI' and resid 113 through 133 Processing helix chain 'LK' and resid 7 through 10 No H-bonds generated for 'chain 'LK' and resid 7 through 10' Processing helix chain 'LK' and resid 61 through 65 Processing helix chain 'LK' and resid 75 through 81 Processing helix chain 'LK' and resid 84 through 92 Processing helix chain 'LK' and resid 131 through 139 Processing helix chain 'LL' and resid 3 through 10 Processing helix chain 'LL' and resid 73 through 75 No H-bonds generated for 'chain 'LL' and resid 73 through 75' Processing helix chain 'LL' and resid 86 through 98 Processing helix chain 'LL' and resid 104 through 121 removed outlier: 5.210A pdb=" N METLL 108 " --> pdb=" O ASPLL 105 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALALL 109 " --> pdb=" O LEULL 106 " (cutoff:3.500A) Processing helix chain 'LN' and resid 112 through 118 removed outlier: 4.255A pdb=" N ARGLN 117 " --> pdb=" O GLULN 113 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHELN 118 " --> pdb=" O CYSLN 114 " (cutoff:3.500A) Processing helix chain 'LN' and resid 134 through 138 removed outlier: 3.526A pdb=" N GLNLN 138 " --> pdb=" O LYSLN 135 " (cutoff:3.500A) Processing helix chain 'LN' and resid 140 through 156 Processing helix chain 'LN' and resid 168 through 170 No H-bonds generated for 'chain 'LN' and resid 168 through 170' Processing helix chain 'LN' and resid 190 through 200 Processing helix chain 'LN' and resid 207 through 210 No H-bonds generated for 'chain 'LN' and resid 207 through 210' Processing helix chain 'LN' and resid 237 through 239 No H-bonds generated for 'chain 'LN' and resid 237 through 239' Processing helix chain 'LN' and resid 248 through 250 No H-bonds generated for 'chain 'LN' and resid 248 through 250' Processing helix chain 'LN' and resid 382 through 389 Processing helix chain 'LN' and resid 393 through 402 Processing helix chain 'LQ' and resid 44 through 47 No H-bonds generated for 'chain 'LQ' and resid 44 through 47' Processing helix chain 'LQ' and resid 58 through 60 No H-bonds generated for 'chain 'LQ' and resid 58 through 60' Processing helix chain 'LQ' and resid 82 through 91 removed outlier: 4.020A pdb=" N VALLQ 87 " --> pdb=" O LYSLQ 83 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEULQ 88 " --> pdb=" O GLULQ 84 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEULQ 89 " --> pdb=" O LEULQ 85 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N METLQ 90 " --> pdb=" O GLULQ 86 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N CYSLQ 91 " --> pdb=" O VALLQ 87 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 105 through 118 Processing helix chain 'LS' and resid 6 through 9 No H-bonds generated for 'chain 'LS' and resid 6 through 9' Processing helix chain 'LS' and resid 14 through 36 Processing helix chain 'LS' and resid 41 through 73 removed outlier: 4.001A pdb=" N ARGLS 48 " --> pdb=" O LEULS 44 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VALLS 49 " --> pdb=" O SERLS 45 " (cutoff:3.500A) Processing helix chain 'LS' and resid 89 through 92 No H-bonds generated for 'chain 'LS' and resid 89 through 92' Processing helix chain 'LS' and resid 97 through 100 No H-bonds generated for 'chain 'LS' and resid 97 through 100' Processing helix chain 'LS' and resid 105 through 113 Processing helix chain 'LT' and resid 36 through 42 removed outlier: 3.586A pdb=" N GLULT 40 " --> pdb=" O ASPLT 37 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHELT 41 " --> pdb=" O GLULT 38 " (cutoff:3.500A) Processing helix chain 'LT' and resid 94 through 96 No H-bonds generated for 'chain 'LT' and resid 94 through 96' Processing helix chain 'LU' and resid 26 through 29 Processing helix chain 'LU' and resid 35 through 48 Processing helix chain 'LU' and resid 52 through 62 Processing helix chain 'LU' and resid 66 through 77 Processing helix chain 'LU' and resid 80 through 102 Processing helix chain 'LW' and resid 52 through 57 removed outlier: 3.544A pdb=" N ASNLW 57 " --> pdb=" O ALALW 53 " (cutoff:3.500A) Processing helix chain 'LW' and resid 67 through 76 removed outlier: 3.713A pdb=" N ARGLW 75 " --> pdb=" O TYRLW 71 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N HISLW 76 " --> pdb=" O ARGLW 72 " (cutoff:3.500A) Processing helix chain 'NE' and resid 213 through 223 Processing helix chain 'NE' and resid 236 through 256 Processing helix chain 'NE' and resid 258 through 278 removed outlier: 4.021A pdb=" N LYSNE 269 " --> pdb=" O GLUNE 265 " (cutoff:3.500A) Processing helix chain 'NE' and resid 286 through 347 removed outlier: 3.517A pdb=" N LYSNE 309 " --> pdb=" O ARGNE 305 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARGNE 310 " --> pdb=" O ARGNE 306 " (cutoff:3.500A) Processing helix chain 'NE' and resid 352 through 356 Processing helix chain 'NG' and resid 128 through 142 Processing helix chain 'NG' and resid 156 through 191 Processing helix chain 'NG' and resid 195 through 204 Processing helix chain 'NG' and resid 207 through 214 Processing helix chain 'NN' and resid 8 through 27 Processing helix chain 'NN' and resid 41 through 53 Processing helix chain 'NN' and resid 70 through 80 removed outlier: 3.818A pdb=" N GLYNN 78 " --> pdb=" O VALNN 74 " (cutoff:3.500A) Proline residue: NN 79 - end of helix Processing helix chain 'NN' and resid 118 through 124 Processing helix chain 'NN' and resid 134 through 136 No H-bonds generated for 'chain 'NN' and resid 134 through 136' Processing helix chain 'NN' and resid 151 through 163 Processing helix chain 'SA' and resid 26 through 29 Processing helix chain 'SA' and resid 34 through 46 removed outlier: 3.936A pdb=" N LYSSA 46 " --> pdb=" O THRSA 42 " (cutoff:3.500A) Processing helix chain 'SA' and resid 117 through 132 removed outlier: 3.643A pdb=" N ALASA 132 " --> pdb=" O LEUSA 128 " (cutoff:3.500A) Processing helix chain 'SA' and resid 134 through 140 Processing helix chain 'SA' and resid 156 through 160 Processing helix chain 'SA' and resid 164 through 173 Processing helix chain 'SA' and resid 177 through 186 Processing helix chain 'SA' and resid 193 through 197 Processing helix chain 'SA' and resid 217 through 221 Processing helix chain 'SA' and resid 237 through 240 No H-bonds generated for 'chain 'SA' and resid 237 through 240' Processing helix chain 'SA' and resid 254 through 264 removed outlier: 3.696A pdb=" N LEUSA 260 " --> pdb=" O ALASA 256 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ASPSA 261 " --> pdb=" O PHESA 257 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLUSA 262 " --> pdb=" O ARGSA 258 " (cutoff:3.500A) Processing helix chain 'SA' and resid 289 through 293 Processing helix chain 'SA' and resid 296 through 301 removed outlier: 3.837A pdb=" N ALASA 301 " --> pdb=" O GLUSA 297 " (cutoff:3.500A) Processing helix chain 'SA' and resid 322 through 328 Processing helix chain 'SA' and resid 330 through 360 removed outlier: 3.547A pdb=" N ARGSA 337 " --> pdb=" O THRSA 334 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLNSA 343 " --> pdb=" O ILESA 340 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HISSA 347 " --> pdb=" O ALASA 344 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYSSA 353 " --> pdb=" O ARGSA 350 " (cutoff:3.500A) Processing helix chain 'SC' and resid 59 through 66 Processing helix chain 'SC' and resid 133 through 135 No H-bonds generated for 'chain 'SC' and resid 133 through 135' Processing helix chain 'SC' and resid 179 through 182 No H-bonds generated for 'chain 'SC' and resid 179 through 182' Processing helix chain 'SC' and resid 191 through 193 No H-bonds generated for 'chain 'SC' and resid 191 through 193' Processing helix chain 'SC' and resid 214 through 217 No H-bonds generated for 'chain 'SC' and resid 214 through 217' Processing helix chain 'SC' and resid 244 through 263 removed outlier: 3.950A pdb=" N GLNSC 256 " --> pdb=" O ALASC 252 " (cutoff:3.500A) Proline residue: SC 259 - end of helix Processing helix chain 'SC' and resid 267 through 272 Processing helix chain 'SD' and resid 38 through 77 removed outlier: 3.585A pdb=" N ILESD 69 " --> pdb=" O TYRSD 65 " (cutoff:3.500A) Processing helix chain 'SD' and resid 103 through 111 Processing helix chain 'SD' and resid 127 through 135 removed outlier: 3.523A pdb=" N METSD 132 " --> pdb=" O ALASD 128 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILESD 135 " --> pdb=" O ASNSD 131 " (cutoff:3.500A) Processing helix chain 'SD' and resid 137 through 139 No H-bonds generated for 'chain 'SD' and resid 137 through 139' Processing helix chain 'SD' and resid 147 through 157 Processing helix chain 'SD' and resid 172 through 182 removed outlier: 3.603A pdb=" N SERSD 178 " --> pdb=" O LEUSD 174 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LYSSD 181 " --> pdb=" O ARGSD 177 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N TYRSD 182 " --> pdb=" O SERSD 178 " (cutoff:3.500A) Processing helix chain 'SD' and resid 187 through 195 Processing helix chain 'SD' and resid 201 through 207 Processing helix chain 'SD' and resid 227 through 229 No H-bonds generated for 'chain 'SD' and resid 227 through 229' Processing helix chain 'SD' and resid 240 through 247 Processing helix chain 'SE' and resid 59 through 73 removed outlier: 3.681A pdb=" N ALASE 68 " --> pdb=" O GLNSE 64 " (cutoff:3.500A) Processing helix chain 'SE' and resid 78 through 83 removed outlier: 4.566A pdb=" N PHESE 83 " --> pdb=" O ALASE 79 " (cutoff:3.500A) Processing helix chain 'SE' and resid 89 through 102 removed outlier: 3.635A pdb=" N LYSSE 101 " --> pdb=" O LYSSE 97 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYRSE 102 " --> pdb=" O LEUSE 98 " (cutoff:3.500A) Processing helix chain 'SE' and resid 107 through 123 Processing helix chain 'SE' and resid 140 through 148 Processing helix chain 'SE' and resid 164 through 166 No H-bonds generated for 'chain 'SE' and resid 164 through 166' Processing helix chain 'SE' and resid 168 through 177 removed outlier: 4.610A pdb=" N ALASE 172 " --> pdb=" O VALSE 168 " (cutoff:3.500A) Processing helix chain 'SE' and resid 187 through 193 removed outlier: 3.511A pdb=" N LEUSE 193 " --> pdb=" O ARGSE 189 " (cutoff:3.500A) Processing helix chain 'SE' and resid 209 through 225 removed outlier: 3.723A pdb=" N LYSSE 212 " --> pdb=" O SERSE 209 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLYSE 213 " --> pdb=" O GLUSE 210 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEUSE 215 " --> pdb=" O LYSSE 212 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLUSE 220 " --> pdb=" O LYSSE 217 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILESE 222 " --> pdb=" O VALSE 219 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASNSE 225 " --> pdb=" O ILESE 222 " (cutoff:3.500A) Processing helix chain 'SH' and resid 58 through 68 removed outlier: 3.793A pdb=" N GLNSH 67 " --> pdb=" O SERSH 63 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHESH 68 " --> pdb=" O TYRSH 64 " (cutoff:3.500A) Processing helix chain 'SH' and resid 96 through 106 Processing helix chain 'SH' and resid 144 through 150 Processing helix chain 'SH' and resid 155 through 179 Processing helix chain 'SI' and resid 61 through 81 Processing helix chain 'SI' and resid 110 through 118 Processing helix chain 'SI' and resid 134 through 142 Processing helix chain 'SI' and resid 144 through 146 No H-bonds generated for 'chain 'SI' and resid 144 through 146' Processing helix chain 'SI' and resid 154 through 164 Processing helix chain 'SI' and resid 179 through 186 Processing helix chain 'SI' and resid 194 through 202 Processing helix chain 'SI' and resid 208 through 214 Processing helix chain 'SI' and resid 226 through 228 No H-bonds generated for 'chain 'SI' and resid 226 through 228' Processing helix chain 'SI' and resid 230 through 237 Processing helix chain 'SI' and resid 244 through 254 removed outlier: 3.564A pdb=" N ARGSI 252 " --> pdb=" O GLNSI 249 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 665 through 676 Processing helix chain 'SJ' and resid 678 through 688 Processing helix chain 'SJ' and resid 703 through 712 removed outlier: 3.753A pdb=" N GLNSJ 711 " --> pdb=" O GLNSJ 707 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HISSJ 712 " --> pdb=" O GLUSJ 708 " (cutoff:3.500A) Processing helix chain 'SJ' and resid 721 through 730 Processing helix chain 'SK' and resid 13 through 16 No H-bonds generated for 'chain 'SK' and resid 13 through 16' Processing helix chain 'SK' and resid 33 through 42 removed outlier: 3.890A pdb=" N PHESK 38 " --> pdb=" O PHESK 34 " (cutoff:3.500A) Processing helix chain 'SK' and resid 59 through 62 No H-bonds generated for 'chain 'SK' and resid 59 through 62' Processing helix chain 'SK' and resid 78 through 87 Processing helix chain 'SK' and resid 104 through 107 No H-bonds generated for 'chain 'SK' and resid 104 through 107' Processing helix chain 'SK' and resid 123 through 133 Processing helix chain 'SK' and resid 148 through 151 No H-bonds generated for 'chain 'SK' and resid 148 through 151' Processing helix chain 'SK' and resid 167 through 177 removed outlier: 3.706A pdb=" N LEUSK 176 " --> pdb=" O GLUSK 172 " (cutoff:3.500A) Processing helix chain 'SK' and resid 193 through 196 No H-bonds generated for 'chain 'SK' and resid 193 through 196' Processing helix chain 'SK' and resid 212 through 221 Processing helix chain 'SL' and resid 33 through 49 Processing helix chain 'SL' and resid 107 through 120 Processing helix chain 'SL' and resid 132 through 138 Processing helix chain 'SL' and resid 142 through 151 Processing helix chain 'SL' and resid 159 through 164 removed outlier: 3.648A pdb=" N ARGSL 162 " --> pdb=" O ALASL 159 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ARGSL 163 " --> pdb=" O ARGSL 160 " (cutoff:3.500A) Processing helix chain 'SL' and resid 166 through 169 No H-bonds generated for 'chain 'SL' and resid 166 through 169' Processing helix chain 'SL' and resid 171 through 175 Processing helix chain 'SL' and resid 190 through 199 Processing helix chain 'SL' and resid 223 through 240 removed outlier: 3.512A pdb=" N GLUSL 239 " --> pdb=" O LYSSL 235 " (cutoff:3.500A) Processing helix chain 'SM' and resid 20 through 27 Processing helix chain 'SM' and resid 31 through 41 Processing helix chain 'SM' and resid 67 through 75 removed outlier: 4.072A pdb=" N HISSM 75 " --> pdb=" O ARGSM 71 " (cutoff:3.500A) Processing helix chain 'SM' and resid 77 through 97 removed outlier: 3.649A pdb=" N VALSM 89 " --> pdb=" O LYSSM 86 " (cutoff:3.500A) Processing helix chain 'SM' and resid 101 through 109 Processing helix chain 'SM' and resid 117 through 123 Processing helix chain 'SM' and resid 127 through 146 removed outlier: 3.684A pdb=" N ASPSM 133 " --> pdb=" O ASPSM 129 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEUSM 134 " --> pdb=" O ALASM 130 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ASPSM 135 " --> pdb=" O LEUSM 131 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASPSM 136 " --> pdb=" O ARGSM 132 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALASM 137 " --> pdb=" O ASPSM 133 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THRSM 146 " --> pdb=" O PHESM 142 " (cutoff:3.500A) Processing helix chain 'SM' and resid 155 through 175 Processing helix chain 'SM' and resid 217 through 242 removed outlier: 3.791A pdb=" N LEUSM 242 " --> pdb=" O LEUSM 238 " (cutoff:3.500A) Processing helix chain 'SM' and resid 271 through 278 Processing helix chain 'SM' and resid 308 through 325 removed outlier: 3.678A pdb=" N GLUSM 316 " --> pdb=" O ASPSM 312 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLUSM 321 " --> pdb=" O LEUSM 317 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYSSM 322 " --> pdb=" O GLUSM 318 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYSSM 325 " --> pdb=" O GLUSM 321 " (cutoff:3.500A) Processing helix chain 'SM' and resid 340 through 350 removed outlier: 3.634A pdb=" N PHESM 350 " --> pdb=" O ILESM 346 " (cutoff:3.500A) Processing helix chain 'SM' and resid 395 through 404 removed outlier: 3.609A pdb=" N ASPSM 400 " --> pdb=" O TRPSM 397 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SERSM 401 " --> pdb=" O VALSM 398 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALASM 404 " --> pdb=" O SERSM 401 " (cutoff:3.500A) Processing helix chain 'SM' and resid 437 through 447 Processing helix chain 'SM' and resid 542 through 585 Processing helix chain 'SN' and resid 20 through 28 Processing helix chain 'SN' and resid 50 through 60 Processing helix chain 'SN' and resid 66 through 69 No H-bonds generated for 'chain 'SN' and resid 66 through 69' Processing helix chain 'SN' and resid 101 through 126 Proline residue: SN 121 - end of helix Processing helix chain 'SN' and resid 144 through 175 Processing helix chain 'SN' and resid 240 through 248 Processing helix chain 'SN' and resid 262 through 265 No H-bonds generated for 'chain 'SN' and resid 262 through 265' Processing helix chain 'SO' and resid 72 through 84 Processing helix chain 'SO' and resid 100 through 110 removed outlier: 3.555A pdb=" N METSO 109 " --> pdb=" O VALSO 106 " (cutoff:3.500A) Processing helix chain 'SO' and resid 170 through 174 Processing helix chain 'SO' and resid 176 through 189 removed outlier: 3.531A pdb=" N GLUSO 183 " --> pdb=" O ALASO 179 " (cutoff:3.500A) Processing helix chain 'SO' and resid 262 through 291 removed outlier: 3.526A pdb=" N ARGSO 266 " --> pdb=" O PROSO 262 " (cutoff:3.500A) Processing helix chain 'SO' and resid 338 through 352 Processing helix chain 'SR' and resid 413 through 416 No H-bonds generated for 'chain 'SR' and resid 413 through 416' Processing helix chain 'SR' and resid 422 through 426 removed outlier: 4.164A pdb=" N HISSR 426 " --> pdb=" O SERSR 423 " (cutoff:3.500A) Processing helix chain 'SR' and resid 438 through 441 No H-bonds generated for 'chain 'SR' and resid 438 through 441' Processing helix chain 'SR' and resid 446 through 463 removed outlier: 3.817A pdb=" N LYSSR 455 " --> pdb=" O GLUSR 451 " (cutoff:3.500A) Processing helix chain 'SS' and resid 143 through 145 No H-bonds generated for 'chain 'SS' and resid 143 through 145' Processing helix chain 'SS' and resid 198 through 209 Processing helix chain 'SS' and resid 250 through 265 Processing helix chain 'SS' and resid 324 through 332 Processing helix chain 'SS' and resid 350 through 352 No H-bonds generated for 'chain 'SS' and resid 350 through 352' Processing helix chain 'SS' and resid 359 through 372 removed outlier: 3.753A pdb=" N TYRSS 371 " --> pdb=" O CYSSS 367 " (cutoff:3.500A) Processing helix chain 'ST' and resid 215 through 227 removed outlier: 3.538A pdb=" N GLNST 223 " --> pdb=" O GLYST 219 " (cutoff:3.500A) Processing helix chain 'SV' and resid 34 through 41 Processing helix chain 'SV' and resid 53 through 58 Processing helix chain 'SV' and resid 67 through 71 removed outlier: 3.831A pdb=" N PHESV 71 " --> pdb=" O ASNSV 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'SV' and resid 67 through 71' Processing helix chain 'SV' and resid 83 through 129 removed outlier: 3.781A pdb=" N ASNSV 115 " --> pdb=" O ARGSV 111 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LYSSV 116 " --> pdb=" O LEUSV 112 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLUSV 117 " --> pdb=" O LYSSV 113 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYSSV 128 " --> pdb=" O ILESV 124 " (cutoff:3.500A) Processing helix chain 'SV' and resid 131 through 134 No H-bonds generated for 'chain 'SV' and resid 131 through 134' Processing helix chain 'SW' and resid 179 through 182 Processing helix chain 'SW' and resid 188 through 197 removed outlier: 3.545A pdb=" N LYSSW 192 " --> pdb=" O GLUSW 188 " (cutoff:3.500A) Processing helix chain 'SW' and resid 204 through 215 removed outlier: 4.679A pdb=" N ARGSW 211 " --> pdb=" O HISSW 207 " (cutoff:3.500A) Proline residue: SW 212 - end of helix Processing helix chain 'SW' and resid 229 through 243 removed outlier: 3.652A pdb=" N PHESW 233 " --> pdb=" O LYSSW 229 " (cutoff:3.500A) Proline residue: SW 236 - end of helix Processing helix chain 'SW' and resid 261 through 276 removed outlier: 3.758A pdb=" N THRSW 276 " --> pdb=" O LYSSW 272 " (cutoff:3.500A) Processing helix chain 'SW' and resid 291 through 300 Processing helix chain 'SW' and resid 309 through 318 Processing helix chain 'SW' and resid 335 through 341 Processing helix chain 'SW' and resid 344 through 353 removed outlier: 3.606A pdb=" N GLNSW 349 " --> pdb=" O GLUSW 345 " (cutoff:3.500A) Processing helix chain 'SW' and resid 369 through 378 removed outlier: 3.796A pdb=" N ILESW 377 " --> pdb=" O ASPSW 373 " (cutoff:3.500A) Processing helix chain 'SW' and resid 409 through 422 removed outlier: 3.662A pdb=" N ARGSW 412 " --> pdb=" O SERSW 409 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N PHESW 413 " --> pdb=" O GLUSW 410 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEUSW 414 " --> pdb=" O LYSSW 411 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHESW 417 " --> pdb=" O LEUSW 414 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYSSW 422 " --> pdb=" O PHESW 419 " (cutoff:3.500A) Processing helix chain 'SW' and resid 435 through 447 Processing helix chain 'SW' and resid 461 through 473 Processing helix chain 'SW' and resid 483 through 486 No H-bonds generated for 'chain 'SW' and resid 483 through 486' Processing helix chain 'SW' and resid 506 through 515 removed outlier: 3.625A pdb=" N GLYSW 514 " --> pdb=" O ILESW 510 " (cutoff:3.500A) Processing helix chain 'SW' and resid 532 through 543 removed outlier: 3.652A pdb=" N LEUSW 535 " --> pdb=" O PROSW 532 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLYSW 536 " --> pdb=" O GLUSW 533 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLNSW 543 " --> pdb=" O TYRSW 540 " (cutoff:3.500A) Processing helix chain 'SW' and resid 555 through 557 No H-bonds generated for 'chain 'SW' and resid 555 through 557' Processing helix chain 'SW' and resid 562 through 571 Processing helix chain 'SW' and resid 573 through 592 Processing helix chain 'SW' and resid 601 through 603 No H-bonds generated for 'chain 'SW' and resid 601 through 603' Processing helix chain 'SW' and resid 606 through 613 removed outlier: 3.594A pdb=" N LEUSW 611 " --> pdb=" O PROSW 607 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SERSW 612 " --> pdb=" O GLNSW 608 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHESW 613 " --> pdb=" O VALSW 609 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 5 through 10 removed outlier: 4.659A pdb=" N THRSZ 8 " --> pdb=" O LYSSZ 5 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 19 through 30 Processing helix chain 'SZ' and resid 37 through 41 Processing helix chain 'SZ' and resid 49 through 55 Processing helix chain 'SZ' and resid 62 through 65 No H-bonds generated for 'chain 'SZ' and resid 62 through 65' Processing helix chain 'SZ' and resid 91 through 101 removed outlier: 3.523A pdb=" N ASNSZ 95 " --> pdb=" O TYRSZ 92 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLUSZ 98 " --> pdb=" O ASNSZ 95 " (cutoff:3.500A) Processing helix chain 'SZ' and resid 113 through 126 Processing helix chain 'SZ' and resid 130 through 135 Processing helix chain 'SZ' and resid 145 through 158 Processing helix chain 'SZ' and resid 160 through 177 removed outlier: 3.518A pdb=" N GLNSZ 164 " --> pdb=" O PROSZ 160 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'L6' and resid 58 through 60 Processing sheet with id= B, first strand: chain 'L7' and resid 6 through 10 removed outlier: 6.817A pdb=" N LYSL7 32 " --> pdb=" O LEUL7 7 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N LEUL7 9 " --> pdb=" O LYSL7 32 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VALL7 34 " --> pdb=" O LEUL7 9 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'L7' and resid 42 through 44 Processing sheet with id= D, first strand: chain 'L8' and resid 55 through 57 removed outlier: 4.142A pdb=" N LYSL8 23 " --> pdb=" O VALL8 15 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEUL8 37 " --> pdb=" O VALL8 28 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'L9' and resid 36 through 39 removed outlier: 4.587A pdb=" N ILEL9 61 " --> pdb=" O ALAL9 39 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASNL9 117 " --> pdb=" O ILEL9 133 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILEL9 135 " --> pdb=" O VALL9 115 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N VALL9 115 " --> pdb=" O ILEL9 135 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'LA' and resid 14 through 19 removed outlier: 6.603A pdb=" N THRLA 151 " --> pdb=" O ILELA 114 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ILELA 114 " --> pdb=" O THRLA 151 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'LB' and resid 136 through 139 removed outlier: 6.452A pdb=" N THRLB 79 " --> pdb=" O VALLB 137 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEULB 139 " --> pdb=" O THRLB 79 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VALLB 81 " --> pdb=" O LEULB 139 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYSLB 99 " --> pdb=" O ALALB 80 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N VALLB 82 " --> pdb=" O LYSLB 99 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N CYSLB 101 " --> pdb=" O VALLB 82 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LYSLB 119 " --> pdb=" O VALLB 100 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ALALB 102 " --> pdb=" O LYSLB 119 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEULB 121 " --> pdb=" O ALALB 102 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'LC' and resid 27 through 34 removed outlier: 6.621A pdb=" N ARGLC 15 " --> pdb=" O ILELC 61 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ILELC 61 " --> pdb=" O ARGLC 15 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'LC' and resid 90 through 99 removed outlier: 4.338A pdb=" N ASNLC 77 " --> pdb=" O ILELC 132 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ARGLC 83 " --> pdb=" O ILELC 126 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ILELC 126 " --> pdb=" O ARGLC 83 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'LE' and resid 96 through 98 removed outlier: 7.147A pdb=" N THRLE 61 " --> pdb=" O ASNLE 77 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ASNLE 77 " --> pdb=" O THRLE 61 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLYLE 73 " --> pdb=" O TYRLE 65 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VALLE 67 " --> pdb=" O ALALE 71 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ALALE 71 " --> pdb=" O VALLE 67 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'LG' and resid 25 through 27 removed outlier: 6.867A pdb=" N METLG 62 " --> pdb=" O ILELG 40 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N VALLG 42 " --> pdb=" O METLG 60 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N METLG 60 " --> pdb=" O VALLG 42 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ALALG 102 " --> pdb=" O ILELG 82 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'LI' and resid 31 through 33 Processing sheet with id= M, first strand: chain 'LI' and resid 86 through 88 Processing sheet with id= N, first strand: chain 'LI' and resid 54 through 57 removed outlier: 6.718A pdb=" N GLNLI 56 " --> pdb=" O ILELI 106 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ILELI 106 " --> pdb=" O GLNLI 56 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'LI' and resid 70 through 74 removed outlier: 6.777A pdb=" N TYRLI 81 " --> pdb=" O VALLI 71 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VALLI 73 " --> pdb=" O VALLI 79 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VALLI 79 " --> pdb=" O VALLI 73 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'LK' and resid 72 through 74 removed outlier: 6.657A pdb=" N LYSLK 110 " --> pdb=" O VALLK 73 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'LK' and resid 99 through 102 removed outlier: 6.781A pdb=" N ALALK 143 " --> pdb=" O VALLK 124 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ALALK 126 " --> pdb=" O ALALK 143 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N VALLK 145 " --> pdb=" O ALALK 126 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'LL' and resid 17 through 20 Processing sheet with id= S, first strand: chain 'LL' and resid 49 through 53 Processing sheet with id= T, first strand: chain 'LN' and resid 276 through 279 removed outlier: 5.215A pdb=" N VALLN 222 " --> pdb=" O VALLN 344 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VALLN 344 " --> pdb=" O VALLN 222 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILELN 78 " --> pdb=" O ALALN 51 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N METLN 53 " --> pdb=" O VALLN 76 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VALLN 76 " --> pdb=" O METLN 53 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N HISLN 55 " --> pdb=" O GLULN 74 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLULN 74 " --> pdb=" O HISLN 55 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VALLN 57 " --> pdb=" O VALLN 72 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VALLN 72 " --> pdb=" O VALLN 57 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYSLN 286 " --> pdb=" O METLN 332 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYSLN 334 " --> pdb=" O ILELN 284 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILELN 284 " --> pdb=" O LYSLN 334 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'LN' and resid 180 through 184 removed outlier: 6.811A pdb=" N HISLN 165 " --> pdb=" O VALLN 86 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N VALLN 86 " --> pdb=" O HISLN 165 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYSLN 103 " --> pdb=" O GLYLN 91 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VALLN 93 " --> pdb=" O THRLN 101 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N THRLN 101 " --> pdb=" O VALLN 93 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'LN' and resid 292 through 294 removed outlier: 3.776A pdb=" N LEULN 292 " --> pdb=" O ILELN 299 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'LN' and resid 56 through 58 Processing sheet with id= X, first strand: chain 'LQ' and resid 75 through 79 Processing sheet with id= Y, first strand: chain 'LT' and resid 100 through 104 removed outlier: 6.766A pdb=" N LEULT 27 " --> pdb=" O ALALT 12 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N METLT 83 " --> pdb=" O HISLT 78 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARGLT 76 " --> pdb=" O ARGLT 85 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYSLT 87 " --> pdb=" O VALLT 74 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N VALLT 74 " --> pdb=" O LYSLT 87 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'LW' and resid 16 through 18 Processing sheet with id= AA, first strand: chain 'NN' and resid 31 through 35 removed outlier: 6.673A pdb=" N HISNN 84 " --> pdb=" O PHENN 32 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N PHENN 34 " --> pdb=" O HISNN 84 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LEUNN 86 " --> pdb=" O PHENN 34 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VALNN 95 " --> pdb=" O VALNN 112 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYSNN 285 " --> pdb=" O THRNN 109 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLNNN 111 " --> pdb=" O LEUNN 283 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N LEUNN 283 " --> pdb=" O GLNNN 111 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLUNN 191 " --> pdb=" O ASNNN 186 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEUNN 140 " --> pdb=" O LEUNN 181 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ILENN 183 " --> pdb=" O LEUNN 140 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VALNN 142 " --> pdb=" O ILENN 183 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N TYRNN 185 " --> pdb=" O VALNN 142 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASNNN 144 " --> pdb=" O TYRNN 185 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'NN' and resid 114 through 116 removed outlier: 3.846A pdb=" N LYSNN 114 " --> pdb=" O THRNN 280 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'NN' and resid 197 through 203 Processing sheet with id= AD, first strand: chain 'SA' and resid 7 through 9 Processing sheet with id= AE, first strand: chain 'SA' and resid 152 through 154 removed outlier: 4.295A pdb=" N LEUSA 152 " --> pdb=" O CYSSA 250 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N CYSSA 208 " --> pdb=" O ILESA 251 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N THRSA 253 " --> pdb=" O CYSSA 208 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ILESA 210 " --> pdb=" O THRSA 253 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N THRSA 228 " --> pdb=" O ILESA 209 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N TYRSA 211 " --> pdb=" O THRSA 228 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEUSA 230 " --> pdb=" O TYRSA 211 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'SC' and resid 91 through 93 removed outlier: 3.560A pdb=" N VALSC 107 " --> pdb=" O VALSC 92 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'SC' and resid 194 through 196 removed outlier: 7.041A pdb=" N LEUSC 174 " --> pdb=" O LEUSC 165 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'SD' and resid 120 through 124 Processing sheet with id= AI, first strand: chain 'SD' and resid 159 through 162 Processing sheet with id= AJ, first strand: chain 'SE' and resid 180 through 184 Processing sheet with id= AK, first strand: chain 'SH' and resid 117 through 121 removed outlier: 4.709A pdb=" N VALSH 46 " --> pdb=" O METSH 121 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARGSH 73 " --> pdb=" O GLUSH 92 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'SH' and resid 109 through 111 Processing sheet with id= AM, first strand: chain 'SI' and resid 127 through 131 Processing sheet with id= AN, first strand: chain 'SI' and resid 167 through 169 Processing sheet with id= AO, first strand: chain 'SK' and resid 2 through 5 removed outlier: 6.908A pdb=" N ALASK 204 " --> pdb=" O VALSK 3 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ALASK 5 " --> pdb=" O ALASK 204 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N CYSSK 206 " --> pdb=" O ALASK 5 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'SK' and resid 17 through 19 removed outlier: 7.877A pdb=" N VALSK 26 " --> pdb=" O PROSK 47 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VALSK 49 " --> pdb=" O VALSK 26 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'SK' and resid 69 through 72 removed outlier: 6.793A pdb=" N GLNSK 93 " --> pdb=" O LEUSK 70 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N VALSK 72 " --> pdb=" O GLNSK 93 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ARGSK 95 " --> pdb=" O VALSK 72 " (cutoff:3.500A) No H-bonds generated for sheet with id= AQ Processing sheet with id= AR, first strand: chain 'SK' and resid 108 through 110 removed outlier: 6.505A pdb=" N GLUSK 136 " --> pdb=" O ALASK 115 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N VALSK 117 " --> pdb=" O GLUSK 136 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N PHESK 138 " --> pdb=" O VALSK 117 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'SK' and resid 158 through 161 removed outlier: 7.045A pdb=" N VALSK 161 " --> pdb=" O PROSK 180 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VALSK 182 " --> pdb=" O VALSK 161 " (cutoff:3.500A) No H-bonds generated for sheet with id= AS Processing sheet with id= AT, first strand: chain 'SL' and resid 78 through 82 removed outlier: 3.522A pdb=" N LEUSL 78 " --> pdb=" O ILESL 205 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VALSL 80 " --> pdb=" O LEUSL 203 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'SL' and resid 128 through 131 removed outlier: 6.754A pdb=" N PHESL 154 " --> pdb=" O CYSSL 96 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N PHESL 98 " --> pdb=" O PHESL 154 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEUSL 156 " --> pdb=" O PHESL 98 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N VALSL 181 " --> pdb=" O THRSL 157 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'SL' and resid 211 through 218 removed outlier: 6.791A pdb=" N LEUSL 64 " --> pdb=" O ILESL 216 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHESL 264 " --> pdb=" O LEUSL 251 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VALSL 253 " --> pdb=" O PROSL 262 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'SM' and resid 197 through 204 removed outlier: 6.255A pdb=" N GLUSM 193 " --> pdb=" O LEUSM 178 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LEUSM 178 " --> pdb=" O GLUSM 193 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'SM' and resid 353 through 356 removed outlier: 7.077A pdb=" N HISSM 375 " --> pdb=" O PHESM 333 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N CYSSM 391 " --> pdb=" O GLNSM 376 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'SO' and resid 88 through 90 removed outlier: 6.398A pdb=" N ILESO 62 " --> pdb=" O LYSSO 89 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LYSSO 114 " --> pdb=" O LEUSO 63 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N PHESO 65 " --> pdb=" O LYSSO 114 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILESO 116 " --> pdb=" O PHESO 65 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N LEUSO 126 " --> pdb=" O VALSO 143 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYSSO 242 " --> pdb=" O LYSSO 140 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEUSO 142 " --> pdb=" O LEUSO 240 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N LEUSO 240 " --> pdb=" O LEUSO 142 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLNSO 144 " --> pdb=" O LEUSO 238 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LEUSO 238 " --> pdb=" O GLNSO 144 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHESO 236 " --> pdb=" O PHESO 217 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEUSO 165 " --> pdb=" O PHESO 206 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHESO 208 " --> pdb=" O LEUSO 165 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N SERSO 167 " --> pdb=" O PHESO 208 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N ILESO 210 " --> pdb=" O SERSO 167 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'SO' and resid 220 through 222 Processing sheet with id= BA, first strand: chain 'SO' and resid 242 through 244 Processing sheet with id= BB, first strand: chain 'SV' and resid 19 through 22 Processing sheet with id= BC, first strand: chain 'SW' and resid 384 through 387 removed outlier: 3.750A pdb=" N LEUSW 219 " --> pdb=" O THRSW 360 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'SW' and resid 404 through 406 removed outlier: 7.441A pdb=" N VALSW 405 " --> pdb=" O ALASW 526 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEUSW 528 " --> pdb=" O VALSW 405 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILESW 529 " --> pdb=" O GLNSW 499 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLYSW 477 " --> pdb=" O LEUSW 428 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N VALSW 430 " --> pdb=" O GLYSW 477 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEUSW 479 " --> pdb=" O VALSW 430 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N PHESW 432 " --> pdb=" O LEUSW 479 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N CYSSW 481 " --> pdb=" O PHESW 432 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEUSW 453 " --> pdb=" O LEUSW 480 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N THRSW 482 " --> pdb=" O LEUSW 453 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ILESW 455 " --> pdb=" O THRSW 482 " (cutoff:3.500A) 2052 hydrogen bonds defined for protein. 5708 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1552 hydrogen bonds 2732 hydrogen bond angles 0 basepair planarities 581 basepair parallelities 846 stacking parallelities Total time for adding SS restraints: 67.54 Time building geometry restraints manager: 38.22 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: 17457 1.33 - 1.45: 32008 1.45 - 1.57: 45910 1.57 - 1.69: 3537 1.69 - 1.81: 375 Bond restraints: 99287 Sorted by residual: bond pdb=" CE1 HICLN 245 " pdb=" NE2 HICLN 245 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.42e+00 bond pdb=" N ARGSR 367 " pdb=" CA ARGSR 367 " ideal model delta sigma weight residual 1.458 1.486 -0.029 1.25e-02 6.40e+03 5.31e+00 bond pdb=" CG HICLN 245 " pdb=" CD2 HICLN 245 " ideal model delta sigma weight residual 1.369 1.410 -0.041 2.00e-02 2.50e+03 4.25e+00 bond pdb=" CB PROLU 6 " pdb=" CG PROLU 6 " ideal model delta sigma weight residual 1.506 1.582 -0.076 3.90e-02 6.57e+02 3.78e+00 bond pdb=" ND1 HICLN 245 " pdb=" CE1 HICLN 245 " ideal model delta sigma weight residual 1.309 1.346 -0.037 2.00e-02 2.50e+03 3.47e+00 ... (remaining 99282 not shown) Histogram of bond angle deviations from ideal: 99.59 - 106.50: 11872 106.50 - 113.41: 56203 113.41 - 120.32: 37252 120.32 - 127.23: 32838 127.23 - 134.14: 4295 Bond angle restraints: 142460 Sorted by residual: angle pdb=" N ILESC 203 " pdb=" CA ILESC 203 " pdb=" C ILESC 203 " ideal model delta sigma weight residual 113.20 109.25 3.95 9.60e-01 1.09e+00 1.69e+01 angle pdb=" CG ARGSJ 661 " pdb=" CD ARGSJ 661 " pdb=" NE ARGSJ 661 " ideal model delta sigma weight residual 112.00 120.58 -8.58 2.20e+00 2.07e-01 1.52e+01 angle pdb=" N ILESO 232 " pdb=" CA ILESO 232 " pdb=" C ILESO 232 " ideal model delta sigma weight residual 111.90 108.77 3.13 8.10e-01 1.52e+00 1.49e+01 angle pdb=" N ARGSR 367 " pdb=" CA ARGSR 367 " pdb=" C ARGSR 367 " ideal model delta sigma weight residual 109.59 115.23 -5.64 1.47e+00 4.63e-01 1.47e+01 angle pdb=" N ILENN 275 " pdb=" CA ILENN 275 " pdb=" C ILENN 275 " ideal model delta sigma weight residual 111.90 108.90 3.00 8.10e-01 1.52e+00 1.37e+01 ... (remaining 142455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.33: 58339 35.33 - 70.66: 4467 70.66 - 105.99: 666 105.99 - 141.32: 9 141.32 - 176.66: 11 Dihedral angle restraints: 63492 sinusoidal: 43445 harmonic: 20047 Sorted by residual: dihedral pdb=" O4' UL3 45 " pdb=" C1' UL3 45 " pdb=" N1 UL3 45 " pdb=" C2 UL3 45 " ideal model delta sinusoidal sigma weight residual 200.00 23.34 176.66 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' UL31381 " pdb=" C1' UL31381 " pdb=" N1 UL31381 " pdb=" C2 UL31381 " ideal model delta sinusoidal sigma weight residual 200.00 27.37 172.63 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' CL35008 " pdb=" C1' CL35008 " pdb=" N1 CL35008 " pdb=" C2 CL35008 " ideal model delta sinusoidal sigma weight residual -160.00 9.98 -169.98 1 1.50e+01 4.44e-03 8.47e+01 ... (remaining 63489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 15087 0.047 - 0.095: 1555 0.095 - 0.142: 503 0.142 - 0.189: 30 0.189 - 0.237: 2 Chirality restraints: 17177 Sorted by residual: chirality pdb=" C1' AL34762 " pdb=" O4' AL34762 " pdb=" C2' AL34762 " pdb=" N9 AL34762 " both_signs ideal model delta sigma weight residual False 2.46 2.22 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C1' UL3 416 " pdb=" O4' UL3 416 " pdb=" C2' UL3 416 " pdb=" N1 UL3 416 " both_signs ideal model delta sigma weight residual False 2.47 2.27 0.20 2.00e-01 2.50e+01 9.59e-01 chirality pdb=" C1' CL2 92 " pdb=" O4' CL2 92 " pdb=" C2' CL2 92 " pdb=" N1 CL2 92 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.18 2.00e-01 2.50e+01 8.09e-01 ... (remaining 17174 not shown) Planarity restraints: 11468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GL1 39 " 0.050 2.00e-02 2.50e+03 2.06e-02 1.27e+01 pdb=" N9 GL1 39 " -0.046 2.00e-02 2.50e+03 pdb=" C8 GL1 39 " -0.009 2.00e-02 2.50e+03 pdb=" N7 GL1 39 " 0.001 2.00e-02 2.50e+03 pdb=" C5 GL1 39 " -0.001 2.00e-02 2.50e+03 pdb=" C6 GL1 39 " 0.007 2.00e-02 2.50e+03 pdb=" O6 GL1 39 " 0.015 2.00e-02 2.50e+03 pdb=" N1 GL1 39 " 0.004 2.00e-02 2.50e+03 pdb=" C2 GL1 39 " -0.003 2.00e-02 2.50e+03 pdb=" N2 GL1 39 " -0.002 2.00e-02 2.50e+03 pdb=" N3 GL1 39 " -0.007 2.00e-02 2.50e+03 pdb=" C4 GL1 39 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRPSR 417 " 0.030 2.00e-02 2.50e+03 2.07e-02 1.07e+01 pdb=" CG TRPSR 417 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TRPSR 417 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRPSR 417 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRPSR 417 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRPSR 417 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRPSR 417 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRPSR 417 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRPSR 417 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRPSR 417 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' AL34762 " -0.041 2.00e-02 2.50e+03 1.83e-02 9.16e+00 pdb=" N9 AL34762 " 0.040 2.00e-02 2.50e+03 pdb=" C8 AL34762 " 0.003 2.00e-02 2.50e+03 pdb=" N7 AL34762 " 0.001 2.00e-02 2.50e+03 pdb=" C5 AL34762 " 0.003 2.00e-02 2.50e+03 pdb=" C6 AL34762 " -0.007 2.00e-02 2.50e+03 pdb=" N6 AL34762 " -0.011 2.00e-02 2.50e+03 pdb=" N1 AL34762 " -0.004 2.00e-02 2.50e+03 pdb=" C2 AL34762 " 0.004 2.00e-02 2.50e+03 pdb=" N3 AL34762 " 0.009 2.00e-02 2.50e+03 pdb=" C4 AL34762 " 0.005 2.00e-02 2.50e+03 ... (remaining 11465 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 527 2.58 - 3.16: 72494 3.16 - 3.74: 161014 3.74 - 4.32: 230666 4.32 - 4.90: 335976 Nonbonded interactions: 800677 Sorted by model distance: nonbonded pdb=" OD1 ASNLT 65 " pdb="MG MGLT 201 " model vdw 2.001 2.170 nonbonded pdb=" O6 GL3 356 " pdb="MG MGL35110 " model vdw 2.006 2.170 nonbonded pdb=" O2' CL3 172 " pdb=" O5' CL3 173 " model vdw 2.019 2.440 nonbonded pdb=" OP2 CL31369 " pdb=" O2' GL31370 " model vdw 2.055 2.440 nonbonded pdb=" OG1 THRLN 95 " pdb=" O GLYLN 98 " model vdw 2.063 2.440 ... (remaining 800672 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: 6.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 24.460 Check model and map are aligned: 1.040 Set scattering table: 0.660 Process input model: 261.230 Find NCS groups from input model: 2.470 Set up NCS constraints: 0.330 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:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 308.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 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 0.076 99287 Z= 0.187 Angle : 0.548 10.512 142460 Z= 0.289 Chirality : 0.035 0.237 17177 Planarity : 0.004 0.078 11468 Dihedral : 20.658 176.655 50476 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.02 % Allowed : 0.12 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.47 (0.10), residues: 6742 helix: 2.00 (0.10), residues: 2785 sheet: 0.39 (0.17), residues: 863 loop : 0.30 (0.11), residues: 3094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.001 TRPSR 417 HIS 0.012 0.001 HISSR 436 PHE 0.021 0.001 PHENN 135 TYR 0.023 0.001 TYRSR 441 ARG 0.013 0.001 ARGSJ 661 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13484 Ramachandran restraints generated. 6742 Oldfield, 0 Emsley, 6742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13484 Ramachandran restraints generated. 6742 Oldfield, 0 Emsley, 6742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 6049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 858 time to evaluate : 5.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: LA 14 SER cc_start: 0.8298 (p) cc_final: 0.7884 (m) REVERT: LA 108 ASP cc_start: 0.7280 (p0) cc_final: 0.6470 (p0) REVERT: LC 94 TYR cc_start: 0.8439 (t80) cc_final: 0.8093 (t80) REVERT: LN 19 ARG cc_start: 0.6939 (ptm160) cc_final: 0.6737 (ptt180) REVERT: LS 7 ARG cc_start: 0.7368 (mtm180) cc_final: 0.7080 (mtp180) REVERT: SD 41 MET cc_start: 0.7741 (mmm) cc_final: 0.7437 (mmt) REVERT: SD 187 MET cc_start: 0.8507 (mmm) cc_final: 0.8151 (mmt) REVERT: SD 220 MET cc_start: 0.7898 (ttp) cc_final: 0.7450 (ttm) REVERT: SI 74 ASP cc_start: 0.7816 (m-30) cc_final: 0.7563 (m-30) REVERT: SK 59 ILE cc_start: 0.8679 (tt) cc_final: 0.8169 (tp) REVERT: SO 343 MET cc_start: 0.5710 (mtt) cc_final: 0.4919 (ttm) REVERT: SS 208 GLN cc_start: 0.8184 (mt0) cc_final: 0.7729 (mt0) outliers start: 1 outliers final: 1 residues processed: 858 average time/residue: 1.7840 time to fit residues: 2059.8350 Evaluate side-chains 674 residues out of total 6049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 673 time to evaluate : 5.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L8 residue 61 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 714 optimal weight: 4.9990 chunk 641 optimal weight: 3.9990 chunk 355 optimal weight: 4.9990 chunk 219 optimal weight: 3.9990 chunk 432 optimal weight: 0.8980 chunk 342 optimal weight: 3.9990 chunk 663 optimal weight: 2.9990 chunk 256 optimal weight: 0.7980 chunk 403 optimal weight: 6.9990 chunk 493 optimal weight: 0.0870 chunk 768 optimal weight: 1.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L6 19 GLN L7 90 HIS L7 96 GLN L7 150 GLN L7 180 GLN L8 69 HIS L8 125 ASN L9 196 ASN LE 131 GLN LG 36 ASN LI 43 ASN LI 72 GLN LN 289 GLN LQ 102 ASN LS 101 ASN LS 108 GLN LT 21 GLN LU 26 HIS LW 16 HIS NE 235 ASN NG 172 GLN NG 178 GLN NN 84 HIS NN 134 GLN NN 186 ASN SC 135 GLN SC 136 HIS SC 190 HIS SC 211 HIS SC 250 GLN SH 67 GLN SI 113 GLN ** SI 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SJ 711 GLN SJ 726 HIS SK 33 ASN SK 82 GLN SK 83 HIS ** SK 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SL 30 GLN SL 35 GLN SL 104 ASN SL 218 HIS ** SN 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SS 296 HIS SS 310 HIS SV 110 ASN SW 207 HIS SW 402 GLN SZ 171 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 99287 Z= 0.179 Angle : 0.497 7.676 142460 Z= 0.257 Chirality : 0.034 0.267 17177 Planarity : 0.004 0.053 11468 Dihedral : 22.099 179.038 36057 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.55 % Allowed : 7.34 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.56 (0.10), residues: 6742 helix: 2.04 (0.09), residues: 2825 sheet: 0.44 (0.17), residues: 865 loop : 0.36 (0.11), residues: 3052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRPSR 417 HIS 0.012 0.001 HISSJ 726 PHE 0.020 0.001 PHESK 154 TYR 0.023 0.001 TYRNN 185 ARG 0.007 0.000 ARGSJ 661 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13484 Ramachandran restraints generated. 6742 Oldfield, 0 Emsley, 6742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13484 Ramachandran restraints generated. 6742 Oldfield, 0 Emsley, 6742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 6049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 701 time to evaluate : 5.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L6 115 GLN cc_start: 0.6992 (OUTLIER) cc_final: 0.6760 (mt0) REVERT: L7 57 PHE cc_start: 0.3440 (OUTLIER) cc_final: 0.2577 (t80) REVERT: L8 33 GLN cc_start: 0.8022 (pt0) cc_final: 0.7698 (pm20) REVERT: L8 70 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7679 (tt0) REVERT: LA 14 SER cc_start: 0.8314 (p) cc_final: 0.7888 (m) REVERT: LC 92 ASN cc_start: 0.8009 (OUTLIER) cc_final: 0.7495 (m-40) REVERT: LN 19 ARG cc_start: 0.7104 (ptm160) cc_final: 0.6864 (ptt180) REVERT: LS 7 ARG cc_start: 0.7369 (mtm180) cc_final: 0.7090 (mtp180) REVERT: NN 131 HIS cc_start: 0.6042 (OUTLIER) cc_final: 0.5496 (m90) REVERT: SD 41 MET cc_start: 0.7523 (mmm) cc_final: 0.7080 (mmt) REVERT: SD 187 MET cc_start: 0.8577 (mmm) cc_final: 0.8297 (mmt) REVERT: SJ 708 GLU cc_start: 0.7452 (tp30) cc_final: 0.7244 (tp30) REVERT: SL 272 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.7119 (m-30) REVERT: SS 138 ASN cc_start: 0.7767 (p0) cc_final: 0.7475 (p0) REVERT: SS 361 GLN cc_start: 0.7784 (mp10) cc_final: 0.7206 (mp10) REVERT: ST 213 GLN cc_start: 0.8112 (mt0) cc_final: 0.7658 (mt0) REVERT: ST 217 GLU cc_start: 0.7898 (tt0) cc_final: 0.7552 (tt0) REVERT: SW 277 HIS cc_start: 0.7606 (m-70) cc_final: 0.7179 (m170) outliers start: 91 outliers final: 22 residues processed: 730 average time/residue: 1.8540 time to fit residues: 1818.0461 Evaluate side-chains 672 residues out of total 6049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 644 time to evaluate : 5.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L6 residue 115 GLN Chi-restraints excluded: chain L7 residue 57 PHE Chi-restraints excluded: chain L7 residue 132 THR Chi-restraints excluded: chain L8 residue 43 THR Chi-restraints excluded: chain L8 residue 70 GLN Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LB residue 5 ILE Chi-restraints excluded: chain LC residue 92 ASN Chi-restraints excluded: chain LG residue 30 ASP Chi-restraints excluded: chain LG residue 108 ASN Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LL residue 52 GLU Chi-restraints excluded: chain LQ residue 21 ILE Chi-restraints excluded: chain LU residue 22 SER Chi-restraints excluded: chain NG residue 211 ILE Chi-restraints excluded: chain NN residue 131 HIS Chi-restraints excluded: chain NN residue 174 LEU Chi-restraints excluded: chain SK residue 28 ILE Chi-restraints excluded: chain SK residue 121 LEU Chi-restraints excluded: chain SL residue 244 LYS Chi-restraints excluded: chain SL residue 272 ASP Chi-restraints excluded: chain SN residue 73 THR Chi-restraints excluded: chain SN residue 128 VAL Chi-restraints excluded: chain SN residue 267 ASP Chi-restraints excluded: chain SR residue 369 ASP Chi-restraints excluded: chain ST residue 207 LEU Chi-restraints excluded: chain ST residue 214 SER Chi-restraints excluded: chain ST residue 228 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 426 optimal weight: 0.9990 chunk 238 optimal weight: 9.9990 chunk 639 optimal weight: 4.9990 chunk 523 optimal weight: 3.9990 chunk 211 optimal weight: 8.9990 chunk 769 optimal weight: 6.9990 chunk 831 optimal weight: 7.9990 chunk 685 optimal weight: 2.9990 chunk 763 optimal weight: 5.9990 chunk 262 optimal weight: 4.9990 chunk 617 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L7 50 ASN L7 96 GLN L8 83 ASN LA 93 HIS LB 93 GLN LC 37 HIS LG 36 ASN LG 135 ASN LI 14 ASN LK 62 HIS LL 83 ASN LN 289 GLN LN 328 ASN LQ 102 ASN LQ 126 ASN LW 16 HIS NG 178 GLN NN 298 HIS SC 250 GLN ** SD 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 248 ASN SE 225 ASN SI 113 GLN ** SI 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SI 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 253 GLN SJ 711 GLN SJ 726 HIS SK 82 GLN ** SK 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SK 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SL 30 GLN SL 46 HIS SL 104 ASN SL 121 HIS SM 209 HIS SN 148 GLN SO 340 GLN ** SS 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SV 129 GLN SW 207 HIS SZ 171 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 99287 Z= 0.387 Angle : 0.594 8.392 142460 Z= 0.305 Chirality : 0.040 0.238 17177 Planarity : 0.005 0.061 11468 Dihedral : 22.047 179.925 36055 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.38 % Allowed : 8.97 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.03 (0.10), residues: 6742 helix: 1.60 (0.09), residues: 2854 sheet: 0.21 (0.17), residues: 917 loop : 0.04 (0.11), residues: 2971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRPSR 417 HIS 0.018 0.002 HISL6 67 PHE 0.026 0.002 PHESH 111 TYR 0.032 0.002 TYRNN 185 ARG 0.010 0.001 ARGLS 89 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13484 Ramachandran restraints generated. 6742 Oldfield, 0 Emsley, 6742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13484 Ramachandran restraints generated. 6742 Oldfield, 0 Emsley, 6742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 6049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 675 time to evaluate : 6.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L6 115 GLN cc_start: 0.7143 (OUTLIER) cc_final: 0.6900 (mt0) REVERT: L7 57 PHE cc_start: 0.3622 (OUTLIER) cc_final: 0.2724 (t80) REVERT: L8 33 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7803 (pm20) REVERT: L8 70 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7898 (tt0) REVERT: LC 92 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.7831 (m-40) REVERT: LN 198 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7009 (ttp80) REVERT: SC 62 MET cc_start: 0.7909 (mmm) cc_final: 0.7660 (tmm) REVERT: SC 250 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.6896 (tp40) REVERT: SD 41 MET cc_start: 0.7592 (mmm) cc_final: 0.7069 (mmt) REVERT: SD 187 MET cc_start: 0.8519 (mmm) cc_final: 0.8173 (mmt) REVERT: SL 272 ASP cc_start: 0.7374 (OUTLIER) cc_final: 0.7071 (m-30) REVERT: SO 128 MET cc_start: 0.7720 (ttm) cc_final: 0.7445 (ttm) REVERT: SO 343 MET cc_start: 0.5725 (OUTLIER) cc_final: 0.4900 (mtt) REVERT: ST 213 GLN cc_start: 0.8214 (mt0) cc_final: 0.7815 (mt0) REVERT: ST 217 GLU cc_start: 0.8029 (tt0) cc_final: 0.7780 (tt0) REVERT: SW 277 HIS cc_start: 0.7541 (m-70) cc_final: 0.7004 (m170) REVERT: SW 353 LEU cc_start: 0.8671 (mt) cc_final: 0.8443 (mt) outliers start: 140 outliers final: 50 residues processed: 736 average time/residue: 1.8545 time to fit residues: 1827.2499 Evaluate side-chains 686 residues out of total 6049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 627 time to evaluate : 5.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 115 GLN Chi-restraints excluded: chain L6 residue 118 LYS Chi-restraints excluded: chain L7 residue 57 PHE Chi-restraints excluded: chain L7 residue 132 THR Chi-restraints excluded: chain L8 residue 33 GLN Chi-restraints excluded: chain L8 residue 43 THR Chi-restraints excluded: chain L8 residue 61 ILE Chi-restraints excluded: chain L8 residue 70 GLN Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 12 THR Chi-restraints excluded: chain LB residue 5 ILE Chi-restraints excluded: chain LC residue 92 ASN Chi-restraints excluded: chain LC residue 124 ILE Chi-restraints excluded: chain LG residue 30 ASP Chi-restraints excluded: chain LG residue 31 ASN Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LG residue 108 ASN Chi-restraints excluded: chain LI residue 93 THR Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LL residue 52 GLU Chi-restraints excluded: chain LN residue 39 LYS Chi-restraints excluded: chain LN residue 198 ARG Chi-restraints excluded: chain LN residue 381 THR Chi-restraints excluded: chain LN residue 382 MET Chi-restraints excluded: chain LQ residue 21 ILE Chi-restraints excluded: chain LQ residue 129 LEU Chi-restraints excluded: chain LS residue 53 SER Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LU residue 22 SER Chi-restraints excluded: chain NE residue 203 VAL Chi-restraints excluded: chain NN residue 19 LEU Chi-restraints excluded: chain NN residue 131 HIS Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SA residue 276 ASN Chi-restraints excluded: chain SC residue 50 LEU Chi-restraints excluded: chain SC residue 194 VAL Chi-restraints excluded: chain SC residue 250 GLN Chi-restraints excluded: chain SE residue 70 LEU Chi-restraints excluded: chain SE residue 115 LEU Chi-restraints excluded: chain SE residue 210 GLU Chi-restraints excluded: chain SH residue 72 THR Chi-restraints excluded: chain SJ residue 719 VAL Chi-restraints excluded: chain SK residue 28 ILE Chi-restraints excluded: chain SL residue 94 ASP Chi-restraints excluded: chain SL residue 244 LYS Chi-restraints excluded: chain SL residue 272 ASP Chi-restraints excluded: chain SM residue 21 ASN Chi-restraints excluded: chain SN residue 73 THR Chi-restraints excluded: chain SN residue 143 SER Chi-restraints excluded: chain SO residue 343 MET Chi-restraints excluded: chain SR residue 369 ASP Chi-restraints excluded: chain SS residue 228 SER Chi-restraints excluded: chain SV residue 64 THR Chi-restraints excluded: chain SW residue 316 MET Chi-restraints excluded: chain SZ residue 8 THR Chi-restraints excluded: chain SZ residue 88 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 760 optimal weight: 6.9990 chunk 578 optimal weight: 4.9990 chunk 399 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 367 optimal weight: 0.9980 chunk 516 optimal weight: 0.1980 chunk 772 optimal weight: 9.9990 chunk 817 optimal weight: 4.9990 chunk 403 optimal weight: 6.9990 chunk 732 optimal weight: 5.9990 chunk 220 optimal weight: 0.9980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L7 50 ASN L7 96 GLN LC 173 ASN LG 36 ASN LI 14 ASN LN 289 GLN LQ 102 ASN LW 16 HIS NG 154 GLN NG 178 GLN ** SD 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 64 GLN ** SI 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SI 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 253 GLN SJ 687 ASN SJ 711 GLN SJ 726 HIS ** SK 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SL 30 GLN SL 104 ASN SO 265 HIS SS 208 GLN ** SS 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SS 332 GLN SV 110 ASN SW 207 HIS SZ 171 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 99287 Z= 0.231 Angle : 0.506 9.233 142460 Z= 0.262 Chirality : 0.035 0.226 17177 Planarity : 0.004 0.048 11468 Dihedral : 22.016 178.555 36055 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.07 % Allowed : 10.69 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.10), residues: 6742 helix: 1.70 (0.10), residues: 2840 sheet: 0.23 (0.17), residues: 891 loop : 0.06 (0.11), residues: 3011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRPSR 417 HIS 0.013 0.001 HISL6 67 PHE 0.020 0.001 PHESK 154 TYR 0.029 0.001 TYRNN 185 ARG 0.005 0.000 ARGL6 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13484 Ramachandran restraints generated. 6742 Oldfield, 0 Emsley, 6742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13484 Ramachandran restraints generated. 6742 Oldfield, 0 Emsley, 6742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 6049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 669 time to evaluate : 5.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L6 115 GLN cc_start: 0.7028 (OUTLIER) cc_final: 0.6798 (mt0) REVERT: L7 141 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7259 (tt) REVERT: L8 33 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7751 (pm20) REVERT: L8 70 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7847 (tt0) REVERT: LC 92 ASN cc_start: 0.8402 (m-40) cc_final: 0.7953 (m-40) REVERT: LG 62 MET cc_start: 0.8083 (mmm) cc_final: 0.7518 (mmt) REVERT: SC 62 MET cc_start: 0.7985 (mmm) cc_final: 0.7693 (tmm) REVERT: SC 250 GLN cc_start: 0.6762 (tp40) cc_final: 0.6276 (tp40) REVERT: SD 41 MET cc_start: 0.7595 (mmm) cc_final: 0.7011 (mmt) REVERT: SD 187 MET cc_start: 0.8537 (mmm) cc_final: 0.8118 (mmt) REVERT: SO 128 MET cc_start: 0.7698 (ttm) cc_final: 0.7439 (ttm) REVERT: SO 231 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7469 (tt0) REVERT: SO 343 MET cc_start: 0.5849 (OUTLIER) cc_final: 0.5043 (ttm) REVERT: ST 213 GLN cc_start: 0.8155 (mt0) cc_final: 0.7637 (mt0) REVERT: ST 217 GLU cc_start: 0.7930 (tt0) cc_final: 0.7587 (tt0) REVERT: SV 93 MET cc_start: 0.7545 (ttm) cc_final: 0.7283 (ptm) REVERT: SW 353 LEU cc_start: 0.8674 (mt) cc_final: 0.8438 (mt) outliers start: 122 outliers final: 49 residues processed: 729 average time/residue: 1.8445 time to fit residues: 1804.8054 Evaluate side-chains 679 residues out of total 6049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 624 time to evaluate : 6.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L6 residue 115 GLN Chi-restraints excluded: chain L7 residue 57 PHE Chi-restraints excluded: chain L7 residue 132 THR Chi-restraints excluded: chain L7 residue 141 LEU Chi-restraints excluded: chain L8 residue 33 GLN Chi-restraints excluded: chain L8 residue 43 THR Chi-restraints excluded: chain L8 residue 70 GLN Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 36 ILE Chi-restraints excluded: chain LB residue 5 ILE Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LC residue 124 ILE Chi-restraints excluded: chain LE residue 147 GLU Chi-restraints excluded: chain LG residue 30 ASP Chi-restraints excluded: chain LG residue 31 ASN Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LG residue 108 ASN Chi-restraints excluded: chain LI residue 56 GLN Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LI residue 112 ASP Chi-restraints excluded: chain LL residue 52 GLU Chi-restraints excluded: chain LN residue 39 LYS Chi-restraints excluded: chain LN residue 329 ASP Chi-restraints excluded: chain LN residue 382 MET Chi-restraints excluded: chain LS residue 53 SER Chi-restraints excluded: chain LU residue 22 SER Chi-restraints excluded: chain NE residue 273 LEU Chi-restraints excluded: chain NG residue 211 ILE Chi-restraints excluded: chain NN residue 131 HIS Chi-restraints excluded: chain SA residue 22 VAL Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SA residue 276 ASN Chi-restraints excluded: chain SC residue 268 GLN Chi-restraints excluded: chain SE residue 70 LEU Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SJ residue 674 ILE Chi-restraints excluded: chain SJ residue 709 GLU Chi-restraints excluded: chain SK residue 28 ILE Chi-restraints excluded: chain SK residue 137 VAL Chi-restraints excluded: chain SL residue 244 LYS Chi-restraints excluded: chain SM residue 427 VAL Chi-restraints excluded: chain SN residue 73 THR Chi-restraints excluded: chain SN residue 116 VAL Chi-restraints excluded: chain SN residue 143 SER Chi-restraints excluded: chain SN residue 267 ASP Chi-restraints excluded: chain SO residue 231 GLU Chi-restraints excluded: chain SO residue 343 MET Chi-restraints excluded: chain SR residue 369 ASP Chi-restraints excluded: chain SS residue 228 SER Chi-restraints excluded: chain SS residue 232 MET Chi-restraints excluded: chain SS residue 265 MET Chi-restraints excluded: chain ST residue 214 SER Chi-restraints excluded: chain SV residue 22 VAL Chi-restraints excluded: chain SZ residue 88 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 681 optimal weight: 7.9990 chunk 464 optimal weight: 0.9980 chunk 11 optimal weight: 30.0000 chunk 608 optimal weight: 8.9990 chunk 337 optimal weight: 4.9990 chunk 697 optimal weight: 30.0000 chunk 565 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 417 optimal weight: 0.9990 chunk 733 optimal weight: 8.9990 chunk 206 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L7 96 GLN L8 125 ASN ** LA 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LG 36 ASN LI 14 ASN LN 289 GLN LQ 102 ASN LW 16 HIS NN 68 ASN ** SD 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 64 GLN SJ 687 ASN SJ 726 HIS ** SK 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SL 30 GLN SL 104 ASN SL 133 GLN SM 243 ASN SS 208 GLN ** SS 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SW 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SW 402 GLN SZ 171 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 99287 Z= 0.382 Angle : 0.575 8.166 142460 Z= 0.295 Chirality : 0.039 0.226 17177 Planarity : 0.005 0.055 11468 Dihedral : 21.990 179.263 36055 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.50 % Allowed : 11.64 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.10), residues: 6742 helix: 1.53 (0.10), residues: 2823 sheet: 0.14 (0.17), residues: 911 loop : -0.09 (0.11), residues: 3008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRPSR 417 HIS 0.011 0.001 HISSJ 726 PHE 0.023 0.002 PHESH 111 TYR 0.028 0.002 TYRNN 185 ARG 0.006 0.001 ARGSS 239 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13484 Ramachandran restraints generated. 6742 Oldfield, 0 Emsley, 6742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13484 Ramachandran restraints generated. 6742 Oldfield, 0 Emsley, 6742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 6049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 637 time to evaluate : 6.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L6 115 GLN cc_start: 0.7095 (OUTLIER) cc_final: 0.6852 (mt0) REVERT: L7 141 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7266 (tt) REVERT: L8 33 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7831 (pm20) REVERT: L8 70 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7921 (tt0) REVERT: L8 83 ASN cc_start: 0.7872 (m110) cc_final: 0.7623 (m-40) REVERT: LC 92 ASN cc_start: 0.8447 (OUTLIER) cc_final: 0.7967 (m-40) REVERT: LG 62 MET cc_start: 0.8074 (mmm) cc_final: 0.7575 (mmt) REVERT: LI 37 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6861 (tm-30) REVERT: LN 198 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.6891 (ttp80) REVERT: SC 62 MET cc_start: 0.7989 (mmm) cc_final: 0.7658 (tmm) REVERT: SD 41 MET cc_start: 0.7648 (mmm) cc_final: 0.7066 (mmt) REVERT: SD 187 MET cc_start: 0.8528 (mmm) cc_final: 0.8184 (mmt) REVERT: SD 229 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7300 (mt-10) REVERT: SI 57 ARG cc_start: 0.5724 (OUTLIER) cc_final: 0.5401 (ttp-170) REVERT: SL 272 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7300 (m-30) REVERT: SO 343 MET cc_start: 0.5843 (OUTLIER) cc_final: 0.5308 (ttm) REVERT: ST 213 GLN cc_start: 0.8145 (mt0) cc_final: 0.7859 (mt0) REVERT: SV 93 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7323 (ptm) REVERT: SZ 171 GLN cc_start: 0.7339 (mm110) cc_final: 0.7114 (tp40) outliers start: 147 outliers final: 72 residues processed: 718 average time/residue: 1.8466 time to fit residues: 1785.6155 Evaluate side-chains 699 residues out of total 6049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 615 time to evaluate : 5.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 115 GLN Chi-restraints excluded: chain L7 residue 57 PHE Chi-restraints excluded: chain L7 residue 132 THR Chi-restraints excluded: chain L7 residue 141 LEU Chi-restraints excluded: chain L8 residue 33 GLN Chi-restraints excluded: chain L8 residue 43 THR Chi-restraints excluded: chain L8 residue 61 ILE Chi-restraints excluded: chain L8 residue 70 GLN Chi-restraints excluded: chain L8 residue 130 LEU Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 12 THR Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 109 VAL Chi-restraints excluded: chain LB residue 5 ILE Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 111 SER Chi-restraints excluded: chain LC residue 92 ASN Chi-restraints excluded: chain LC residue 124 ILE Chi-restraints excluded: chain LE residue 143 THR Chi-restraints excluded: chain LE residue 147 GLU Chi-restraints excluded: chain LG residue 30 ASP Chi-restraints excluded: chain LG residue 64 THR Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LI residue 37 GLU Chi-restraints excluded: chain LI residue 56 GLN Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LI residue 112 ASP Chi-restraints excluded: chain LL residue 52 GLU Chi-restraints excluded: chain LN residue 198 ARG Chi-restraints excluded: chain LN residue 208 ASN Chi-restraints excluded: chain LN residue 329 ASP Chi-restraints excluded: chain LN residue 381 THR Chi-restraints excluded: chain LN residue 382 MET Chi-restraints excluded: chain LQ residue 21 ILE Chi-restraints excluded: chain LS residue 53 SER Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LU residue 22 SER Chi-restraints excluded: chain NE residue 273 LEU Chi-restraints excluded: chain NG residue 211 ILE Chi-restraints excluded: chain NN residue 19 LEU Chi-restraints excluded: chain NN residue 131 HIS Chi-restraints excluded: chain SA residue 22 VAL Chi-restraints excluded: chain SA residue 138 MET Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SA residue 276 ASN Chi-restraints excluded: chain SC residue 50 LEU Chi-restraints excluded: chain SC residue 194 VAL Chi-restraints excluded: chain SD residue 67 THR Chi-restraints excluded: chain SD residue 229 GLU Chi-restraints excluded: chain SE residue 70 LEU Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SH residue 72 THR Chi-restraints excluded: chain SH residue 156 THR Chi-restraints excluded: chain SI residue 57 ARG Chi-restraints excluded: chain SI residue 147 VAL Chi-restraints excluded: chain SJ residue 674 ILE Chi-restraints excluded: chain SJ residue 701 LEU Chi-restraints excluded: chain SJ residue 709 GLU Chi-restraints excluded: chain SJ residue 719 VAL Chi-restraints excluded: chain SK residue 28 ILE Chi-restraints excluded: chain SK residue 137 VAL Chi-restraints excluded: chain SK residue 192 VAL Chi-restraints excluded: chain SL residue 64 LEU Chi-restraints excluded: chain SL residue 94 ASP Chi-restraints excluded: chain SL residue 244 LYS Chi-restraints excluded: chain SL residue 272 ASP Chi-restraints excluded: chain SM residue 21 ASN Chi-restraints excluded: chain SM residue 67 ILE Chi-restraints excluded: chain SM residue 86 LYS Chi-restraints excluded: chain SM residue 427 VAL Chi-restraints excluded: chain SN residue 73 THR Chi-restraints excluded: chain SN residue 116 VAL Chi-restraints excluded: chain SN residue 143 SER Chi-restraints excluded: chain SN residue 267 ASP Chi-restraints excluded: chain SO residue 343 MET Chi-restraints excluded: chain SR residue 369 ASP Chi-restraints excluded: chain SS residue 228 SER Chi-restraints excluded: chain ST residue 214 SER Chi-restraints excluded: chain SV residue 22 VAL Chi-restraints excluded: chain SV residue 28 VAL Chi-restraints excluded: chain SV residue 64 THR Chi-restraints excluded: chain SV residue 93 MET Chi-restraints excluded: chain SZ residue 88 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 275 optimal weight: 7.9990 chunk 736 optimal weight: 5.9990 chunk 161 optimal weight: 40.0000 chunk 480 optimal weight: 0.0670 chunk 201 optimal weight: 9.9990 chunk 818 optimal weight: 4.9990 chunk 679 optimal weight: 2.9990 chunk 378 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 270 optimal weight: 0.8980 chunk 429 optimal weight: 1.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L7 96 GLN ** LA 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LC 117 HIS LG 36 ASN LI 14 ASN LN 289 GLN LQ 102 ASN NN 68 ASN ** NN 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SD 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 64 GLN ** SI 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SI 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SJ 726 HIS ** SK 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SL 30 GLN SL 104 ASN SM 243 ASN SS 208 GLN ** SS 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SS 332 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 99287 Z= 0.189 Angle : 0.494 8.973 142460 Z= 0.255 Chirality : 0.034 0.216 17177 Planarity : 0.004 0.045 11468 Dihedral : 21.970 179.229 36055 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.97 % Allowed : 12.78 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.07 (0.10), residues: 6742 helix: 1.71 (0.10), residues: 2814 sheet: 0.15 (0.17), residues: 893 loop : 0.02 (0.11), residues: 3035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRPSR 417 HIS 0.012 0.001 HISSJ 726 PHE 0.020 0.001 PHESK 154 TYR 0.020 0.001 TYRNN 185 ARG 0.006 0.000 ARGSJ 728 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13484 Ramachandran restraints generated. 6742 Oldfield, 0 Emsley, 6742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13484 Ramachandran restraints generated. 6742 Oldfield, 0 Emsley, 6742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 6049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 655 time to evaluate : 5.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L6 115 GLN cc_start: 0.7037 (OUTLIER) cc_final: 0.6816 (mt0) REVERT: L8 33 GLN cc_start: 0.8042 (pt0) cc_final: 0.7752 (pm20) REVERT: L8 70 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7749 (tt0) REVERT: LC 92 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.8018 (m-40) REVERT: LI 37 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6821 (tm-30) REVERT: SD 41 MET cc_start: 0.7554 (mmm) cc_final: 0.6910 (mmt) REVERT: SD 187 MET cc_start: 0.8526 (mmm) cc_final: 0.8176 (mmt) REVERT: SO 343 MET cc_start: 0.5815 (OUTLIER) cc_final: 0.5290 (ttm) REVERT: SR 441 TYR cc_start: 0.5487 (m-10) cc_final: 0.5271 (m-10) REVERT: ST 213 GLN cc_start: 0.8276 (mt0) cc_final: 0.7933 (mt0) REVERT: ST 217 GLU cc_start: 0.7718 (tt0) cc_final: 0.7512 (tt0) REVERT: SV 109 MET cc_start: 0.6051 (OUTLIER) cc_final: 0.5671 (mmt) REVERT: SZ 171 GLN cc_start: 0.7290 (mm110) cc_final: 0.7079 (tp40) outliers start: 116 outliers final: 63 residues processed: 723 average time/residue: 1.8175 time to fit residues: 1773.3979 Evaluate side-chains 693 residues out of total 6049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 624 time to evaluate : 5.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 115 GLN Chi-restraints excluded: chain L7 residue 57 PHE Chi-restraints excluded: chain L7 residue 132 THR Chi-restraints excluded: chain L8 residue 43 THR Chi-restraints excluded: chain L8 residue 61 ILE Chi-restraints excluded: chain L8 residue 70 GLN Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 12 THR Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 36 ILE Chi-restraints excluded: chain LB residue 5 ILE Chi-restraints excluded: chain LC residue 92 ASN Chi-restraints excluded: chain LC residue 124 ILE Chi-restraints excluded: chain LE residue 147 GLU Chi-restraints excluded: chain LG residue 30 ASP Chi-restraints excluded: chain LG residue 31 ASN Chi-restraints excluded: chain LG residue 65 VAL Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LI residue 37 GLU Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LI residue 112 ASP Chi-restraints excluded: chain LL residue 52 GLU Chi-restraints excluded: chain LL residue 56 ASP Chi-restraints excluded: chain LN residue 208 ASN Chi-restraints excluded: chain LN residue 329 ASP Chi-restraints excluded: chain LN residue 344 VAL Chi-restraints excluded: chain LN residue 381 THR Chi-restraints excluded: chain LQ residue 21 ILE Chi-restraints excluded: chain LS residue 53 SER Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LU residue 22 SER Chi-restraints excluded: chain NE residue 273 LEU Chi-restraints excluded: chain NG residue 211 ILE Chi-restraints excluded: chain NN residue 131 HIS Chi-restraints excluded: chain SA residue 22 VAL Chi-restraints excluded: chain SA residue 154 VAL Chi-restraints excluded: chain SA residue 276 ASN Chi-restraints excluded: chain SC residue 194 VAL Chi-restraints excluded: chain SD residue 67 THR Chi-restraints excluded: chain SE residue 70 LEU Chi-restraints excluded: chain SE residue 207 VAL Chi-restraints excluded: chain SH residue 156 THR Chi-restraints excluded: chain SH residue 190 LEU Chi-restraints excluded: chain SI residue 147 VAL Chi-restraints excluded: chain SI residue 255 ASN Chi-restraints excluded: chain SJ residue 674 ILE Chi-restraints excluded: chain SJ residue 709 GLU Chi-restraints excluded: chain SK residue 28 ILE Chi-restraints excluded: chain SK residue 137 VAL Chi-restraints excluded: chain SK residue 198 VAL Chi-restraints excluded: chain SL residue 64 LEU Chi-restraints excluded: chain SL residue 94 ASP Chi-restraints excluded: chain SL residue 179 VAL Chi-restraints excluded: chain SL residue 244 LYS Chi-restraints excluded: chain SM residue 67 ILE Chi-restraints excluded: chain SM residue 427 VAL Chi-restraints excluded: chain SN residue 73 THR Chi-restraints excluded: chain SN residue 116 VAL Chi-restraints excluded: chain SN residue 143 SER Chi-restraints excluded: chain SN residue 267 ASP Chi-restraints excluded: chain SO residue 343 MET Chi-restraints excluded: chain SR residue 369 ASP Chi-restraints excluded: chain SS residue 228 SER Chi-restraints excluded: chain SV residue 22 VAL Chi-restraints excluded: chain SV residue 28 VAL Chi-restraints excluded: chain SV residue 64 THR Chi-restraints excluded: chain SV residue 109 MET Chi-restraints excluded: chain SZ residue 88 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 789 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 466 optimal weight: 6.9990 chunk 597 optimal weight: 2.9990 chunk 463 optimal weight: 4.9990 chunk 689 optimal weight: 0.0040 chunk 457 optimal weight: 0.7980 chunk 815 optimal weight: 0.9990 chunk 510 optimal weight: 3.9990 chunk 497 optimal weight: 0.0670 chunk 376 optimal weight: 0.6980 overall best weight: 0.5132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L7 96 GLN L7 150 GLN ** LA 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LC 117 HIS LE 114 GLN LG 36 ASN LI 14 ASN LN 289 GLN ** SD 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 248 ASN SE 64 GLN ** SI 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SI 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SJ 687 ASN SJ 726 HIS ** SK 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SL 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SL 104 ASN SM 243 ASN SN 146 GLN SO 265 HIS SS 208 GLN ** SS 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SS 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ST 236 GLN ** SV 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 99287 Z= 0.125 Angle : 0.473 11.633 142460 Z= 0.244 Chirality : 0.033 0.245 17177 Planarity : 0.003 0.044 11468 Dihedral : 21.912 179.175 36055 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.39 % Allowed : 13.66 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.22 (0.10), residues: 6742 helix: 1.78 (0.10), residues: 2826 sheet: 0.25 (0.17), residues: 905 loop : 0.16 (0.11), residues: 3011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRPL9 120 HIS 0.016 0.001 HISSJ 726 PHE 0.015 0.001 PHEL7 57 TYR 0.032 0.001 TYRLK 61 ARG 0.006 0.000 ARGL6 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13484 Ramachandran restraints generated. 6742 Oldfield, 0 Emsley, 6742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13484 Ramachandran restraints generated. 6742 Oldfield, 0 Emsley, 6742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 6049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 662 time to evaluate : 6.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L6 115 GLN cc_start: 0.7011 (OUTLIER) cc_final: 0.6775 (mt0) REVERT: L7 113 ASP cc_start: 0.7633 (p0) cc_final: 0.7140 (p0) REVERT: L8 33 GLN cc_start: 0.8069 (pt0) cc_final: 0.7802 (pm20) REVERT: LC 92 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.8111 (m-40) REVERT: SD 41 MET cc_start: 0.7430 (mmm) cc_final: 0.6836 (mmt) REVERT: SD 187 MET cc_start: 0.8558 (mmm) cc_final: 0.8196 (mmt) REVERT: SH 106 MET cc_start: 0.7622 (mmt) cc_final: 0.7401 (mmt) REVERT: SI 57 ARG cc_start: 0.5722 (OUTLIER) cc_final: 0.5408 (ttp-170) REVERT: SJ 668 LEU cc_start: 0.8097 (mp) cc_final: 0.7848 (mt) REVERT: SO 343 MET cc_start: 0.5905 (mtt) cc_final: 0.5324 (ttm) REVERT: ST 213 GLN cc_start: 0.8283 (mt0) cc_final: 0.7902 (mt0) REVERT: ST 217 GLU cc_start: 0.7693 (tt0) cc_final: 0.7475 (tt0) outliers start: 82 outliers final: 35 residues processed: 710 average time/residue: 1.8581 time to fit residues: 1785.9728 Evaluate side-chains 649 residues out of total 6049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 611 time to evaluate : 6.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L6 residue 115 GLN Chi-restraints excluded: chain L8 residue 43 THR Chi-restraints excluded: chain L8 residue 61 ILE Chi-restraints excluded: chain LA residue 36 ILE Chi-restraints excluded: chain LB residue 5 ILE Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 92 VAL Chi-restraints excluded: chain LC residue 92 ASN Chi-restraints excluded: chain LC residue 124 ILE Chi-restraints excluded: chain LG residue 65 VAL Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LI residue 112 ASP Chi-restraints excluded: chain LQ residue 21 ILE Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain NG residue 211 ILE Chi-restraints excluded: chain NN residue 131 HIS Chi-restraints excluded: chain SA residue 276 ASN Chi-restraints excluded: chain SE residue 207 VAL Chi-restraints excluded: chain SH residue 190 LEU Chi-restraints excluded: chain SI residue 57 ARG Chi-restraints excluded: chain SJ residue 674 ILE Chi-restraints excluded: chain SJ residue 719 VAL Chi-restraints excluded: chain SK residue 28 ILE Chi-restraints excluded: chain SK residue 147 LEU Chi-restraints excluded: chain SK residue 192 VAL Chi-restraints excluded: chain SK residue 198 VAL Chi-restraints excluded: chain SL residue 64 LEU Chi-restraints excluded: chain SL residue 179 VAL Chi-restraints excluded: chain SL residue 244 LYS Chi-restraints excluded: chain SM residue 67 ILE Chi-restraints excluded: chain SN residue 73 THR Chi-restraints excluded: chain SN residue 143 SER Chi-restraints excluded: chain SN residue 268 VAL Chi-restraints excluded: chain SO residue 265 HIS Chi-restraints excluded: chain SR residue 369 ASP Chi-restraints excluded: chain SV residue 22 VAL Chi-restraints excluded: chain SV residue 110 ASN Chi-restraints excluded: chain SW residue 304 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 504 optimal weight: 2.9990 chunk 325 optimal weight: 7.9990 chunk 487 optimal weight: 1.9990 chunk 245 optimal weight: 3.9990 chunk 160 optimal weight: 20.0000 chunk 157 optimal weight: 30.0000 chunk 518 optimal weight: 1.9990 chunk 555 optimal weight: 5.9990 chunk 403 optimal weight: 7.9990 chunk 75 optimal weight: 20.0000 chunk 640 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L7 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L7 96 GLN L7 150 GLN L8 125 ASN ** LA 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LG 36 ASN LI 14 ASN LQ 102 ASN ** NN 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SD 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 64 GLN SI 71 GLN SI 249 GLN SI 253 GLN SJ 687 ASN ** SJ 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SK 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SL 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SL 104 ASN SL 112 GLN SM 243 ASN SS 138 ASN SS 208 GLN ** SS 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SZ 171 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 99287 Z= 0.304 Angle : 0.540 11.369 142460 Z= 0.276 Chirality : 0.037 0.212 17177 Planarity : 0.004 0.048 11468 Dihedral : 21.859 179.884 36055 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.72 % Allowed : 13.78 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.07 (0.10), residues: 6742 helix: 1.67 (0.10), residues: 2808 sheet: 0.18 (0.17), residues: 911 loop : 0.06 (0.11), residues: 3023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPLC 81 HIS 0.015 0.001 HISSO 265 PHE 0.023 0.002 PHESK 222 TYR 0.022 0.002 TYRLB 32 ARG 0.014 0.001 ARGSM 313 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13484 Ramachandran restraints generated. 6742 Oldfield, 0 Emsley, 6742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13484 Ramachandran restraints generated. 6742 Oldfield, 0 Emsley, 6742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 6049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 636 time to evaluate : 6.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L6 115 GLN cc_start: 0.7011 (OUTLIER) cc_final: 0.6752 (mt0) REVERT: L7 113 ASP cc_start: 0.7733 (p0) cc_final: 0.7244 (p0) REVERT: L8 33 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7810 (pm20) REVERT: L8 70 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7768 (tt0) REVERT: LA 23 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.7685 (mpp80) REVERT: LC 92 ASN cc_start: 0.8429 (OUTLIER) cc_final: 0.8065 (m-40) REVERT: SD 187 MET cc_start: 0.8543 (mmm) cc_final: 0.8208 (mmt) REVERT: SI 57 ARG cc_start: 0.5750 (OUTLIER) cc_final: 0.5411 (ttp-170) REVERT: SJ 668 LEU cc_start: 0.8167 (mp) cc_final: 0.7925 (mt) REVERT: SR 451 GLU cc_start: 0.5601 (tp30) cc_final: 0.5396 (tp30) REVERT: ST 213 GLN cc_start: 0.8263 (mt0) cc_final: 0.7786 (mt0) REVERT: ST 217 GLU cc_start: 0.7815 (tt0) cc_final: 0.7578 (tt0) REVERT: SV 111 ARG cc_start: 0.7001 (mtp-110) cc_final: 0.6782 (ttp80) outliers start: 101 outliers final: 64 residues processed: 696 average time/residue: 1.8046 time to fit residues: 1694.0371 Evaluate side-chains 688 residues out of total 6049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 618 time to evaluate : 5.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 115 GLN Chi-restraints excluded: chain L8 residue 33 GLN Chi-restraints excluded: chain L8 residue 43 THR Chi-restraints excluded: chain L8 residue 61 ILE Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 70 GLN Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain LA residue 5 SER Chi-restraints excluded: chain LA residue 12 THR Chi-restraints excluded: chain LA residue 23 ARG Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 36 ILE Chi-restraints excluded: chain LB residue 5 ILE Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 92 VAL Chi-restraints excluded: chain LB residue 111 SER Chi-restraints excluded: chain LC residue 92 ASN Chi-restraints excluded: chain LC residue 124 ILE Chi-restraints excluded: chain LC residue 156 HIS Chi-restraints excluded: chain LE residue 147 GLU Chi-restraints excluded: chain LG residue 30 ASP Chi-restraints excluded: chain LG residue 65 VAL Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LG residue 108 ASN Chi-restraints excluded: chain LI residue 86 GLN Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LI residue 112 ASP Chi-restraints excluded: chain LK residue 5 LEU Chi-restraints excluded: chain LL residue 52 GLU Chi-restraints excluded: chain LN residue 53 MET Chi-restraints excluded: chain LN residue 208 ASN Chi-restraints excluded: chain LN residue 237 THR Chi-restraints excluded: chain LN residue 329 ASP Chi-restraints excluded: chain LN residue 344 VAL Chi-restraints excluded: chain LQ residue 21 ILE Chi-restraints excluded: chain LS residue 53 SER Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain NG residue 211 ILE Chi-restraints excluded: chain NN residue 131 HIS Chi-restraints excluded: chain SA residue 22 VAL Chi-restraints excluded: chain SA residue 276 ASN Chi-restraints excluded: chain SC residue 50 LEU Chi-restraints excluded: chain SC residue 194 VAL Chi-restraints excluded: chain SD residue 196 THR Chi-restraints excluded: chain SE residue 70 LEU Chi-restraints excluded: chain SE residue 207 VAL Chi-restraints excluded: chain SH residue 133 ASP Chi-restraints excluded: chain SH residue 190 LEU Chi-restraints excluded: chain SI residue 57 ARG Chi-restraints excluded: chain SI residue 255 ASN Chi-restraints excluded: chain SJ residue 674 ILE Chi-restraints excluded: chain SJ residue 701 LEU Chi-restraints excluded: chain SJ residue 719 VAL Chi-restraints excluded: chain SK residue 28 ILE Chi-restraints excluded: chain SK residue 192 VAL Chi-restraints excluded: chain SK residue 198 VAL Chi-restraints excluded: chain SL residue 179 VAL Chi-restraints excluded: chain SL residue 244 LYS Chi-restraints excluded: chain SM residue 67 ILE Chi-restraints excluded: chain SN residue 73 THR Chi-restraints excluded: chain SN residue 143 SER Chi-restraints excluded: chain SR residue 369 ASP Chi-restraints excluded: chain SS residue 228 SER Chi-restraints excluded: chain SV residue 22 VAL Chi-restraints excluded: chain SV residue 28 VAL Chi-restraints excluded: chain SW residue 304 ILE Chi-restraints excluded: chain SZ residue 88 VAL Chi-restraints excluded: chain SZ residue 150 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 741 optimal weight: 0.6980 chunk 781 optimal weight: 8.9990 chunk 712 optimal weight: 0.9990 chunk 759 optimal weight: 1.9990 chunk 780 optimal weight: 6.9990 chunk 457 optimal weight: 0.9990 chunk 331 optimal weight: 6.9990 chunk 596 optimal weight: 3.9990 chunk 233 optimal weight: 0.9990 chunk 686 optimal weight: 3.9990 chunk 718 optimal weight: 4.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L7 96 GLN ** LA 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LC 117 HIS LE 114 GLN LG 36 ASN LI 14 ASN ** NN 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SD 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 64 GLN SI 71 GLN ** SI 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SI 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SI 253 GLN ** SJ 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SL 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SL 104 ASN SL 112 GLN SM 243 ASN SR 421 ASN SS 149 HIS SS 208 GLN SV 110 ASN ** SV 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SZ 171 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 99287 Z= 0.162 Angle : 0.489 12.836 142460 Z= 0.250 Chirality : 0.033 0.230 17177 Planarity : 0.004 0.044 11468 Dihedral : 21.863 179.112 36055 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.39 % Allowed : 14.36 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.10), residues: 6742 helix: 1.78 (0.10), residues: 2803 sheet: 0.27 (0.17), residues: 886 loop : 0.11 (0.11), residues: 3053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRPLC 81 HIS 0.013 0.001 HISSJ 726 PHE 0.014 0.001 PHELK 69 TYR 0.025 0.001 TYRLG 38 ARG 0.008 0.000 ARGNN 271 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13484 Ramachandran restraints generated. 6742 Oldfield, 0 Emsley, 6742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13484 Ramachandran restraints generated. 6742 Oldfield, 0 Emsley, 6742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 6049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 629 time to evaluate : 6.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L6 115 GLN cc_start: 0.7012 (OUTLIER) cc_final: 0.6790 (mt0) REVERT: L8 33 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7849 (pm20) REVERT: L8 70 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7715 (tt0) REVERT: LA 23 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7672 (mpp80) REVERT: LC 92 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.8049 (m-40) REVERT: LC 99 ASP cc_start: 0.7306 (t0) cc_final: 0.7024 (t0) REVERT: LE 120 LYS cc_start: 0.6145 (mmtp) cc_final: 0.5643 (tppt) REVERT: LI 37 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6797 (tm-30) REVERT: SD 41 MET cc_start: 0.7497 (mmm) cc_final: 0.6863 (mmt) REVERT: SD 187 MET cc_start: 0.8534 (mmm) cc_final: 0.8191 (mmt) REVERT: SJ 668 LEU cc_start: 0.8129 (mp) cc_final: 0.7884 (mt) REVERT: ST 213 GLN cc_start: 0.8247 (mt0) cc_final: 0.7768 (mt0) REVERT: ST 217 GLU cc_start: 0.7772 (tt0) cc_final: 0.7505 (tt0) outliers start: 82 outliers final: 55 residues processed: 677 average time/residue: 1.8723 time to fit residues: 1715.1165 Evaluate side-chains 676 residues out of total 6049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 615 time to evaluate : 5.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L6 residue 115 GLN Chi-restraints excluded: chain L8 residue 33 GLN Chi-restraints excluded: chain L8 residue 43 THR Chi-restraints excluded: chain L8 residue 61 ILE Chi-restraints excluded: chain L8 residue 70 GLN Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain LA residue 12 THR Chi-restraints excluded: chain LA residue 23 ARG Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 36 ILE Chi-restraints excluded: chain LB residue 5 ILE Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 92 VAL Chi-restraints excluded: chain LC residue 92 ASN Chi-restraints excluded: chain LC residue 124 ILE Chi-restraints excluded: chain LC residue 156 HIS Chi-restraints excluded: chain LG residue 30 ASP Chi-restraints excluded: chain LG residue 65 VAL Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LI residue 37 GLU Chi-restraints excluded: chain LI residue 86 GLN Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LI residue 112 ASP Chi-restraints excluded: chain LK residue 5 LEU Chi-restraints excluded: chain LL residue 56 ASP Chi-restraints excluded: chain LN residue 67 VAL Chi-restraints excluded: chain LN residue 208 ASN Chi-restraints excluded: chain LN residue 237 THR Chi-restraints excluded: chain LN residue 329 ASP Chi-restraints excluded: chain LN residue 344 VAL Chi-restraints excluded: chain LQ residue 21 ILE Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LU residue 22 SER Chi-restraints excluded: chain NG residue 211 ILE Chi-restraints excluded: chain NN residue 131 HIS Chi-restraints excluded: chain SA residue 22 VAL Chi-restraints excluded: chain SA residue 276 ASN Chi-restraints excluded: chain SC residue 194 VAL Chi-restraints excluded: chain SE residue 207 VAL Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SH residue 133 ASP Chi-restraints excluded: chain SH residue 190 LEU Chi-restraints excluded: chain SJ residue 674 ILE Chi-restraints excluded: chain SJ residue 701 LEU Chi-restraints excluded: chain SJ residue 719 VAL Chi-restraints excluded: chain SK residue 28 ILE Chi-restraints excluded: chain SK residue 192 VAL Chi-restraints excluded: chain SK residue 198 VAL Chi-restraints excluded: chain SL residue 64 LEU Chi-restraints excluded: chain SL residue 179 VAL Chi-restraints excluded: chain SL residue 244 LYS Chi-restraints excluded: chain SM residue 67 ILE Chi-restraints excluded: chain SN residue 73 THR Chi-restraints excluded: chain SN residue 143 SER Chi-restraints excluded: chain SO residue 289 LEU Chi-restraints excluded: chain SR residue 369 ASP Chi-restraints excluded: chain SV residue 22 VAL Chi-restraints excluded: chain SV residue 28 VAL Chi-restraints excluded: chain SV residue 64 THR Chi-restraints excluded: chain SZ residue 150 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 757 optimal weight: 1.9990 chunk 498 optimal weight: 0.9980 chunk 803 optimal weight: 9.9990 chunk 490 optimal weight: 0.9990 chunk 381 optimal weight: 1.9990 chunk 558 optimal weight: 2.9990 chunk 842 optimal weight: 3.9990 chunk 775 optimal weight: 3.9990 chunk 671 optimal weight: 2.9990 chunk 69 optimal weight: 20.0000 chunk 518 optimal weight: 7.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L7 96 GLN L8 125 ASN ** LA 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LC 117 HIS LE 114 GLN LG 36 ASN LI 14 ASN LQ 102 ASN NN 137 HIS ** SD 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SD 248 ASN SE 64 GLN SI 71 GLN SI 253 GLN ** SJ 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SL 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SL 104 ASN SL 112 GLN SM 243 ASN SS 208 GLN ** SV 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SZ 171 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 99287 Z= 0.215 Angle : 0.508 15.250 142460 Z= 0.259 Chirality : 0.035 0.236 17177 Planarity : 0.004 0.045 11468 Dihedral : 21.836 179.182 36055 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.29 % Allowed : 14.48 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: 1.14 (0.10), residues: 6742 helix: 1.74 (0.10), residues: 2805 sheet: 0.27 (0.17), residues: 870 loop : 0.08 (0.11), residues: 3067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRPLC 81 HIS 0.014 0.001 HISSJ 726 PHE 0.023 0.001 PHESK 154 TYR 0.021 0.001 TYRLK 61 ARG 0.010 0.000 ARGST 234 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13484 Ramachandran restraints generated. 6742 Oldfield, 0 Emsley, 6742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13484 Ramachandran restraints generated. 6742 Oldfield, 0 Emsley, 6742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 6049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 621 time to evaluate : 5.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L6 115 GLN cc_start: 0.7015 (OUTLIER) cc_final: 0.6777 (mt0) REVERT: L7 113 ASP cc_start: 0.7671 (p0) cc_final: 0.7154 (p0) REVERT: L7 186 GLU cc_start: 0.7021 (mp0) cc_final: 0.6650 (mm-30) REVERT: L8 33 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7870 (pm20) REVERT: L8 70 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7766 (tt0) REVERT: LA 23 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7681 (mpp80) REVERT: LC 92 ASN cc_start: 0.8399 (OUTLIER) cc_final: 0.8048 (m-40) REVERT: LC 99 ASP cc_start: 0.7339 (t0) cc_final: 0.7052 (t0) REVERT: LE 120 LYS cc_start: 0.6386 (mmtp) cc_final: 0.5876 (tppt) REVERT: SD 41 MET cc_start: 0.7523 (mmm) cc_final: 0.6881 (mmt) REVERT: SD 187 MET cc_start: 0.8541 (mmm) cc_final: 0.8203 (mmt) REVERT: SJ 668 LEU cc_start: 0.8146 (mp) cc_final: 0.7908 (mt) REVERT: SR 432 ILE cc_start: 0.7718 (pp) cc_final: 0.7510 (pt) REVERT: ST 213 GLN cc_start: 0.8245 (mt0) cc_final: 0.7773 (mt0) REVERT: ST 217 GLU cc_start: 0.7784 (tt0) cc_final: 0.7441 (tt0) outliers start: 76 outliers final: 59 residues processed: 667 average time/residue: 1.8755 time to fit residues: 1686.0677 Evaluate side-chains 679 residues out of total 6049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 615 time to evaluate : 5.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L6 residue 115 GLN Chi-restraints excluded: chain L8 residue 33 GLN Chi-restraints excluded: chain L8 residue 43 THR Chi-restraints excluded: chain L8 residue 61 ILE Chi-restraints excluded: chain L8 residue 67 SER Chi-restraints excluded: chain L8 residue 70 GLN Chi-restraints excluded: chain L9 residue 60 VAL Chi-restraints excluded: chain LA residue 12 THR Chi-restraints excluded: chain LA residue 23 ARG Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 36 ILE Chi-restraints excluded: chain LB residue 5 ILE Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 92 VAL Chi-restraints excluded: chain LC residue 92 ASN Chi-restraints excluded: chain LC residue 124 ILE Chi-restraints excluded: chain LC residue 156 HIS Chi-restraints excluded: chain LE residue 143 THR Chi-restraints excluded: chain LG residue 30 ASP Chi-restraints excluded: chain LG residue 65 VAL Chi-restraints excluded: chain LG residue 81 VAL Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LI residue 86 GLN Chi-restraints excluded: chain LI residue 94 THR Chi-restraints excluded: chain LI residue 112 ASP Chi-restraints excluded: chain LK residue 5 LEU Chi-restraints excluded: chain LL residue 56 ASP Chi-restraints excluded: chain LN residue 53 MET Chi-restraints excluded: chain LN residue 67 VAL Chi-restraints excluded: chain LN residue 208 ASN Chi-restraints excluded: chain LN residue 237 THR Chi-restraints excluded: chain LN residue 329 ASP Chi-restraints excluded: chain LN residue 344 VAL Chi-restraints excluded: chain LQ residue 21 ILE Chi-restraints excluded: chain LS residue 53 SER Chi-restraints excluded: chain LT residue 33 VAL Chi-restraints excluded: chain LU residue 22 SER Chi-restraints excluded: chain NN residue 131 HIS Chi-restraints excluded: chain SA residue 22 VAL Chi-restraints excluded: chain SA residue 276 ASN Chi-restraints excluded: chain SC residue 50 LEU Chi-restraints excluded: chain SC residue 194 VAL Chi-restraints excluded: chain SE residue 207 VAL Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SH residue 133 ASP Chi-restraints excluded: chain SH residue 190 LEU Chi-restraints excluded: chain SI residue 231 VAL Chi-restraints excluded: chain SJ residue 674 ILE Chi-restraints excluded: chain SJ residue 719 VAL Chi-restraints excluded: chain SK residue 28 ILE Chi-restraints excluded: chain SK residue 192 VAL Chi-restraints excluded: chain SK residue 198 VAL Chi-restraints excluded: chain SL residue 64 LEU Chi-restraints excluded: chain SL residue 179 VAL Chi-restraints excluded: chain SL residue 244 LYS Chi-restraints excluded: chain SM residue 67 ILE Chi-restraints excluded: chain SN residue 73 THR Chi-restraints excluded: chain SN residue 143 SER Chi-restraints excluded: chain SR residue 369 ASP Chi-restraints excluded: chain SS residue 328 LEU Chi-restraints excluded: chain SV residue 22 VAL Chi-restraints excluded: chain SV residue 28 VAL Chi-restraints excluded: chain SV residue 64 THR Chi-restraints excluded: chain SZ residue 150 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 411 optimal weight: 3.9990 chunk 533 optimal weight: 2.9990 chunk 714 optimal weight: 4.9990 chunk 205 optimal weight: 8.9990 chunk 618 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 186 optimal weight: 5.9990 chunk 672 optimal weight: 0.7980 chunk 281 optimal weight: 50.0000 chunk 690 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L7 96 GLN L8 125 ASN ** LA 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LC 117 HIS LE 114 GLN LG 36 ASN LI 14 ASN LQ 102 ASN NN 68 ASN ** SD 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 64 GLN SI 71 GLN SI 253 GLN ** SJ 726 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SK 82 GLN ** SL 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SL 104 ASN SL 112 GLN SM 243 ASN SS 208 GLN SZ 171 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.093824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.063378 restraints weight = 244817.543| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.71 r_work: 0.2891 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 99287 Z= 0.359 Angle : 0.583 15.977 142460 Z= 0.296 Chirality : 0.039 0.255 17177 Planarity : 0.005 0.049 11468 Dihedral : 21.880 179.840 36055 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.51 % Allowed : 14.38 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.10), residues: 6742 helix: 1.50 (0.10), residues: 2812 sheet: 0.13 (0.17), residues: 876 loop : -0.07 (0.11), residues: 3054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRPLC 81 HIS 0.013 0.001 HISSJ 726 PHE 0.024 0.002 PHENN 194 TYR 0.027 0.002 TYRLG 38 ARG 0.008 0.001 ARGNN 271 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29485.61 seconds wall clock time: 516 minutes 27.04 seconds (30987.04 seconds total)