Starting phenix.real_space_refine on Sun Mar 17 09:40:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eup_24410/03_2024/8eup_24410.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eup_24410/03_2024/8eup_24410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eup_24410/03_2024/8eup_24410.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eup_24410/03_2024/8eup_24410.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eup_24410/03_2024/8eup_24410.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eup_24410/03_2024/8eup_24410.pdb" } resolution = 3.1 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= 0.000 sd= 0.008 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1623 5.49 5 S 99 5.16 5 C 43129 2.51 5 N 14617 2.21 5 O 19253 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "3 TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 24": "OE1" <-> "OE2" Residue "4 GLU 175": "OE1" <-> "OE2" Residue "5 GLU 52": "OE1" <-> "OE2" Residue "5 PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 360": "OD1" <-> "OD2" Residue "E TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 77": "OE1" <-> "OE2" Residue "E ASP 110": "OD1" <-> "OD2" Residue "E GLU 152": "OE1" <-> "OE2" Residue "E ASP 156": "OD1" <-> "OD2" Residue "E ASP 188": "OD1" <-> "OD2" Residue "F TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 87": "OE1" <-> "OE2" Residue "F ASP 190": "OD1" <-> "OD2" Residue "F TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 99": "OE1" <-> "OE2" Residue "P ASP 108": "OD1" <-> "OD2" Residue "S TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 108": "OD1" <-> "OD2" Residue "Y TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 127": "OE1" <-> "OE2" Residue "h PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 22": "OE1" <-> "OE2" Residue "h GLU 62": "OE1" <-> "OE2" Residue "i GLU 44": "OE1" <-> "OE2" Residue "m GLU 212": "OE1" <-> "OE2" Residue "m GLU 231": "OE1" <-> "OE2" Residue "m GLU 251": "OE1" <-> "OE2" Residue "v TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 136": "OE1" <-> "OE2" Residue "v GLU 143": "OE1" <-> "OE2" Residue "v TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 184": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 78722 Number of models: 1 Model: "" Number of chains: 41 Chain: "1" Number of atoms: 30438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1422, 30438 Classifications: {'RNA': 1422} Modifications used: {'rna2p_pur': 148, 'rna2p_pyr': 95, 'rna3p_pur': 650, 'rna3p_pyr': 529} Link IDs: {'rna2p': 242, 'rna3p': 1179} Chain breaks: 25 Chain: "2" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3109 Classifications: {'RNA': 146} Modifications used: {'rna2p_pur': 16, 'rna2p_pyr': 10, 'rna3p_pur': 61, 'rna3p_pyr': 59} Link IDs: {'rna2p': 25, 'rna3p': 120} Chain breaks: 3 Chain: "3" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1613 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 7, 'TRANS': 186} Chain: "4" Number of atoms: 1746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1746 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 8, 'TRANS': 198} Chain: "5" Number of atoms: 2669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2669 Classifications: {'peptide': 338} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 323} Chain breaks: 1 Chain: "6" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1167 Classifications: {'RNA': 55} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 9, 'rna3p_pur': 19, 'rna3p_pyr': 17} Link IDs: {'rna2p': 19, 'rna3p': 35} Chain breaks: 2 Chain: "A" Number of atoms: 2049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2049 Classifications: {'peptide': 253} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 240} Chain breaks: 1 Chain: "B" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 1552 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 269} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 302} Chain breaks: 1 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1014 Unresolved non-hydrogen angles: 1280 Unresolved non-hydrogen dihedrals: 861 Unresolved non-hydrogen chiralities: 87 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 13, 'TYR:plan': 9, 'ASN:plan1': 9, 'TRP:plan': 4, 'HIS:plan': 10, 'PHE:plan': 13, 'GLU:plan': 19, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 526 Chain: "C" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2568 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 310} Chain breaks: 1 Chain: "D" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3055 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 16, 'TRANS': 383} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "E" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1328 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 156} Chain: "F" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1939 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 227} Chain: "G" Number of atoms: 1277 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 163, 1261 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 163, 1261 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain breaks: 1 bond proxies already assigned to first conformer: 1261 Chain: "H" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 862 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 157} Link IDs: {'PTRANS': 4, 'TRANS': 170} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 551 Unresolved non-hydrogen angles: 704 Unresolved non-hydrogen dihedrals: 442 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 16, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 5, 'GLU:plan': 9, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 281 Chain: "J" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 469 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 3, 'TRANS': 90} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 6, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 182 Chain: "K" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1225 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 220} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 232} Chain breaks: 1 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 753 Unresolved non-hydrogen angles: 955 Unresolved non-hydrogen dihedrals: 627 Unresolved non-hydrogen chiralities: 74 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 12, 'TRP:plan': 3, 'ASP:plan': 11, 'PHE:plan': 7, 'GLU:plan': 16, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 351 Chain: "L" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 942 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 9, 'TRANS': 106} Chain: "M" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 609 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 404 Unresolved non-hydrogen angles: 509 Unresolved non-hydrogen dihedrals: 344 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 6, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 3, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 209 Chain: "N" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1406 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain breaks: 2 Chain: "O" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1437 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 172} Chain breaks: 1 Chain: "P" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1037 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain breaks: 2 Chain: "Q" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1041 Classifications: {'peptide': 134} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 128} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1408 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 156} Chain breaks: 1 Chain: "V" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 619 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 342 Unresolved non-hydrogen angles: 433 Unresolved non-hydrogen dihedrals: 288 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 149 Chain: "Y" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 998 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "b" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 749 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 137} Link IDs: {'PTRANS': 2, 'TRANS': 148} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 514 Unresolved non-hydrogen angles: 649 Unresolved non-hydrogen dihedrals: 423 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 5, 'GLU:plan': 7, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 282 Chain: "e" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 995 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "f" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 839 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "h" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 993 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "i" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 783 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "j" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 563 Classifications: {'peptide': 71} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 68} Chain: "m" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 595 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 6, 'TRANS': 66} Chain breaks: 1 Chain: "o" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 673 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'PTRANS': 6, 'TRANS': 129} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 482 Unresolved non-hydrogen angles: 600 Unresolved non-hydrogen dihedrals: 416 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 5, 'HIS:plan': 7, 'PHE:plan': 7, 'GLU:plan': 8, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 253 Chain: "r" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 278 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'TRANS': 55} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 140 Chain: "t" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 167 Classifications: {'peptide': 23} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 22} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 35 Chain: "u" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 506 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 373 Unresolved non-hydrogen angles: 463 Unresolved non-hydrogen dihedrals: 331 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 6, 'GLU:plan': 2, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 211 Chain: "v" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1276 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 7, 'TRANS': 150} Chain breaks: 1 Chain: "x" Number of atoms: 2524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2524 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 294} Chain: "y" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1092 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 187} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 607 Unresolved non-hydrogen angles: 793 Unresolved non-hydrogen dihedrals: 469 Unresolved non-hydrogen chiralities: 79 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 14, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 7, 'GLU:plan': 16, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 328 Chain: "T" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 125 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 15} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "j" 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 70968 SG CYS j 19 89.105 92.703 164.308 1.00 57.49 S ATOM 70996 SG CYS j 22 90.908 93.585 161.483 1.00 37.55 S ATOM 71092 SG CYS j 34 90.107 90.050 161.484 1.00 41.22 S ATOM 71109 SG CYS j 37 92.818 91.522 163.890 1.00 41.58 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AASP G 227 " occ=0.20 ... (14 atoms not shown) pdb=" OD2BASP G 227 " occ=0.80 Time building chain proxies: 32.65, per 1000 atoms: 0.41 Number of scatterers: 78722 At special positions: 0 Unit cell: (226.84, 196.1, 311.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 99 16.00 P 1623 15.00 O 19253 8.00 N 14617 7.00 C 43129 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: 34.14 Conformation dependent library (CDL) restraints added in 7.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN j 101 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 22 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 19 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 34 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 37 " Number of angles added : 6 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11664 Finding SS restraints... Secondary structure from input PDB file: 224 helices and 57 sheets defined 42.0% alpha, 15.4% beta 487 base pairs and 883 stacking pairs defined. Time for finding SS restraints: 26.60 Creating SS restraints... Processing helix chain '3' and resid 3 through 12 Processing helix chain '3' and resid 66 through 70 Processing helix chain '3' and resid 85 through 97 Processing helix chain '3' and resid 101 through 128 Processing helix chain '3' and resid 137 through 156 removed outlier: 3.525A pdb=" N HIS 3 142 " --> pdb=" O PRO 3 138 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS 3 156 " --> pdb=" O LEU 3 152 " (cutoff:3.500A) Processing helix chain '3' and resid 156 through 172 Processing helix chain '3' and resid 182 through 194 removed outlier: 4.251A pdb=" N LYS 3 188 " --> pdb=" O GLU 3 184 " (cutoff:3.500A) Processing helix chain '4' and resid 8 through 12 removed outlier: 3.919A pdb=" N ALA 4 12 " --> pdb=" O ILE 4 8 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 8 through 12' Processing helix chain '4' and resid 15 through 30 removed outlier: 4.138A pdb=" N LYS 4 21 " --> pdb=" O LYS 4 17 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU 4 23 " --> pdb=" O ARG 4 19 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU 4 24 " --> pdb=" O ASP 4 20 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG 4 28 " --> pdb=" O GLU 4 24 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE 4 29 " --> pdb=" O SER 4 25 " (cutoff:3.500A) Processing helix chain '4' and resid 37 through 54 removed outlier: 3.505A pdb=" N PHE 4 41 " --> pdb=" O GLU 4 37 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET 4 54 " --> pdb=" O TYR 4 50 " (cutoff:3.500A) Processing helix chain '4' and resid 57 through 70 removed outlier: 3.890A pdb=" N SER 4 65 " --> pdb=" O GLN 4 61 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP 4 66 " --> pdb=" O GLN 4 62 " (cutoff:3.500A) Processing helix chain '4' and resid 79 through 93 Processing helix chain '4' and resid 99 through 101 No H-bonds generated for 'chain '4' and resid 99 through 101' Processing helix chain '4' and resid 102 through 128 removed outlier: 4.062A pdb=" N PHE 4 106 " --> pdb=" O ARG 4 102 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU 4 108 " --> pdb=" O ASP 4 104 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE 4 118 " --> pdb=" O CYS 4 114 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS 4 126 " --> pdb=" O GLN 4 122 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR 4 127 " --> pdb=" O THR 4 123 " (cutoff:3.500A) Processing helix chain '4' and resid 129 through 143 Processing helix chain '4' and resid 154 through 173 removed outlier: 3.974A pdb=" N LEU 4 158 " --> pdb=" O PRO 4 154 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR 4 166 " --> pdb=" O ALA 4 162 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N GLU 4 167 " --> pdb=" O ASP 4 163 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS 4 171 " --> pdb=" O GLU 4 167 " (cutoff:3.500A) Processing helix chain '4' and resid 183 through 188 Processing helix chain '4' and resid 195 through 202 Processing helix chain '5' and resid 40 through 43 Processing helix chain '5' and resid 166 through 170 Processing helix chain 'A' and resid 54 through 68 Processing helix chain 'A' and resid 85 through 94 Processing helix chain 'A' and resid 105 through 107 No H-bonds generated for 'chain 'A' and resid 105 through 107' Processing helix chain 'A' and resid 152 through 158 removed outlier: 4.328A pdb=" N ASP A 156 " --> pdb=" O ASP A 152 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 158 " --> pdb=" O THR A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 254 through 283 removed outlier: 3.894A pdb=" N ILE A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLN A 264 " --> pdb=" O ASN A 260 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ARG A 265 " --> pdb=" O GLN A 261 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N TYR A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL A 267 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN A 268 " --> pdb=" O GLN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 293 removed outlier: 4.094A pdb=" N ASN A 292 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL A 293 " --> pdb=" O LEU A 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 119 Processing helix chain 'B' and resid 130 through 140 Processing helix chain 'B' and resid 141 through 154 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.724A pdb=" N THR B 208 " --> pdb=" O ASP B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 33 through 45 removed outlier: 4.061A pdb=" N ALA C 43 " --> pdb=" O SER C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 130 Processing helix chain 'C' and resid 133 through 139 removed outlier: 3.535A pdb=" N LEU C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 161 removed outlier: 3.502A pdb=" N PHE C 161 " --> pdb=" O VAL C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 174 removed outlier: 3.503A pdb=" N GLU C 173 " --> pdb=" O ALA C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 185 removed outlier: 4.079A pdb=" N VAL C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN C 185 " --> pdb=" O ILE C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 222 removed outlier: 3.671A pdb=" N ARG C 222 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 241 Processing helix chain 'C' and resid 242 through 245 Processing helix chain 'C' and resid 254 through 264 removed outlier: 4.395A pdb=" N ASP C 261 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N SER C 262 " --> pdb=" O GLY C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 294 Processing helix chain 'C' and resid 295 through 300 Processing helix chain 'C' and resid 323 through 331 Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'D' and resid 97 through 107 removed outlier: 3.628A pdb=" N GLU D 106 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N MET D 107 " --> pdb=" O ALA D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 124 removed outlier: 3.974A pdb=" N ARG D 118 " --> pdb=" O GLU D 114 " (cutoff:3.500A) Proline residue: D 121 - end of helix Processing helix chain 'D' and resid 138 through 143 removed outlier: 3.578A pdb=" N ALA D 142 " --> pdb=" O GLY D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 155 Processing helix chain 'D' and resid 170 through 185 Processing helix chain 'D' and resid 205 through 210 Processing helix chain 'D' and resid 218 through 229 Processing helix chain 'D' and resid 244 through 252 removed outlier: 3.781A pdb=" N GLY D 252 " --> pdb=" O ILE D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 264 removed outlier: 3.597A pdb=" N LYS D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 288 removed outlier: 3.512A pdb=" N ILE D 288 " --> pdb=" O ASP D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 334 removed outlier: 4.309A pdb=" N PHE D 324 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU D 325 " --> pdb=" O ASP D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 359 Processing helix chain 'D' and resid 371 through 385 Processing helix chain 'D' and resid 416 through 425 Processing helix chain 'D' and resid 446 through 456 Processing helix chain 'D' and resid 465 through 469 Processing helix chain 'D' and resid 472 through 483 removed outlier: 4.110A pdb=" N LYS D 478 " --> pdb=" O SER D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 503 Processing helix chain 'D' and resid 516 through 525 removed outlier: 3.571A pdb=" N GLY D 525 " --> pdb=" O ALA D 521 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 53 Processing helix chain 'E' and resid 138 through 142 removed outlier: 4.241A pdb=" N GLU E 142 " --> pdb=" O PHE E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 171 Proline residue: E 166 - end of helix removed outlier: 3.568A pdb=" N LYS E 169 " --> pdb=" O LEU E 165 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALA E 170 " --> pdb=" O PRO E 166 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE E 171 " --> pdb=" O ALA E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 180 Processing helix chain 'F' and resid 16 through 80 removed outlier: 3.524A pdb=" N LEU F 20 " --> pdb=" O PRO F 16 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS F 22 " --> pdb=" O SER F 18 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA F 38 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU F 39 " --> pdb=" O ALA F 35 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS F 46 " --> pdb=" O SER F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 113 Processing helix chain 'F' and resid 127 through 134 removed outlier: 3.889A pdb=" N LYS F 131 " --> pdb=" O ASN F 127 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU F 132 " --> pdb=" O LYS F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 139 No H-bonds generated for 'chain 'F' and resid 137 through 139' Processing helix chain 'F' and resid 147 through 159 removed outlier: 3.519A pdb=" N ILE F 155 " --> pdb=" O VAL F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 181 removed outlier: 4.413A pdb=" N ILE F 176 " --> pdb=" O ASP F 172 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU F 177 " --> pdb=" O ASN F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 184 No H-bonds generated for 'chain 'F' and resid 182 through 184' Processing helix chain 'F' and resid 187 through 197 Processing helix chain 'F' and resid 201 through 209 Processing helix chain 'F' and resid 228 through 232 Processing helix chain 'F' and resid 241 through 247 removed outlier: 3.604A pdb=" N LEU F 245 " --> pdb=" O HIS F 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 77 removed outlier: 3.629A pdb=" N GLN G 77 " --> pdb=" O PRO G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 80 No H-bonds generated for 'chain 'G' and resid 78 through 80' Processing helix chain 'G' and resid 83 through 95 Processing helix chain 'G' and resid 96 through 98 No H-bonds generated for 'chain 'G' and resid 96 through 98' Processing helix chain 'G' and resid 101 through 119 Processing helix chain 'G' and resid 135 through 145 Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 165 through 173 Processing helix chain 'G' and resid 183 through 190 Processing helix chain 'G' and resid 204 through 206 No H-bonds generated for 'chain 'G' and resid 204 through 206' Processing helix chain 'G' and resid 207 through 222 removed outlier: 3.708A pdb=" N SER G 213 " --> pdb=" O ASN G 209 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE G 214 " --> pdb=" O GLU G 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 23 No H-bonds generated for 'chain 'H' and resid 21 through 23' Processing helix chain 'H' and resid 61 through 84 Processing helix chain 'H' and resid 114 through 118 removed outlier: 3.530A pdb=" N GLY H 117 " --> pdb=" O ASN H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 163 Processing helix chain 'J' and resid 96 through 107 Processing helix chain 'J' and resid 114 through 119 Processing helix chain 'J' and resid 134 through 160 Processing helix chain 'J' and resid 177 through 187 Processing helix chain 'K' and resid 14 through 27 Processing helix chain 'K' and resid 42 through 46 removed outlier: 3.753A pdb=" N GLU K 46 " --> pdb=" O LEU K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 106 removed outlier: 3.734A pdb=" N TYR K 98 " --> pdb=" O PRO K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 124 removed outlier: 3.575A pdb=" N TRP K 124 " --> pdb=" O LEU K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 137 removed outlier: 3.677A pdb=" N PHE K 137 " --> pdb=" O LEU K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 150 Processing helix chain 'K' and resid 155 through 160 Processing helix chain 'K' and resid 174 through 187 Processing helix chain 'K' and resid 209 through 228 Processing helix chain 'K' and resid 256 through 262 removed outlier: 3.533A pdb=" N ALA K 262 " --> pdb=" O LYS K 258 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 46 removed outlier: 3.515A pdb=" N LYS L 42 " --> pdb=" O ALA L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 84 Processing helix chain 'L' and resid 86 through 91 removed outlier: 3.948A pdb=" N SER L 91 " --> pdb=" O ARG L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 122 removed outlier: 3.690A pdb=" N ASN L 112 " --> pdb=" O SER L 108 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG L 115 " --> pdb=" O ARG L 111 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS L 122 " --> pdb=" O VAL L 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 82 Processing helix chain 'M' and resid 90 through 104 Processing helix chain 'M' and resid 106 through 122 Processing helix chain 'N' and resid 3 through 11 Processing helix chain 'N' and resid 16 through 33 removed outlier: 3.503A pdb=" N MET N 33 " --> pdb=" O GLU N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 52 Processing helix chain 'N' and resid 97 through 110 Processing helix chain 'N' and resid 139 through 144 Processing helix chain 'N' and resid 148 through 157 removed outlier: 3.615A pdb=" N ASN N 153 " --> pdb=" O TRP N 150 " (cutoff:3.500A) Proline residue: N 154 - end of helix Processing helix chain 'N' and resid 158 through 163 removed outlier: 3.531A pdb=" N ARG N 162 " --> pdb=" O HIS N 158 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 172 Processing helix chain 'N' and resid 190 through 194 Processing helix chain 'O' and resid 16 through 30 Processing helix chain 'O' and resid 38 through 41 Processing helix chain 'O' and resid 47 through 58 Processing helix chain 'O' and resid 76 through 87 Processing helix chain 'O' and resid 93 through 102 removed outlier: 3.883A pdb=" N GLU O 101 " --> pdb=" O GLN O 97 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N HIS O 102 " --> pdb=" O ALA O 98 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 115 removed outlier: 4.346A pdb=" N LYS O 115 " --> pdb=" O PRO O 111 " (cutoff:3.500A) Processing helix chain 'O' and resid 121 through 125 Processing helix chain 'O' and resid 139 through 144 Processing helix chain 'O' and resid 150 through 186 Processing helix chain 'O' and resid 192 through 196 removed outlier: 3.502A pdb=" N PHE O 195 " --> pdb=" O LEU O 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 37 Processing helix chain 'P' and resid 40 through 53 Processing helix chain 'P' and resid 85 through 106 Processing helix chain 'P' and resid 108 through 112 removed outlier: 3.531A pdb=" N LYS P 111 " --> pdb=" O ASP P 108 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 39 removed outlier: 3.717A pdb=" N LYS Q 30 " --> pdb=" O LYS Q 26 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE Q 34 " --> pdb=" O LYS Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 51 removed outlier: 3.828A pdb=" N LYS Q 45 " --> pdb=" O SER Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 71 Processing helix chain 'Q' and resid 108 through 118 removed outlier: 3.672A pdb=" N ALA Q 118 " --> pdb=" O ARG Q 114 " (cutoff:3.500A) Processing helix chain 'Q' and resid 124 through 130 Processing helix chain 'S' and resid 32 through 48 Processing helix chain 'S' and resid 97 through 113 Processing helix chain 'S' and resid 136 through 142 Processing helix chain 'V' and resid 121 through 128 Processing helix chain 'V' and resid 128 through 135 Processing helix chain 'Y' and resid 10 through 20 Processing helix chain 'Y' and resid 22 through 30 removed outlier: 5.005A pdb=" N VAL Y 28 " --> pdb=" O SER Y 24 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU Y 29 " --> pdb=" O VAL Y 25 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 43 Processing helix chain 'Y' and resid 74 through 77 Processing helix chain 'Y' and resid 111 through 121 Processing helix chain 'b' and resid 15 through 30 Processing helix chain 'b' and resid 41 through 68 Processing helix chain 'b' and resid 94 through 120 Processing helix chain 'b' and resid 122 through 160 removed outlier: 3.666A pdb=" N SER b 146 " --> pdb=" O LYS b 142 " (cutoff:3.500A) Processing helix chain 'b' and resid 424 through 430 Processing helix chain 'b' and resid 440 through 445 Processing helix chain 'e' and resid 51 through 55 Processing helix chain 'e' and resid 75 through 81 removed outlier: 3.682A pdb=" N VAL e 79 " --> pdb=" O ASN e 75 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU e 80 " --> pdb=" O VAL e 76 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU e 81 " --> pdb=" O SER e 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 75 through 81' Processing helix chain 'e' and resid 82 through 84 No H-bonds generated for 'chain 'e' and resid 82 through 84' Processing helix chain 'e' and resid 98 through 113 removed outlier: 3.576A pdb=" N GLU e 104 " --> pdb=" O ARG e 100 " (cutoff:3.500A) Processing helix chain 'f' and resid 38 through 43 removed outlier: 3.540A pdb=" N GLN f 43 " --> pdb=" O LYS f 39 " (cutoff:3.500A) Processing helix chain 'f' and resid 44 through 46 No H-bonds generated for 'chain 'f' and resid 44 through 46' Processing helix chain 'f' and resid 91 through 95 removed outlier: 4.041A pdb=" N PHE f 95 " --> pdb=" O ALA f 92 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 9 Processing helix chain 'h' and resid 12 through 36 removed outlier: 4.234A pdb=" N LEU h 16 " --> pdb=" O SER h 12 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU h 22 " --> pdb=" O GLU h 18 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU h 23 " --> pdb=" O GLN h 19 " (cutoff:3.500A) Processing helix chain 'h' and resid 39 through 72 removed outlier: 4.013A pdb=" N LYS h 47 " --> pdb=" O LEU h 43 " (cutoff:3.500A) Processing helix chain 'h' and resid 87 through 92 Processing helix chain 'h' and resid 95 through 100 Processing helix chain 'h' and resid 103 through 113 Processing helix chain 'i' and resid 32 through 47 removed outlier: 3.659A pdb=" N PHE i 37 " --> pdb=" O LYS i 33 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY i 47 " --> pdb=" O ARG i 43 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 62 Processing helix chain 'i' and resid 63 through 76 Processing helix chain 'i' and resid 77 through 99 Processing helix chain 'j' and resid 50 through 57 Processing helix chain 'j' and resid 66 through 74 removed outlier: 3.957A pdb=" N ARG j 72 " --> pdb=" O LYS j 68 " (cutoff:3.500A) Processing helix chain 'm' and resid 228 through 244 Processing helix chain 'm' and resid 249 through 256 Processing helix chain 'o' and resid 117 through 129 removed outlier: 3.614A pdb=" N PHE o 128 " --> pdb=" O TYR o 124 " (cutoff:3.500A) Processing helix chain 'o' and resid 155 through 167 Processing helix chain 'o' and resid 187 through 192 Processing helix chain 'o' and resid 202 through 213 Processing helix chain 'o' and resid 216 through 225 Processing helix chain 'o' and resid 226 through 238 Processing helix chain 'r' and resid 5 through 14 Processing helix chain 'r' and resid 19 through 42 removed outlier: 4.184A pdb=" N ALA r 32 " --> pdb=" O ALA r 28 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N HIS r 33 " --> pdb=" O ALA r 29 " (cutoff:3.500A) Processing helix chain 'r' and resid 43 through 57 removed outlier: 3.577A pdb=" N LYS r 48 " --> pdb=" O GLY r 44 " (cutoff:3.500A) Processing helix chain 't' and resid 53 through 72 removed outlier: 3.985A pdb=" N PHE t 57 " --> pdb=" O ARG t 53 " (cutoff:3.500A) Processing helix chain 'u' and resid 33 through 42 Processing helix chain 'u' and resid 45 through 49 removed outlier: 3.633A pdb=" N VAL u 49 " --> pdb=" O PRO u 46 " (cutoff:3.500A) Processing helix chain 'u' and resid 52 through 58 removed outlier: 3.506A pdb=" N ARG u 56 " --> pdb=" O THR u 52 " (cutoff:3.500A) Processing helix chain 'u' and resid 83 through 114 removed outlier: 3.589A pdb=" N LEU u 113 " --> pdb=" O TYR u 109 " (cutoff:3.500A) Processing helix chain 'v' and resid 3 through 12 removed outlier: 3.988A pdb=" N LYS v 9 " --> pdb=" O ARG v 5 " (cutoff:3.500A) Processing helix chain 'v' and resid 33 through 39 Processing helix chain 'v' and resid 45 through 53 Processing helix chain 'v' and resid 135 through 152 Processing helix chain 'v' and resid 160 through 172 Processing helix chain 'v' and resid 178 through 185 Processing helix chain 'v' and resid 194 through 207 removed outlier: 3.687A pdb=" N LYS v 206 " --> pdb=" O TYR v 202 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA v 207 " --> pdb=" O ILE v 203 " (cutoff:3.500A) Processing helix chain 'x' and resid 6 through 39 Processing helix chain 'x' and resid 39 through 50 removed outlier: 3.757A pdb=" N LYS x 43 " --> pdb=" O ASP x 39 " (cutoff:3.500A) Processing helix chain 'x' and resid 71 through 79 removed outlier: 3.524A pdb=" N GLN x 75 " --> pdb=" O ASP x 71 " (cutoff:3.500A) Processing helix chain 'x' and resid 83 through 88 Processing helix chain 'x' and resid 105 through 110 removed outlier: 4.044A pdb=" N TYR x 109 " --> pdb=" O SER x 105 " (cutoff:3.500A) Processing helix chain 'x' and resid 111 through 119 Processing helix chain 'x' and resid 132 through 144 removed outlier: 3.848A pdb=" N GLU x 138 " --> pdb=" O HIS x 134 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS x 142 " --> pdb=" O GLU x 138 " (cutoff:3.500A) Processing helix chain 'x' and resid 205 through 218 Processing helix chain 'x' and resid 296 through 300 Processing helix chain 'y' and resid 12 through 17 Processing helix chain 'y' and resid 31 through 42 Processing helix chain 'y' and resid 58 through 63 Processing helix chain 'y' and resid 77 through 88 Processing helix chain 'y' and resid 103 through 108 Processing helix chain 'y' and resid 122 through 133 Processing helix chain 'y' and resid 141 through 145 removed outlier: 3.824A pdb=" N GLY y 144 " --> pdb=" O THR y 141 " (cutoff:3.500A) Processing helix chain 'y' and resid 147 through 151 Processing helix chain 'y' and resid 166 through 178 Processing helix chain 'y' and resid 192 through 197 Processing helix chain 'y' and resid 211 through 222 Processing sheet with id=AA1, first strand: chain '3' and resid 19 through 21 Processing sheet with id=AA2, first strand: chain '3' and resid 50 through 55 Processing sheet with id=AA3, first strand: chain '3' and resid 132 through 135 Processing sheet with id=AA4, first strand: chain '5' and resid 33 through 36 removed outlier: 3.900A pdb=" N SER 5 338 " --> pdb=" O GLY 5 6 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '5' and resid 45 through 51 removed outlier: 5.037A pdb=" N PHE 5 47 " --> pdb=" O ALA 5 58 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA 5 58 " --> pdb=" O PHE 5 47 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG 5 59 " --> pdb=" O THR 5 63 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR 5 63 " --> pdb=" O ARG 5 59 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER 5 78 " --> pdb=" O CYS 5 66 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASN 5 68 " --> pdb=" O LEU 5 76 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU 5 76 " --> pdb=" O ASN 5 68 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '5' and resid 92 through 97 removed outlier: 7.592A pdb=" N ALA 5 105 " --> pdb=" O VAL 5 93 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N MET 5 95 " --> pdb=" O MET 5 103 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N MET 5 103 " --> pdb=" O MET 5 95 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU 5 112 " --> pdb=" O LEU 5 104 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '5' and resid 132 through 135 removed outlier: 5.420A pdb=" N GLY 5 147 " --> pdb=" O ASP 5 151 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ASP 5 151 " --> pdb=" O GLY 5 147 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE 5 180 " --> pdb=" O LEU 5 154 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N SER 5 156 " --> pdb=" O LYS 5 178 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LYS 5 178 " --> pdb=" O SER 5 156 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '5' and resid 198 through 203 removed outlier: 4.588A pdb=" N GLY 5 200 " --> pdb=" O ILE 5 228 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N GLN 5 233 " --> pdb=" O THR 5 229 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '5' and resid 256 through 262 removed outlier: 3.860A pdb=" N HIS 5 258 " --> pdb=" O ALA 5 271 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU 5 268 " --> pdb=" O PHE 5 280 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE 5 279 " --> pdb=" O ILE 5 288 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS 5 286 " --> pdb=" O ASP 5 281 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '5' and resid 298 through 304 removed outlier: 4.019A pdb=" N GLY 5 312 " --> pdb=" O ASN 5 316 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASN 5 316 " --> pdb=" O GLY 5 312 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 45 through 46 removed outlier: 6.228A pdb=" N LEU A 46 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N PHE A 101 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU A 109 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN A 231 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N HIS A 125 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ILE A 229 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N GLU A 127 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N MET A 227 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR A 243 " --> pdb=" O ILE A 232 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 45 through 46 removed outlier: 6.228A pdb=" N LEU A 46 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N PHE A 101 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU A 109 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN A 231 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N HIS A 125 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ILE A 229 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N GLU A 127 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N MET A 227 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE A 221 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N GLU A 204 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A 200 " --> pdb=" O PHE A 225 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ARG A 146 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ARG A 187 " --> pdb=" O ARG A 146 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 191 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL J 121 " --> pdb=" O PRO A 147 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N LEU A 149 " --> pdb=" O VAL J 121 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 356 through 359 removed outlier: 6.492A pdb=" N LEU B 356 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ASP B 59 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG B 334 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N VAL B 220 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL B 217 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU B 278 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N GLY B 219 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N THR B 276 " --> pdb=" O GLY B 219 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE B 282 " --> pdb=" O ASN B 325 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASN B 325 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLU B 80 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N LYS B 50 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 98 through 106 removed outlier: 6.960A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N TRP B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N VAL B 87 " --> pdb=" O TRP B 106 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N VAL B 86 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N HIS B 163 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 98 through 106 removed outlier: 6.960A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N TRP B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N VAL B 87 " --> pdb=" O TRP B 106 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 17 through 23 removed outlier: 6.037A pdb=" N GLU C 20 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE C 10 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N VAL C 153 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU C 152 " --> pdb=" O TRP C 252 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU C 208 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR C 253 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL C 210 " --> pdb=" O THR C 253 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE C 211 " --> pdb=" O VAL C 230 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 192 through 195 removed outlier: 6.337A pdb=" N VAL D 164 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ALA D 217 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE D 166 " --> pdb=" O ALA D 217 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 364 through 365 Processing sheet with id=AC1, first strand: chain 'E' and resid 94 through 97 removed outlier: 7.001A pdb=" N THR E 83 " --> pdb=" O VAL E 72 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N VAL E 72 " --> pdb=" O THR E 83 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 82 through 84 removed outlier: 3.819A pdb=" N VAL F 84 " --> pdb=" O HIS T 139 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS T 139 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 121 through 125 removed outlier: 6.653A pdb=" N VAL F 141 " --> pdb=" O GLY F 236 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 160 through 162 Processing sheet with id=AC5, first strand: chain 'G' and resid 133 through 134 Processing sheet with id=AC6, first strand: chain 'H' and resid 6 through 12 Processing sheet with id=AC7, first strand: chain 'H' and resid 18 through 20 removed outlier: 3.867A pdb=" N ASP H 20 " --> pdb=" O THR H 27 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 130 through 132 removed outlier: 5.860A pdb=" N ARG H 91 " --> pdb=" O VAL H 179 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N VAL H 179 " --> pdb=" O ARG H 91 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL H 93 " --> pdb=" O ILE H 177 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ILE H 177 " --> pdb=" O VAL H 93 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 100 through 104 Processing sheet with id=AD1, first strand: chain 'K' and resid 198 through 205 removed outlier: 6.115A pdb=" N VAL K 53 " --> pdb=" O CYS K 203 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU K 241 " --> pdb=" O PRO K 250 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 74 through 75 Processing sheet with id=AD3, first strand: chain 'K' and resid 111 through 116 removed outlier: 6.924A pdb=" N ALA K 87 " --> pdb=" O ARG K 113 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ILE K 115 " --> pdb=" O ALA K 87 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU K 89 " --> pdb=" O ILE K 115 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N CYS K 88 " --> pdb=" O LEU K 141 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ASP K 143 " --> pdb=" O CYS K 88 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ILE K 90 " --> pdb=" O ASP K 143 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 22 through 24 removed outlier: 6.408A pdb=" N LYS L 23 " --> pdb=" O LEU N 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'L' and resid 57 through 58 Processing sheet with id=AD6, first strand: chain 'L' and resid 123 through 125 Processing sheet with id=AD7, first strand: chain 'M' and resid 49 through 52 removed outlier: 7.983A pdb=" N ARG M 36 " --> pdb=" O ILE M 31 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE M 31 " --> pdb=" O ARG M 36 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LEU M 38 " --> pdb=" O VAL M 29 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG M 12 " --> pdb=" O ILE M 28 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL M 13 " --> pdb=" O THR M 59 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR M 59 " --> pdb=" O VAL M 13 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 36 through 38 removed outlier: 7.534A pdb=" N TYR N 127 " --> pdb=" O ASN N 122 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ASN N 122 " --> pdb=" O TYR N 127 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N PHE N 129 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N TRP N 120 " --> pdb=" O PHE N 129 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLU N 131 " --> pdb=" O SER N 118 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER N 118 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE N 133 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 7 through 11 removed outlier: 6.114A pdb=" N VAL O 8 " --> pdb=" O VAL O 35 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N VAL O 37 " --> pdb=" O VAL O 8 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE O 10 " --> pdb=" O VAL O 37 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 43 through 45 Processing sheet with id=AE2, first strand: chain 'P' and resid 15 through 22 removed outlier: 4.552A pdb=" N TYR P 21 " --> pdb=" O SER P 144 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA P 151 " --> pdb=" O ILE P 114 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ILE P 114 " --> pdb=" O ALA P 151 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 58 through 59 Processing sheet with id=AE4, first strand: chain 'Q' and resid 121 through 123 removed outlier: 6.199A pdb=" N ILE Q 102 " --> pdb=" O LEU Q 123 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR Q 82 " --> pdb=" O ALA Q 103 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N LEU Q 105 " --> pdb=" O THR Q 82 " (cutoff:3.500A) removed outlier: 9.623A pdb=" N VAL Q 84 " --> pdb=" O LEU Q 105 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N PHE Q 107 " --> pdb=" O VAL Q 84 " (cutoff:3.500A) removed outlier: 9.827A pdb=" N GLY Q 86 " --> pdb=" O PHE Q 107 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'S' and resid 55 through 62 removed outlier: 5.140A pdb=" N ILE S 57 " --> pdb=" O ARG S 11 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ARG S 11 " --> pdb=" O ILE S 57 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'S' and resid 87 through 95 removed outlier: 3.743A pdb=" N VAL S 73 " --> pdb=" O VAL S 128 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ARG S 79 " --> pdb=" O ILE S 122 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE S 122 " --> pdb=" O ARG S 79 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'V' and resid 24 through 25 removed outlier: 5.981A pdb=" N ASN V 35 " --> pdb=" O LYS V 65 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'V' and resid 86 through 88 Processing sheet with id=AE9, first strand: chain 'Y' and resid 31 through 33 Processing sheet with id=AF1, first strand: chain 'Y' and resid 66 through 67 removed outlier: 6.760A pdb=" N GLN Y 54 " --> pdb=" O THR Y 106 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Y' and resid 69 through 73 removed outlier: 7.173A pdb=" N LEU Y 80 " --> pdb=" O THR Y 70 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N VAL Y 72 " --> pdb=" O LEU Y 78 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU Y 78 " --> pdb=" O VAL Y 72 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'e' and resid 69 through 73 removed outlier: 4.627A pdb=" N LYS e 115 " --> pdb=" O TYR e 89 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'f' and resid 9 through 19 removed outlier: 5.784A pdb=" N HIS f 14 " --> pdb=" O LYS f 32 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LYS f 32 " --> pdb=" O HIS f 14 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER f 16 " --> pdb=" O ILE f 30 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR f 28 " --> pdb=" O GLN f 18 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N GLY f 27 " --> pdb=" O PHE f 86 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N PHE f 86 " --> pdb=" O GLY f 27 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA f 81 " --> pdb=" O PRO f 75 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ARG f 83 " --> pdb=" O ALA f 73 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N LYS f 64 " --> pdb=" O SER f 56 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG f 49 " --> pdb=" O MET f 102 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N VAL f 53 " --> pdb=" O SER f 98 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER f 98 " --> pdb=" O VAL f 53 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER f 97 " --> pdb=" O HIS f 14 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'j' and resid 16 through 18 Processing sheet with id=AF6, first strand: chain 'o' and resid 131 through 134 removed outlier: 3.756A pdb=" N LYS o 179 " --> pdb=" O TYR o 108 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'u' and resid 4 through 5 Processing sheet with id=AF8, first strand: chain 'u' and resid 19 through 22 Processing sheet with id=AF9, first strand: chain 'x' and resid 122 through 124 removed outlier: 5.958A pdb=" N LEU x 96 " --> pdb=" O GLU x 123 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LEU x 97 " --> pdb=" O LEU x 149 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU x 151 " --> pdb=" O LEU x 97 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N THR x 99 " --> pdb=" O LEU x 151 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLU x 153 " --> pdb=" O THR x 99 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA x 160 " --> pdb=" O ASN x 152 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASP x 154 " --> pdb=" O THR x 158 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N THR x 158 " --> pdb=" O ASP x 154 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET x 276 " --> pdb=" O TYR x 173 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N THR x 175 " --> pdb=" O LEU x 274 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU x 274 " --> pdb=" O THR x 175 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N ARG x 275 " --> pdb=" O GLU x 292 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N GLU x 292 " --> pdb=" O ARG x 275 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL x 277 " --> pdb=" O PHE x 290 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU x 288 " --> pdb=" O LYS x 279 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'x' and resid 177 through 180 removed outlier: 6.091A pdb=" N ASN x 178 " --> pdb=" O THR x 271 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N THR x 271 " --> pdb=" O ASN x 178 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ARG x 244 " --> pdb=" O LEU x 266 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N PHE x 242 " --> pdb=" O PRO x 268 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE x 270 " --> pdb=" O LEU x 240 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU x 240 " --> pdb=" O PHE x 270 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'y' and resid 64 through 66 Processing sheet with id=AG3, first strand: chain 'y' and resid 152 through 153 2088 hydrogen bonds defined for protein. 5958 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1148 hydrogen bonds 1842 hydrogen bond angles 0 basepair planarities 487 basepair parallelities 883 stacking parallelities Total time for adding SS restraints: 60.40 Time building geometry restraints manager: 36.57 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: 14561 1.33 - 1.45: 29136 1.45 - 1.58: 36403 1.58 - 1.70: 3212 1.70 - 1.83: 160 Bond restraints: 83472 Sorted by residual: bond pdb=" CA ILE D 120 " pdb=" CB ILE D 120 " ideal model delta sigma weight residual 1.539 1.559 -0.020 5.40e-03 3.43e+04 1.35e+01 bond pdb=" C VAL 3 11 " pdb=" O VAL 3 11 " ideal model delta sigma weight residual 1.237 1.206 0.031 1.17e-02 7.31e+03 7.07e+00 bond pdb=" CA MET Y 30 " pdb=" CB MET Y 30 " ideal model delta sigma weight residual 1.526 1.489 0.037 1.76e-02 3.23e+03 4.52e+00 bond pdb=" CA ASP Q 90 " pdb=" C ASP Q 90 " ideal model delta sigma weight residual 1.528 1.505 0.022 1.33e-02 5.65e+03 2.81e+00 bond pdb=" O3' G 1 711 " pdb=" P U 1 712 " ideal model delta sigma weight residual 1.607 1.582 0.025 1.50e-02 4.44e+03 2.70e+00 ... (remaining 83467 not shown) Histogram of bond angle deviations from ideal: 99.22 - 106.20: 9892 106.20 - 113.17: 47706 113.17 - 120.15: 29251 120.15 - 127.12: 30084 127.12 - 134.09: 3927 Bond angle restraints: 120860 Sorted by residual: angle pdb=" C ASN C 331 " pdb=" CA ASN C 331 " pdb=" CB ASN C 331 " ideal model delta sigma weight residual 110.65 104.61 6.04 1.04e+00 9.25e-01 3.37e+01 angle pdb=" N LYS 4 46 " pdb=" CA LYS 4 46 " pdb=" C LYS 4 46 " ideal model delta sigma weight residual 111.07 105.19 5.88 1.07e+00 8.73e-01 3.02e+01 angle pdb=" O3' U 11159 " pdb=" C3' U 11159 " pdb=" C2' U 11159 " ideal model delta sigma weight residual 109.50 116.67 -7.17 1.50e+00 4.44e-01 2.29e+01 angle pdb=" CB MET D 439 " pdb=" CG MET D 439 " pdb=" SD MET D 439 " ideal model delta sigma weight residual 112.70 126.46 -13.76 3.00e+00 1.11e-01 2.10e+01 angle pdb=" O3' A 1 488 " pdb=" C3' A 1 488 " pdb=" C2' A 1 488 " ideal model delta sigma weight residual 109.50 116.26 -6.76 1.50e+00 4.44e-01 2.03e+01 ... (remaining 120855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 47168 35.64 - 71.27: 4580 71.27 - 106.91: 478 106.91 - 142.55: 16 142.55 - 178.19: 19 Dihedral angle restraints: 52261 sinusoidal: 34358 harmonic: 17903 Sorted by residual: dihedral pdb=" O4' U 13314 " pdb=" C1' U 13314 " pdb=" N1 U 13314 " pdb=" C2 U 13314 " ideal model delta sinusoidal sigma weight residual -160.00 7.50 -167.50 1 1.50e+01 4.44e-03 8.43e+01 dihedral pdb=" O4' U 13153 " pdb=" C1' U 13153 " pdb=" N1 U 13153 " pdb=" C2 U 13153 " ideal model delta sinusoidal sigma weight residual 200.00 54.37 145.63 1 1.50e+01 4.44e-03 7.79e+01 dihedral pdb=" O4' U 1 761 " pdb=" C1' U 1 761 " pdb=" N1 U 1 761 " pdb=" C2 U 1 761 " ideal model delta sinusoidal sigma weight residual -128.00 50.05 -178.05 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 52258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 13855 0.066 - 0.132: 1166 0.132 - 0.197: 62 0.197 - 0.263: 7 0.263 - 0.329: 2 Chirality restraints: 15092 Sorted by residual: chirality pdb=" C3' A 1 488 " pdb=" C4' A 1 488 " pdb=" O3' A 1 488 " pdb=" C2' A 1 488 " both_signs ideal model delta sigma weight residual False -2.74 -2.42 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" C3' U 11159 " pdb=" C4' U 11159 " pdb=" O3' U 11159 " pdb=" C2' U 11159 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" C3' U 1 706 " pdb=" C4' U 1 706 " pdb=" O3' U 1 706 " pdb=" C2' U 1 706 " both_signs ideal model delta sigma weight residual False -2.48 -2.73 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 15089 not shown) Planarity restraints: 9549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR 4 173 " -0.041 5.00e-02 4.00e+02 6.29e-02 6.33e+00 pdb=" N PRO 4 174 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO 4 174 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO 4 174 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE L 46 " -0.011 2.00e-02 2.50e+03 2.10e-02 4.42e+00 pdb=" C ILE L 46 " 0.036 2.00e-02 2.50e+03 pdb=" O ILE L 46 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA L 47 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 1 414 " -0.024 2.00e-02 2.50e+03 1.16e-02 4.05e+00 pdb=" N9 G 1 414 " 0.030 2.00e-02 2.50e+03 pdb=" C8 G 1 414 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G 1 414 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G 1 414 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G 1 414 " -0.010 2.00e-02 2.50e+03 pdb=" O6 G 1 414 " -0.000 2.00e-02 2.50e+03 pdb=" N1 G 1 414 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G 1 414 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G 1 414 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G 1 414 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G 1 414 " 0.003 2.00e-02 2.50e+03 ... (remaining 9546 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 3344 2.67 - 3.23: 73594 3.23 - 3.78: 149434 3.78 - 4.34: 196484 4.34 - 4.90: 276450 Nonbonded interactions: 699306 Sorted by model distance: nonbonded pdb=" OP2 A 13367 " pdb=" N6 A 13368 " model vdw 2.108 2.520 nonbonded pdb=" OH TYR 3 86 " pdb=" OG1 THR 3 113 " model vdw 2.197 2.440 nonbonded pdb=" OG1 THR C 267 " pdb=" OE1 GLU C 281 " model vdw 2.198 2.440 nonbonded pdb=" N2 G 11416 " pdb=" O GLY C 243 " model vdw 2.203 2.520 nonbonded pdb=" O2' A 11012 " pdb=" O4' U 11013 " model vdw 2.204 2.440 ... (remaining 699301 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 27.690 Check model and map are aligned: 0.870 Set scattering table: 0.570 Process input model: 230.850 Find NCS groups from input model: 1.980 Set up NCS constraints: 0.240 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:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 271.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 83472 Z= 0.289 Angle : 0.555 13.756 120860 Z= 0.296 Chirality : 0.036 0.329 15092 Planarity : 0.004 0.063 9549 Dihedral : 22.511 178.186 40597 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.29 % Favored : 94.56 % Rotamer: Outliers : 0.40 % Allowed : 22.54 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.11), residues: 6040 helix: 0.78 (0.11), residues: 2286 sheet: -0.07 (0.19), residues: 860 loop : -0.71 (0.12), residues: 2894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP 5 80 HIS 0.006 0.001 HIS C 314 PHE 0.023 0.001 PHE D 143 TYR 0.026 0.002 TYR E 86 ARG 0.011 0.001 ARG e 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 362 time to evaluate : 4.910 Fit side-chains revert: symmetry clash REVERT: i 44 GLU cc_start: 0.7451 (tm-30) cc_final: 0.7131 (tm-30) REVERT: x 218 LEU cc_start: 0.8559 (tp) cc_final: 0.8349 (tp) outliers start: 14 outliers final: 5 residues processed: 367 average time/residue: 0.7559 time to fit residues: 478.2140 Evaluate side-chains 344 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 339 time to evaluate : 4.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain O residue 150 TYR Chi-restraints excluded: chain v residue 123 VAL Chi-restraints excluded: chain T residue 151 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 641 optimal weight: 0.4980 chunk 576 optimal weight: 8.9990 chunk 319 optimal weight: 9.9990 chunk 196 optimal weight: 10.0000 chunk 388 optimal weight: 1.9990 chunk 307 optimal weight: 0.9990 chunk 595 optimal weight: 50.0000 chunk 230 optimal weight: 20.0000 chunk 362 optimal weight: 3.9990 chunk 443 optimal weight: 0.0770 chunk 690 optimal weight: 20.0000 overall best weight: 1.5144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN ** C 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS D 200 ASN D 270 GLN E 75 GLN E 186 ASN ** N 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 ASN ** Q 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 GLN v 33 ASN v 152 GLN x 264 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 83472 Z= 0.221 Angle : 0.587 7.332 120860 Z= 0.298 Chirality : 0.037 0.270 15092 Planarity : 0.004 0.052 9549 Dihedral : 22.849 178.878 31573 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.59 % Favored : 95.26 % Rotamer: Outliers : 2.69 % Allowed : 22.52 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: 0.12 (0.11), residues: 6040 helix: 1.07 (0.11), residues: 2361 sheet: -0.03 (0.19), residues: 845 loop : -0.68 (0.12), residues: 2834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP 4 76 HIS 0.004 0.001 HIS N 192 PHE 0.020 0.001 PHE A 248 TYR 0.016 0.001 TYR 4 183 ARG 0.012 0.000 ARG h 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 365 time to evaluate : 5.043 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: 3 79 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.5986 (ttp-170) REVERT: 3 104 GLN cc_start: 0.7005 (OUTLIER) cc_final: 0.6777 (mt0) REVERT: C 100 ARG cc_start: 0.4918 (OUTLIER) cc_final: 0.2719 (tpt170) REVERT: D 156 PHE cc_start: 0.7247 (OUTLIER) cc_final: 0.6422 (m-80) REVERT: D 200 ASN cc_start: 0.6940 (OUTLIER) cc_final: 0.6721 (t0) REVERT: E 86 TYR cc_start: 0.4304 (OUTLIER) cc_final: 0.2749 (m-10) REVERT: F 247 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.6997 (mt0) REVERT: L 106 GLU cc_start: 0.5910 (tp30) cc_final: 0.5462 (tp30) REVERT: N 4 TYR cc_start: 0.8410 (m-80) cc_final: 0.8157 (m-80) REVERT: x 218 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8376 (tp) outliers start: 100 outliers final: 47 residues processed: 440 average time/residue: 0.7325 time to fit residues: 558.7568 Evaluate side-chains 387 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 332 time to evaluate : 4.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 43 CYS Chi-restraints excluded: chain 3 residue 79 ARG Chi-restraints excluded: chain 3 residue 104 GLN Chi-restraints excluded: chain 3 residue 136 ILE Chi-restraints excluded: chain 3 residue 163 LYS Chi-restraints excluded: chain 4 residue 15 ASP Chi-restraints excluded: chain 4 residue 99 ASP Chi-restraints excluded: chain 4 residue 177 VAL Chi-restraints excluded: chain 4 residue 196 VAL Chi-restraints excluded: chain 5 residue 83 ASP Chi-restraints excluded: chain 5 residue 130 LEU Chi-restraints excluded: chain 5 residue 258 HIS Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain D residue 156 PHE Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 392 CYS Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain N residue 192 HIS Chi-restraints excluded: chain O residue 73 HIS Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 150 TYR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 108 ILE Chi-restraints excluded: chain h residue 25 GLN Chi-restraints excluded: chain h residue 78 ILE Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain v residue 123 VAL Chi-restraints excluded: chain v residue 130 ILE Chi-restraints excluded: chain v residue 137 VAL Chi-restraints excluded: chain v residue 167 ILE Chi-restraints excluded: chain v residue 178 ASP Chi-restraints excluded: chain v residue 190 SER Chi-restraints excluded: chain x residue 118 CYS Chi-restraints excluded: chain x residue 161 LEU Chi-restraints excluded: chain x residue 218 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 383 optimal weight: 8.9990 chunk 214 optimal weight: 2.9990 chunk 574 optimal weight: 50.0000 chunk 469 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 chunk 691 optimal weight: 30.0000 chunk 746 optimal weight: 9.9990 chunk 615 optimal weight: 0.7980 chunk 685 optimal weight: 20.0000 chunk 235 optimal weight: 4.9990 chunk 554 optimal weight: 0.0010 overall best weight: 1.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 233 GLN ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN F 193 HIS ** Q 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 14 GLN ** m 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 152 GLN x 50 ASN ** x 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 83472 Z= 0.201 Angle : 0.547 7.925 120860 Z= 0.278 Chirality : 0.036 0.266 15092 Planarity : 0.004 0.049 9549 Dihedral : 22.711 179.696 31569 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.67 % Favored : 95.18 % Rotamer: Outliers : 3.49 % Allowed : 22.78 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: 0.25 (0.11), residues: 6040 helix: 1.23 (0.11), residues: 2359 sheet: -0.05 (0.19), residues: 858 loop : -0.63 (0.12), residues: 2823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP 4 76 HIS 0.004 0.001 HIS P 116 PHE 0.026 0.001 PHE h 6 TYR 0.015 0.001 TYR m 202 ARG 0.008 0.000 ARG D 201 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 366 time to evaluate : 4.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 79 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.5867 (ttp-170) REVERT: 3 104 GLN cc_start: 0.6970 (OUTLIER) cc_final: 0.6748 (mt0) REVERT: 3 129 HIS cc_start: 0.6821 (OUTLIER) cc_final: 0.6537 (m170) REVERT: 4 163 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7449 (t0) REVERT: 5 95 MET cc_start: 0.6415 (OUTLIER) cc_final: 0.5933 (pmm) REVERT: C 100 ARG cc_start: 0.4821 (OUTLIER) cc_final: 0.2661 (tpt170) REVERT: D 156 PHE cc_start: 0.7271 (OUTLIER) cc_final: 0.6643 (m-80) REVERT: E 86 TYR cc_start: 0.4315 (OUTLIER) cc_final: 0.2960 (m-80) REVERT: Y 80 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7499 (mm) REVERT: e 96 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.5991 (m-40) REVERT: j 21 ARG cc_start: 0.6447 (ttp-170) cc_final: 0.5890 (ttp-170) REVERT: x 103 ARG cc_start: 0.5938 (OUTLIER) cc_final: 0.5712 (ttm-80) outliers start: 130 outliers final: 73 residues processed: 463 average time/residue: 0.7471 time to fit residues: 600.0178 Evaluate side-chains 426 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 342 time to evaluate : 4.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 43 CYS Chi-restraints excluded: chain 3 residue 79 ARG Chi-restraints excluded: chain 3 residue 104 GLN Chi-restraints excluded: chain 3 residue 129 HIS Chi-restraints excluded: chain 3 residue 136 ILE Chi-restraints excluded: chain 3 residue 163 LYS Chi-restraints excluded: chain 4 residue 15 ASP Chi-restraints excluded: chain 4 residue 99 ASP Chi-restraints excluded: chain 4 residue 163 ASP Chi-restraints excluded: chain 4 residue 177 VAL Chi-restraints excluded: chain 4 residue 196 VAL Chi-restraints excluded: chain 5 residue 51 HIS Chi-restraints excluded: chain 5 residue 83 ASP Chi-restraints excluded: chain 5 residue 95 MET Chi-restraints excluded: chain 5 residue 114 ARG Chi-restraints excluded: chain 5 residue 130 LEU Chi-restraints excluded: chain 5 residue 152 VAL Chi-restraints excluded: chain 5 residue 168 LEU Chi-restraints excluded: chain 5 residue 176 VAL Chi-restraints excluded: chain 5 residue 196 VAL Chi-restraints excluded: chain 5 residue 258 HIS Chi-restraints excluded: chain 5 residue 307 VAL Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 156 PHE Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 392 CYS Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 58 CYS Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain N residue 149 ASN Chi-restraints excluded: chain N residue 192 HIS Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 73 HIS Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 150 TYR Chi-restraints excluded: chain O residue 152 ASP Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain Y residue 80 LEU Chi-restraints excluded: chain Y residue 110 LEU Chi-restraints excluded: chain e residue 96 ASN Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 107 ASN Chi-restraints excluded: chain f residue 108 ILE Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 78 ILE Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain m residue 210 VAL Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain v residue 46 LEU Chi-restraints excluded: chain v residue 63 THR Chi-restraints excluded: chain v residue 123 VAL Chi-restraints excluded: chain v residue 130 ILE Chi-restraints excluded: chain v residue 137 VAL Chi-restraints excluded: chain v residue 167 ILE Chi-restraints excluded: chain v residue 178 ASP Chi-restraints excluded: chain v residue 190 SER Chi-restraints excluded: chain x residue 103 ARG Chi-restraints excluded: chain x residue 115 LEU Chi-restraints excluded: chain x residue 118 CYS Chi-restraints excluded: chain x residue 161 LEU Chi-restraints excluded: chain x residue 179 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 683 optimal weight: 20.0000 chunk 519 optimal weight: 8.9990 chunk 358 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 329 optimal weight: 5.9990 chunk 464 optimal weight: 50.0000 chunk 693 optimal weight: 0.0470 chunk 734 optimal weight: 4.9990 chunk 362 optimal weight: 0.6980 chunk 657 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 overall best weight: 2.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 292 GLN ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN C 344 ASN D 188 HIS ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 ASN O 189 ASN ** Q 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 230 HIS ** x 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 83472 Z= 0.300 Angle : 0.608 9.008 120860 Z= 0.308 Chirality : 0.039 0.312 15092 Planarity : 0.005 0.051 9549 Dihedral : 22.710 179.141 31569 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.14 % Favored : 94.71 % Rotamer: Outliers : 4.52 % Allowed : 23.45 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: 0.20 (0.11), residues: 6040 helix: 1.22 (0.11), residues: 2365 sheet: -0.14 (0.19), residues: 841 loop : -0.67 (0.12), residues: 2834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP 4 76 HIS 0.006 0.001 HIS C 314 PHE 0.028 0.002 PHE h 6 TYR 0.018 0.002 TYR Q 32 ARG 0.008 0.000 ARG F 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 359 time to evaluate : 4.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 31 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7635 (pt0) REVERT: 3 79 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.6150 (ttp-170) REVERT: 3 104 GLN cc_start: 0.7025 (OUTLIER) cc_final: 0.6777 (mt0) REVERT: 3 129 HIS cc_start: 0.6922 (OUTLIER) cc_final: 0.6540 (m170) REVERT: 4 93 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7329 (ptt90) REVERT: 4 212 TYR cc_start: 0.4943 (OUTLIER) cc_final: 0.3561 (p90) REVERT: 5 95 MET cc_start: 0.6650 (OUTLIER) cc_final: 0.6233 (pmm) REVERT: C 100 ARG cc_start: 0.5124 (OUTLIER) cc_final: 0.2882 (tpt170) REVERT: D 156 PHE cc_start: 0.7260 (OUTLIER) cc_final: 0.6716 (m-80) REVERT: D 343 MET cc_start: 0.6306 (ptp) cc_final: 0.5787 (ptp) REVERT: E 86 TYR cc_start: 0.4409 (OUTLIER) cc_final: 0.2992 (m-80) REVERT: F 110 MET cc_start: 0.8202 (mtp) cc_final: 0.7824 (mtm) REVERT: P 54 HIS cc_start: 0.7266 (OUTLIER) cc_final: 0.6922 (m90) REVERT: Q 127 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7480 (mt0) REVERT: Q 131 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8800 (ttm170) REVERT: Y 2 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7696 (tttp) REVERT: Y 80 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7305 (mm) REVERT: e 58 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8079 (mtpt) REVERT: e 96 ASN cc_start: 0.8866 (OUTLIER) cc_final: 0.7825 (p0) REVERT: j 21 ARG cc_start: 0.6563 (ttp-170) cc_final: 0.6055 (ttp-170) outliers start: 169 outliers final: 112 residues processed: 485 average time/residue: 0.7411 time to fit residues: 621.8872 Evaluate side-chains 470 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 341 time to evaluate : 4.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 31 GLU Chi-restraints excluded: chain 3 residue 34 VAL Chi-restraints excluded: chain 3 residue 35 THR Chi-restraints excluded: chain 3 residue 43 CYS Chi-restraints excluded: chain 3 residue 79 ARG Chi-restraints excluded: chain 3 residue 104 GLN Chi-restraints excluded: chain 3 residue 129 HIS Chi-restraints excluded: chain 3 residue 136 ILE Chi-restraints excluded: chain 3 residue 137 LYS Chi-restraints excluded: chain 3 residue 163 LYS Chi-restraints excluded: chain 4 residue 15 ASP Chi-restraints excluded: chain 4 residue 51 CYS Chi-restraints excluded: chain 4 residue 75 VAL Chi-restraints excluded: chain 4 residue 79 ASN Chi-restraints excluded: chain 4 residue 93 ARG Chi-restraints excluded: chain 4 residue 99 ASP Chi-restraints excluded: chain 4 residue 100 ILE Chi-restraints excluded: chain 4 residue 113 PHE Chi-restraints excluded: chain 4 residue 134 VAL Chi-restraints excluded: chain 4 residue 177 VAL Chi-restraints excluded: chain 4 residue 196 VAL Chi-restraints excluded: chain 4 residue 212 TYR Chi-restraints excluded: chain 5 residue 17 ILE Chi-restraints excluded: chain 5 residue 52 GLU Chi-restraints excluded: chain 5 residue 83 ASP Chi-restraints excluded: chain 5 residue 94 SER Chi-restraints excluded: chain 5 residue 95 MET Chi-restraints excluded: chain 5 residue 130 LEU Chi-restraints excluded: chain 5 residue 152 VAL Chi-restraints excluded: chain 5 residue 168 LEU Chi-restraints excluded: chain 5 residue 196 VAL Chi-restraints excluded: chain 5 residue 199 THR Chi-restraints excluded: chain 5 residue 258 HIS Chi-restraints excluded: chain 5 residue 307 VAL Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain D residue 156 PHE Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 392 CYS Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain N residue 149 ASN Chi-restraints excluded: chain N residue 192 HIS Chi-restraints excluded: chain N residue 195 LEU Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 73 HIS Chi-restraints excluded: chain O residue 88 MET Chi-restraints excluded: chain O residue 150 TYR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 10 LEU Chi-restraints excluded: chain P residue 54 HIS Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 127 GLN Chi-restraints excluded: chain Q residue 131 ARG Chi-restraints excluded: chain S residue 26 MET Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 7 VAL Chi-restraints excluded: chain Y residue 80 LEU Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain Y residue 110 LEU Chi-restraints excluded: chain e residue 19 SER Chi-restraints excluded: chain e residue 49 MET Chi-restraints excluded: chain e residue 58 LYS Chi-restraints excluded: chain e residue 79 VAL Chi-restraints excluded: chain e residue 96 ASN Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 107 ASN Chi-restraints excluded: chain f residue 108 ILE Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 78 ILE Chi-restraints excluded: chain h residue 107 ILE Chi-restraints excluded: chain i residue 15 LEU Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain m residue 210 VAL Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain v residue 46 LEU Chi-restraints excluded: chain v residue 63 THR Chi-restraints excluded: chain v residue 123 VAL Chi-restraints excluded: chain v residue 130 ILE Chi-restraints excluded: chain v residue 137 VAL Chi-restraints excluded: chain v residue 167 ILE Chi-restraints excluded: chain v residue 178 ASP Chi-restraints excluded: chain v residue 190 SER Chi-restraints excluded: chain x residue 26 LEU Chi-restraints excluded: chain x residue 115 LEU Chi-restraints excluded: chain x residue 118 CYS Chi-restraints excluded: chain x residue 161 LEU Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 151 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 611 optimal weight: 2.9990 chunk 417 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 546 optimal weight: 0.6980 chunk 303 optimal weight: 0.7980 chunk 626 optimal weight: 3.9990 chunk 507 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 375 optimal weight: 6.9990 chunk 659 optimal weight: 0.9980 chunk 185 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 233 GLN ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 202 ASN C 331 ASN D 188 HIS ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 GLN O 189 ASN ** Q 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 234 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 83472 Z= 0.193 Angle : 0.537 8.604 120860 Z= 0.273 Chirality : 0.036 0.260 15092 Planarity : 0.004 0.050 9549 Dihedral : 22.603 179.019 31569 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.46 % Favored : 95.39 % Rotamer: Outliers : 3.86 % Allowed : 24.25 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: 0.35 (0.11), residues: 6040 helix: 1.38 (0.11), residues: 2370 sheet: -0.20 (0.19), residues: 857 loop : -0.57 (0.12), residues: 2813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP 4 76 HIS 0.009 0.001 HIS 5 51 PHE 0.023 0.001 PHE O 81 TYR 0.014 0.001 TYR 4 183 ARG 0.004 0.000 ARG Q 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 372 time to evaluate : 4.895 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: 3 79 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.6007 (ttp-170) REVERT: 3 104 GLN cc_start: 0.6930 (OUTLIER) cc_final: 0.6718 (mt0) REVERT: 3 129 HIS cc_start: 0.6870 (OUTLIER) cc_final: 0.6537 (m170) REVERT: 5 95 MET cc_start: 0.6535 (OUTLIER) cc_final: 0.6219 (ptp) REVERT: C 100 ARG cc_start: 0.4828 (OUTLIER) cc_final: 0.2662 (tpt170) REVERT: D 156 PHE cc_start: 0.7282 (OUTLIER) cc_final: 0.6812 (m-80) REVERT: D 170 THR cc_start: 0.7764 (OUTLIER) cc_final: 0.7419 (p) REVERT: D 343 MET cc_start: 0.6128 (ptp) cc_final: 0.5732 (ptp) REVERT: E 86 TYR cc_start: 0.4218 (OUTLIER) cc_final: 0.2901 (m-80) REVERT: F 110 MET cc_start: 0.8122 (mtp) cc_final: 0.7765 (mtm) REVERT: L 129 LYS cc_start: 0.5598 (OUTLIER) cc_final: 0.5359 (ptpp) REVERT: e 58 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8109 (mtpt) REVERT: e 96 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.6045 (m-40) REVERT: i 43 ARG cc_start: 0.7054 (OUTLIER) cc_final: 0.6305 (tpm170) REVERT: j 21 ARG cc_start: 0.6595 (ttp-170) cc_final: 0.6053 (ttp-170) REVERT: j 65 SER cc_start: 0.7863 (t) cc_final: 0.7657 (m) REVERT: x 103 ARG cc_start: 0.5974 (OUTLIER) cc_final: 0.4698 (ttm-80) outliers start: 145 outliers final: 94 residues processed: 475 average time/residue: 0.7398 time to fit residues: 608.8569 Evaluate side-chains 448 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 341 time to evaluate : 4.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 34 VAL Chi-restraints excluded: chain 3 residue 43 CYS Chi-restraints excluded: chain 3 residue 79 ARG Chi-restraints excluded: chain 3 residue 104 GLN Chi-restraints excluded: chain 3 residue 129 HIS Chi-restraints excluded: chain 3 residue 136 ILE Chi-restraints excluded: chain 3 residue 137 LYS Chi-restraints excluded: chain 3 residue 163 LYS Chi-restraints excluded: chain 3 residue 185 ILE Chi-restraints excluded: chain 4 residue 51 CYS Chi-restraints excluded: chain 4 residue 74 ILE Chi-restraints excluded: chain 4 residue 79 ASN Chi-restraints excluded: chain 4 residue 99 ASP Chi-restraints excluded: chain 4 residue 100 ILE Chi-restraints excluded: chain 4 residue 113 PHE Chi-restraints excluded: chain 4 residue 121 ILE Chi-restraints excluded: chain 4 residue 177 VAL Chi-restraints excluded: chain 4 residue 196 VAL Chi-restraints excluded: chain 5 residue 51 HIS Chi-restraints excluded: chain 5 residue 52 GLU Chi-restraints excluded: chain 5 residue 83 ASP Chi-restraints excluded: chain 5 residue 95 MET Chi-restraints excluded: chain 5 residue 130 LEU Chi-restraints excluded: chain 5 residue 168 LEU Chi-restraints excluded: chain 5 residue 176 VAL Chi-restraints excluded: chain 5 residue 196 VAL Chi-restraints excluded: chain 5 residue 199 THR Chi-restraints excluded: chain 5 residue 258 HIS Chi-restraints excluded: chain 5 residue 274 ARG Chi-restraints excluded: chain 5 residue 307 VAL Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 156 PHE Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 392 CYS Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain N residue 149 ASN Chi-restraints excluded: chain N residue 192 HIS Chi-restraints excluded: chain O residue 73 HIS Chi-restraints excluded: chain O residue 150 TYR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain e residue 49 MET Chi-restraints excluded: chain e residue 58 LYS Chi-restraints excluded: chain e residue 79 VAL Chi-restraints excluded: chain e residue 96 ASN Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 107 ASN Chi-restraints excluded: chain f residue 108 ILE Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 78 ILE Chi-restraints excluded: chain i residue 25 SER Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain i residue 43 ARG Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain m residue 210 VAL Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain v residue 46 LEU Chi-restraints excluded: chain v residue 63 THR Chi-restraints excluded: chain v residue 123 VAL Chi-restraints excluded: chain v residue 130 ILE Chi-restraints excluded: chain v residue 137 VAL Chi-restraints excluded: chain v residue 167 ILE Chi-restraints excluded: chain v residue 178 ASP Chi-restraints excluded: chain v residue 190 SER Chi-restraints excluded: chain x residue 26 LEU Chi-restraints excluded: chain x residue 103 ARG Chi-restraints excluded: chain x residue 115 LEU Chi-restraints excluded: chain x residue 118 CYS Chi-restraints excluded: chain x residue 161 LEU Chi-restraints excluded: chain x residue 179 LEU Chi-restraints excluded: chain T residue 143 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 247 optimal weight: 0.0020 chunk 661 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 431 optimal weight: 30.0000 chunk 181 optimal weight: 0.0050 chunk 735 optimal weight: 5.9990 chunk 610 optimal weight: 0.3980 chunk 340 optimal weight: 0.9980 chunk 61 optimal weight: 20.0000 chunk 243 optimal weight: 10.0000 chunk 386 optimal weight: 3.9990 overall best weight: 0.8804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 71 HIS ** 4 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 138 ASN ** 5 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN O 189 ASN ** Q 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 83472 Z= 0.153 Angle : 0.510 10.411 120860 Z= 0.260 Chirality : 0.035 0.247 15092 Planarity : 0.004 0.050 9549 Dihedral : 22.470 179.793 31569 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.23 % Favored : 95.62 % Rotamer: Outliers : 3.83 % Allowed : 24.46 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: 0.51 (0.11), residues: 6040 helix: 1.52 (0.11), residues: 2361 sheet: -0.09 (0.18), residues: 870 loop : -0.51 (0.12), residues: 2809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 407 HIS 0.007 0.001 HIS 5 51 PHE 0.039 0.001 PHE h 6 TYR 0.014 0.001 TYR 4 183 ARG 0.006 0.000 ARG D 258 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 381 time to evaluate : 4.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 31 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7467 (pt0) REVERT: 3 104 GLN cc_start: 0.6760 (OUTLIER) cc_final: 0.6548 (mt0) REVERT: 3 129 HIS cc_start: 0.6847 (OUTLIER) cc_final: 0.6540 (m170) REVERT: D 156 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.6802 (m-80) REVERT: D 170 THR cc_start: 0.7683 (OUTLIER) cc_final: 0.7236 (p) REVERT: E 86 TYR cc_start: 0.4212 (OUTLIER) cc_final: 0.2965 (m-80) REVERT: F 110 MET cc_start: 0.8012 (mtp) cc_final: 0.7677 (mtm) REVERT: L 129 LYS cc_start: 0.5493 (OUTLIER) cc_final: 0.5166 (ptpp) REVERT: P 54 HIS cc_start: 0.7237 (OUTLIER) cc_final: 0.6850 (m90) REVERT: Y 2 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7351 (tttp) REVERT: e 96 ASN cc_start: 0.8713 (OUTLIER) cc_final: 0.6110 (m-40) REVERT: i 43 ARG cc_start: 0.6958 (OUTLIER) cc_final: 0.6222 (tpm170) REVERT: j 21 ARG cc_start: 0.6637 (ttp-170) cc_final: 0.6109 (ttp-170) REVERT: j 65 SER cc_start: 0.7825 (t) cc_final: 0.7624 (m) REVERT: x 103 ARG cc_start: 0.5870 (OUTLIER) cc_final: 0.4573 (ttm-80) outliers start: 144 outliers final: 85 residues processed: 490 average time/residue: 0.7458 time to fit residues: 631.9632 Evaluate side-chains 451 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 354 time to evaluate : 4.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 31 GLU Chi-restraints excluded: chain 3 residue 43 CYS Chi-restraints excluded: chain 3 residue 104 GLN Chi-restraints excluded: chain 3 residue 129 HIS Chi-restraints excluded: chain 3 residue 136 ILE Chi-restraints excluded: chain 3 residue 163 LYS Chi-restraints excluded: chain 3 residue 167 LYS Chi-restraints excluded: chain 3 residue 185 ILE Chi-restraints excluded: chain 4 residue 99 ASP Chi-restraints excluded: chain 4 residue 100 ILE Chi-restraints excluded: chain 4 residue 113 PHE Chi-restraints excluded: chain 4 residue 177 VAL Chi-restraints excluded: chain 4 residue 196 VAL Chi-restraints excluded: chain 5 residue 83 ASP Chi-restraints excluded: chain 5 residue 130 LEU Chi-restraints excluded: chain 5 residue 168 LEU Chi-restraints excluded: chain 5 residue 176 VAL Chi-restraints excluded: chain 5 residue 196 VAL Chi-restraints excluded: chain 5 residue 199 THR Chi-restraints excluded: chain 5 residue 258 HIS Chi-restraints excluded: chain 5 residue 274 ARG Chi-restraints excluded: chain 5 residue 307 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 156 PHE Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 392 CYS Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain L residue 132 GLN Chi-restraints excluded: chain N residue 149 ASN Chi-restraints excluded: chain N residue 192 HIS Chi-restraints excluded: chain O residue 73 HIS Chi-restraints excluded: chain O residue 109 ILE Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 150 TYR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 54 HIS Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 144 ASN Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 7 VAL Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain e residue 19 SER Chi-restraints excluded: chain e residue 49 MET Chi-restraints excluded: chain e residue 79 VAL Chi-restraints excluded: chain e residue 96 ASN Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 107 ASN Chi-restraints excluded: chain f residue 108 ILE Chi-restraints excluded: chain h residue 78 ILE Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain i residue 25 SER Chi-restraints excluded: chain i residue 43 ARG Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain m residue 210 VAL Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain v residue 46 LEU Chi-restraints excluded: chain v residue 63 THR Chi-restraints excluded: chain v residue 123 VAL Chi-restraints excluded: chain v residue 130 ILE Chi-restraints excluded: chain v residue 167 ILE Chi-restraints excluded: chain v residue 178 ASP Chi-restraints excluded: chain v residue 190 SER Chi-restraints excluded: chain x residue 26 LEU Chi-restraints excluded: chain x residue 103 ARG Chi-restraints excluded: chain x residue 115 LEU Chi-restraints excluded: chain x residue 118 CYS Chi-restraints excluded: chain x residue 161 LEU Chi-restraints excluded: chain x residue 179 LEU Chi-restraints excluded: chain T residue 143 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 708 optimal weight: 3.9990 chunk 82 optimal weight: 20.0000 chunk 418 optimal weight: 0.0670 chunk 536 optimal weight: 6.9990 chunk 416 optimal weight: 7.9990 chunk 618 optimal weight: 0.9990 chunk 410 optimal weight: 1.9990 chunk 732 optimal weight: 8.9990 chunk 458 optimal weight: 20.0000 chunk 446 optimal weight: 2.9990 chunk 338 optimal weight: 40.0000 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 127 HIS ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 ASN ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN O 189 ASN ** Q 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 19 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 83472 Z= 0.264 Angle : 0.570 9.243 120860 Z= 0.289 Chirality : 0.037 0.296 15092 Planarity : 0.004 0.051 9549 Dihedral : 22.480 178.900 31569 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.77 % Favored : 95.08 % Rotamer: Outliers : 4.07 % Allowed : 24.67 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: 0.42 (0.11), residues: 6040 helix: 1.46 (0.11), residues: 2370 sheet: -0.11 (0.19), residues: 847 loop : -0.58 (0.12), residues: 2823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP 5 171 HIS 0.008 0.001 HIS 5 51 PHE 0.031 0.001 PHE D 143 TYR 0.019 0.002 TYR Q 32 ARG 0.005 0.000 ARG F 167 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 351 time to evaluate : 5.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 31 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7526 (pt0) REVERT: 3 104 GLN cc_start: 0.6991 (OUTLIER) cc_final: 0.6734 (mt0) REVERT: 3 123 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7423 (ttp80) REVERT: 3 129 HIS cc_start: 0.6871 (OUTLIER) cc_final: 0.6578 (m170) REVERT: 4 212 TYR cc_start: 0.5011 (OUTLIER) cc_final: 0.3723 (p90) REVERT: C 100 ARG cc_start: 0.4922 (OUTLIER) cc_final: 0.2694 (tpt170) REVERT: D 156 PHE cc_start: 0.7269 (OUTLIER) cc_final: 0.6807 (m-80) REVERT: D 170 THR cc_start: 0.7780 (OUTLIER) cc_final: 0.7527 (p) REVERT: D 477 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6899 (pm20) REVERT: E 86 TYR cc_start: 0.4384 (OUTLIER) cc_final: 0.3223 (m-80) REVERT: F 110 MET cc_start: 0.8114 (mtp) cc_final: 0.7794 (mtm) REVERT: P 54 HIS cc_start: 0.7313 (OUTLIER) cc_final: 0.6912 (m90) REVERT: P 112 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7412 (mm) REVERT: Q 127 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7347 (mt0) REVERT: S 175 PHE cc_start: 0.4802 (OUTLIER) cc_final: 0.4281 (t80) REVERT: Y 2 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7341 (tttp) REVERT: e 96 ASN cc_start: 0.8786 (OUTLIER) cc_final: 0.7755 (p0) REVERT: i 43 ARG cc_start: 0.6990 (OUTLIER) cc_final: 0.6213 (tpm170) REVERT: j 21 ARG cc_start: 0.6634 (ttp-170) cc_final: 0.6137 (ttp-170) REVERT: j 65 SER cc_start: 0.7847 (t) cc_final: 0.7643 (m) REVERT: x 103 ARG cc_start: 0.5969 (OUTLIER) cc_final: 0.4484 (ttm-80) outliers start: 153 outliers final: 111 residues processed: 470 average time/residue: 0.7376 time to fit residues: 598.5058 Evaluate side-chains 463 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 334 time to evaluate : 4.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 31 GLU Chi-restraints excluded: chain 3 residue 34 VAL Chi-restraints excluded: chain 3 residue 43 CYS Chi-restraints excluded: chain 3 residue 104 GLN Chi-restraints excluded: chain 3 residue 123 ARG Chi-restraints excluded: chain 3 residue 129 HIS Chi-restraints excluded: chain 3 residue 136 ILE Chi-restraints excluded: chain 3 residue 163 LYS Chi-restraints excluded: chain 3 residue 167 LYS Chi-restraints excluded: chain 3 residue 185 ILE Chi-restraints excluded: chain 4 residue 15 ASP Chi-restraints excluded: chain 4 residue 51 CYS Chi-restraints excluded: chain 4 residue 99 ASP Chi-restraints excluded: chain 4 residue 100 ILE Chi-restraints excluded: chain 4 residue 113 PHE Chi-restraints excluded: chain 4 residue 177 VAL Chi-restraints excluded: chain 4 residue 196 VAL Chi-restraints excluded: chain 4 residue 212 TYR Chi-restraints excluded: chain 5 residue 17 ILE Chi-restraints excluded: chain 5 residue 51 HIS Chi-restraints excluded: chain 5 residue 83 ASP Chi-restraints excluded: chain 5 residue 87 LEU Chi-restraints excluded: chain 5 residue 130 LEU Chi-restraints excluded: chain 5 residue 168 LEU Chi-restraints excluded: chain 5 residue 176 VAL Chi-restraints excluded: chain 5 residue 196 VAL Chi-restraints excluded: chain 5 residue 199 THR Chi-restraints excluded: chain 5 residue 253 THR Chi-restraints excluded: chain 5 residue 258 HIS Chi-restraints excluded: chain 5 residue 304 LEU Chi-restraints excluded: chain 5 residue 307 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain D residue 156 PHE Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 392 CYS Chi-restraints excluded: chain D residue 477 GLU Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain L residue 132 GLN Chi-restraints excluded: chain N residue 149 ASN Chi-restraints excluded: chain N residue 192 HIS Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 73 HIS Chi-restraints excluded: chain O residue 109 ILE Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 150 TYR Chi-restraints excluded: chain O residue 189 ASN Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 54 HIS Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 127 GLN Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 144 ASN Chi-restraints excluded: chain S residue 175 PHE Chi-restraints excluded: chain Y residue 2 LYS Chi-restraints excluded: chain Y residue 7 VAL Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain e residue 19 SER Chi-restraints excluded: chain e residue 49 MET Chi-restraints excluded: chain e residue 79 VAL Chi-restraints excluded: chain e residue 96 ASN Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 125 SER Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 107 ASN Chi-restraints excluded: chain f residue 108 ILE Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 78 ILE Chi-restraints excluded: chain i residue 15 LEU Chi-restraints excluded: chain i residue 25 SER Chi-restraints excluded: chain i residue 43 ARG Chi-restraints excluded: chain i residue 78 LEU Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain m residue 112 THR Chi-restraints excluded: chain m residue 210 VAL Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain v residue 19 ARG Chi-restraints excluded: chain v residue 46 LEU Chi-restraints excluded: chain v residue 63 THR Chi-restraints excluded: chain v residue 123 VAL Chi-restraints excluded: chain v residue 125 ASP Chi-restraints excluded: chain v residue 130 ILE Chi-restraints excluded: chain v residue 137 VAL Chi-restraints excluded: chain v residue 167 ILE Chi-restraints excluded: chain v residue 178 ASP Chi-restraints excluded: chain v residue 190 SER Chi-restraints excluded: chain x residue 26 LEU Chi-restraints excluded: chain x residue 103 ARG Chi-restraints excluded: chain x residue 115 LEU Chi-restraints excluded: chain x residue 118 CYS Chi-restraints excluded: chain x residue 161 LEU Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 151 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 453 optimal weight: 7.9990 chunk 292 optimal weight: 0.7980 chunk 437 optimal weight: 0.0570 chunk 220 optimal weight: 0.2980 chunk 143 optimal weight: 4.9990 chunk 141 optimal weight: 40.0000 chunk 465 optimal weight: 40.0000 chunk 499 optimal weight: 0.0060 chunk 362 optimal weight: 0.6980 chunk 68 optimal weight: 9.9990 chunk 575 optimal weight: 50.0000 overall best weight: 0.3714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN G 107 GLN ** O 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 230 HIS v 152 GLN x 6 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 83472 Z= 0.122 Angle : 0.505 11.457 120860 Z= 0.257 Chirality : 0.034 0.247 15092 Planarity : 0.003 0.052 9549 Dihedral : 22.361 178.232 31569 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.63 % Favored : 96.22 % Rotamer: Outliers : 2.69 % Allowed : 26.00 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: 0.61 (0.11), residues: 6040 helix: 1.61 (0.11), residues: 2372 sheet: 0.05 (0.19), residues: 848 loop : -0.48 (0.12), residues: 2820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP 5 171 HIS 0.007 0.001 HIS 5 51 PHE 0.036 0.001 PHE h 6 TYR 0.029 0.001 TYR F 143 ARG 0.004 0.000 ARG Q 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 385 time to evaluate : 4.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 129 HIS cc_start: 0.6805 (OUTLIER) cc_final: 0.6513 (m170) REVERT: 5 95 MET cc_start: 0.5603 (ptt) cc_final: 0.5199 (ptt) REVERT: C 100 ARG cc_start: 0.4633 (OUTLIER) cc_final: 0.2522 (tpt170) REVERT: D 156 PHE cc_start: 0.7176 (OUTLIER) cc_final: 0.6663 (m-80) REVERT: D 170 THR cc_start: 0.7477 (OUTLIER) cc_final: 0.7211 (p) REVERT: D 477 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6700 (pm20) REVERT: E 86 TYR cc_start: 0.4574 (OUTLIER) cc_final: 0.3461 (m-80) REVERT: F 110 MET cc_start: 0.7901 (mtp) cc_final: 0.7621 (mtm) REVERT: P 112 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7421 (mm) REVERT: S 175 PHE cc_start: 0.4500 (OUTLIER) cc_final: 0.4180 (t80) REVERT: i 43 ARG cc_start: 0.6674 (OUTLIER) cc_final: 0.6142 (tpm170) REVERT: j 21 ARG cc_start: 0.6687 (ttp-170) cc_final: 0.6117 (ttp-170) REVERT: v 128 ILE cc_start: 0.4175 (OUTLIER) cc_final: 0.3871 (tt) REVERT: x 103 ARG cc_start: 0.5839 (OUTLIER) cc_final: 0.4449 (ttm-80) outliers start: 101 outliers final: 68 residues processed: 458 average time/residue: 0.7608 time to fit residues: 599.6636 Evaluate side-chains 434 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 355 time to evaluate : 4.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 129 HIS Chi-restraints excluded: chain 3 residue 163 LYS Chi-restraints excluded: chain 3 residue 167 LYS Chi-restraints excluded: chain 3 residue 185 ILE Chi-restraints excluded: chain 4 residue 51 CYS Chi-restraints excluded: chain 4 residue 79 ASN Chi-restraints excluded: chain 4 residue 99 ASP Chi-restraints excluded: chain 4 residue 100 ILE Chi-restraints excluded: chain 4 residue 113 PHE Chi-restraints excluded: chain 4 residue 177 VAL Chi-restraints excluded: chain 4 residue 196 VAL Chi-restraints excluded: chain 5 residue 51 HIS Chi-restraints excluded: chain 5 residue 83 ASP Chi-restraints excluded: chain 5 residue 87 LEU Chi-restraints excluded: chain 5 residue 168 LEU Chi-restraints excluded: chain 5 residue 176 VAL Chi-restraints excluded: chain 5 residue 199 THR Chi-restraints excluded: chain 5 residue 258 HIS Chi-restraints excluded: chain 5 residue 274 ARG Chi-restraints excluded: chain 5 residue 304 LEU Chi-restraints excluded: chain 5 residue 307 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain D residue 156 PHE Chi-restraints excluded: chain D residue 170 THR Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 392 CYS Chi-restraints excluded: chain D residue 477 GLU Chi-restraints excluded: chain D residue 512 ILE Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain N residue 149 ASN Chi-restraints excluded: chain N residue 192 HIS Chi-restraints excluded: chain O residue 73 HIS Chi-restraints excluded: chain O residue 109 ILE Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 150 TYR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 144 ASN Chi-restraints excluded: chain S residue 175 PHE Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain e residue 19 SER Chi-restraints excluded: chain e residue 58 LYS Chi-restraints excluded: chain e residue 79 VAL Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 108 ILE Chi-restraints excluded: chain i residue 43 ARG Chi-restraints excluded: chain i residue 78 LEU Chi-restraints excluded: chain m residue 210 VAL Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain v residue 46 LEU Chi-restraints excluded: chain v residue 123 VAL Chi-restraints excluded: chain v residue 128 ILE Chi-restraints excluded: chain v residue 130 ILE Chi-restraints excluded: chain v residue 167 ILE Chi-restraints excluded: chain v residue 178 ASP Chi-restraints excluded: chain v residue 190 SER Chi-restraints excluded: chain x residue 26 LEU Chi-restraints excluded: chain x residue 103 ARG Chi-restraints excluded: chain x residue 118 CYS Chi-restraints excluded: chain x residue 154 ASP Chi-restraints excluded: chain x residue 179 LEU Chi-restraints excluded: chain x residue 233 ILE Chi-restraints excluded: chain T residue 143 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 666 optimal weight: 50.0000 chunk 701 optimal weight: 0.9980 chunk 640 optimal weight: 1.9990 chunk 682 optimal weight: 50.0000 chunk 410 optimal weight: 0.8980 chunk 297 optimal weight: 0.6980 chunk 536 optimal weight: 5.9990 chunk 209 optimal weight: 2.9990 chunk 616 optimal weight: 0.9980 chunk 645 optimal weight: 2.9990 chunk 680 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 127 HIS 5 233 GLN ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 152 GLN v 168 GLN x 6 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 83472 Z= 0.175 Angle : 0.518 9.717 120860 Z= 0.263 Chirality : 0.035 0.251 15092 Planarity : 0.004 0.052 9549 Dihedral : 22.302 179.955 31567 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.01 % Favored : 95.84 % Rotamer: Outliers : 2.74 % Allowed : 25.79 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: 0.64 (0.11), residues: 6040 helix: 1.67 (0.11), residues: 2364 sheet: 0.02 (0.19), residues: 851 loop : -0.48 (0.12), residues: 2825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP 5 171 HIS 0.008 0.001 HIS 5 51 PHE 0.032 0.001 PHE D 143 TYR 0.031 0.001 TYR C 333 ARG 0.005 0.000 ARG e 124 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 355 time to evaluate : 5.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 31 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7438 (pt0) REVERT: 3 129 HIS cc_start: 0.6846 (OUTLIER) cc_final: 0.6580 (m170) REVERT: 5 95 MET cc_start: 0.5681 (ptt) cc_final: 0.5321 (ptt) REVERT: C 100 ARG cc_start: 0.4743 (OUTLIER) cc_final: 0.2407 (tpt170) REVERT: D 156 PHE cc_start: 0.7203 (OUTLIER) cc_final: 0.6716 (m-80) REVERT: D 477 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6646 (pm20) REVERT: F 110 MET cc_start: 0.8015 (mtp) cc_final: 0.7716 (mtm) REVERT: P 112 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7293 (mm) REVERT: S 175 PHE cc_start: 0.4580 (OUTLIER) cc_final: 0.4151 (t80) REVERT: i 43 ARG cc_start: 0.6733 (OUTLIER) cc_final: 0.6254 (tpm170) REVERT: j 21 ARG cc_start: 0.6595 (ttp-170) cc_final: 0.6074 (ttp-170) REVERT: x 15 MET cc_start: 0.7744 (tpp) cc_final: 0.7524 (tpt) REVERT: x 103 ARG cc_start: 0.5726 (OUTLIER) cc_final: 0.4364 (ttm-80) outliers start: 103 outliers final: 77 residues processed: 432 average time/residue: 0.7423 time to fit residues: 556.5070 Evaluate side-chains 432 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 346 time to evaluate : 4.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 31 GLU Chi-restraints excluded: chain 3 residue 129 HIS Chi-restraints excluded: chain 3 residue 163 LYS Chi-restraints excluded: chain 3 residue 167 LYS Chi-restraints excluded: chain 3 residue 185 ILE Chi-restraints excluded: chain 4 residue 51 CYS Chi-restraints excluded: chain 4 residue 75 VAL Chi-restraints excluded: chain 4 residue 79 ASN Chi-restraints excluded: chain 4 residue 99 ASP Chi-restraints excluded: chain 4 residue 100 ILE Chi-restraints excluded: chain 4 residue 113 PHE Chi-restraints excluded: chain 4 residue 177 VAL Chi-restraints excluded: chain 4 residue 196 VAL Chi-restraints excluded: chain 5 residue 51 HIS Chi-restraints excluded: chain 5 residue 83 ASP Chi-restraints excluded: chain 5 residue 87 LEU Chi-restraints excluded: chain 5 residue 168 LEU Chi-restraints excluded: chain 5 residue 176 VAL Chi-restraints excluded: chain 5 residue 199 THR Chi-restraints excluded: chain 5 residue 258 HIS Chi-restraints excluded: chain 5 residue 274 ARG Chi-restraints excluded: chain 5 residue 304 LEU Chi-restraints excluded: chain 5 residue 307 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain D residue 156 PHE Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 392 CYS Chi-restraints excluded: chain D residue 477 GLU Chi-restraints excluded: chain D residue 512 ILE Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain N residue 149 ASN Chi-restraints excluded: chain N residue 192 HIS Chi-restraints excluded: chain O residue 73 HIS Chi-restraints excluded: chain O residue 109 ILE Chi-restraints excluded: chain O residue 138 THR Chi-restraints excluded: chain O residue 150 TYR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 144 ASN Chi-restraints excluded: chain S residue 175 PHE Chi-restraints excluded: chain Y residue 7 VAL Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain e residue 19 SER Chi-restraints excluded: chain e residue 49 MET Chi-restraints excluded: chain e residue 79 VAL Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 108 ILE Chi-restraints excluded: chain h residue 25 GLN Chi-restraints excluded: chain h residue 78 ILE Chi-restraints excluded: chain i residue 42 VAL Chi-restraints excluded: chain i residue 43 ARG Chi-restraints excluded: chain i residue 78 LEU Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain m residue 210 VAL Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain v residue 46 LEU Chi-restraints excluded: chain v residue 123 VAL Chi-restraints excluded: chain v residue 130 ILE Chi-restraints excluded: chain v residue 178 ASP Chi-restraints excluded: chain v residue 190 SER Chi-restraints excluded: chain x residue 26 LEU Chi-restraints excluded: chain x residue 103 ARG Chi-restraints excluded: chain x residue 118 CYS Chi-restraints excluded: chain x residue 154 ASP Chi-restraints excluded: chain x residue 179 LEU Chi-restraints excluded: chain x residue 233 ILE Chi-restraints excluded: chain T residue 143 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 448 optimal weight: 50.0000 chunk 721 optimal weight: 4.9990 chunk 440 optimal weight: 20.0000 chunk 342 optimal weight: 9.9990 chunk 501 optimal weight: 0.5980 chunk 757 optimal weight: 50.0000 chunk 696 optimal weight: 1.9990 chunk 602 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 465 optimal weight: 10.0000 chunk 369 optimal weight: 0.0570 overall best weight: 2.5304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 127 HIS ** 5 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 126 GLN x 264 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 83472 Z= 0.317 Angle : 0.612 12.786 120860 Z= 0.309 Chirality : 0.039 0.325 15092 Planarity : 0.004 0.054 9549 Dihedral : 22.385 178.980 31567 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.87 % Favored : 94.98 % Rotamer: Outliers : 2.85 % Allowed : 25.71 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: 0.43 (0.11), residues: 6040 helix: 1.47 (0.11), residues: 2370 sheet: -0.08 (0.19), residues: 844 loop : -0.58 (0.12), residues: 2826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP 5 171 HIS 0.008 0.001 HIS 5 51 PHE 0.033 0.002 PHE h 6 TYR 0.025 0.002 TYR F 143 ARG 0.009 0.001 ARG v 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12080 Ramachandran restraints generated. 6040 Oldfield, 0 Emsley, 6040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 338 time to evaluate : 5.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 31 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7586 (pt0) REVERT: 3 129 HIS cc_start: 0.6833 (OUTLIER) cc_final: 0.6525 (m170) REVERT: 4 52 MET cc_start: 0.8501 (tpt) cc_final: 0.8102 (tpt) REVERT: C 100 ARG cc_start: 0.4865 (OUTLIER) cc_final: 0.2654 (tpt170) REVERT: D 156 PHE cc_start: 0.7167 (OUTLIER) cc_final: 0.6607 (m-80) REVERT: D 477 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6691 (pm20) REVERT: E 86 TYR cc_start: 0.4539 (OUTLIER) cc_final: 0.3511 (m-80) REVERT: F 110 MET cc_start: 0.8173 (mtp) cc_final: 0.7886 (mtm) REVERT: S 42 TYR cc_start: 0.6417 (t80) cc_final: 0.6200 (t80) REVERT: S 175 PHE cc_start: 0.4766 (OUTLIER) cc_final: 0.4109 (t80) REVERT: i 43 ARG cc_start: 0.6942 (OUTLIER) cc_final: 0.6340 (tpm170) REVERT: j 21 ARG cc_start: 0.6570 (ttp-170) cc_final: 0.6147 (ttp-170) REVERT: x 15 MET cc_start: 0.7793 (tpp) cc_final: 0.7494 (tpt) REVERT: x 103 ARG cc_start: 0.6067 (OUTLIER) cc_final: 0.4474 (ttm-80) outliers start: 107 outliers final: 78 residues processed: 419 average time/residue: 0.7358 time to fit residues: 539.0730 Evaluate side-chains 421 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 334 time to evaluate : 4.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 31 GLU Chi-restraints excluded: chain 3 residue 129 HIS Chi-restraints excluded: chain 3 residue 163 LYS Chi-restraints excluded: chain 3 residue 185 ILE Chi-restraints excluded: chain 3 residue 189 VAL Chi-restraints excluded: chain 4 residue 51 CYS Chi-restraints excluded: chain 4 residue 75 VAL Chi-restraints excluded: chain 4 residue 79 ASN Chi-restraints excluded: chain 4 residue 99 ASP Chi-restraints excluded: chain 4 residue 100 ILE Chi-restraints excluded: chain 4 residue 113 PHE Chi-restraints excluded: chain 4 residue 177 VAL Chi-restraints excluded: chain 4 residue 196 VAL Chi-restraints excluded: chain 5 residue 51 HIS Chi-restraints excluded: chain 5 residue 83 ASP Chi-restraints excluded: chain 5 residue 87 LEU Chi-restraints excluded: chain 5 residue 130 LEU Chi-restraints excluded: chain 5 residue 176 VAL Chi-restraints excluded: chain 5 residue 199 THR Chi-restraints excluded: chain 5 residue 234 LEU Chi-restraints excluded: chain 5 residue 278 SER Chi-restraints excluded: chain 5 residue 304 LEU Chi-restraints excluded: chain 5 residue 307 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain D residue 156 PHE Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 392 CYS Chi-restraints excluded: chain D residue 477 GLU Chi-restraints excluded: chain D residue 512 ILE Chi-restraints excluded: chain E residue 34 ASN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 86 TYR Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 163 VAL Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain N residue 149 ASN Chi-restraints excluded: chain N residue 192 HIS Chi-restraints excluded: chain O residue 73 HIS Chi-restraints excluded: chain O residue 109 ILE Chi-restraints excluded: chain O residue 150 TYR Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 119 VAL Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 144 ASN Chi-restraints excluded: chain S residue 175 PHE Chi-restraints excluded: chain Y residue 7 VAL Chi-restraints excluded: chain Y residue 66 GLU Chi-restraints excluded: chain e residue 19 SER Chi-restraints excluded: chain e residue 79 VAL Chi-restraints excluded: chain e residue 83 LEU Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain f residue 60 VAL Chi-restraints excluded: chain f residue 108 ILE Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 25 GLN Chi-restraints excluded: chain h residue 78 ILE Chi-restraints excluded: chain i residue 43 ARG Chi-restraints excluded: chain i residue 78 LEU Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain m residue 210 VAL Chi-restraints excluded: chain v residue 46 LEU Chi-restraints excluded: chain v residue 123 VAL Chi-restraints excluded: chain v residue 130 ILE Chi-restraints excluded: chain v residue 178 ASP Chi-restraints excluded: chain v residue 190 SER Chi-restraints excluded: chain x residue 26 LEU Chi-restraints excluded: chain x residue 103 ARG Chi-restraints excluded: chain x residue 118 CYS Chi-restraints excluded: chain x residue 232 THR Chi-restraints excluded: chain T residue 143 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 478 optimal weight: 10.0000 chunk 642 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 555 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 167 optimal weight: 0.5980 chunk 603 optimal weight: 50.0000 chunk 252 optimal weight: 4.9990 chunk 620 optimal weight: 0.5980 chunk 76 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 127 HIS ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 GLN ** O 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 230 HIS x 264 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.153941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.136988 restraints weight = 231744.472| |-----------------------------------------------------------------------------| r_work (start): 0.4296 rms_B_bonded: 1.56 r_work: 0.3949 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3924 r_free = 0.3924 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3924 r_free = 0.3924 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 83472 Z= 0.169 Angle : 0.523 12.832 120860 Z= 0.266 Chirality : 0.035 0.244 15092 Planarity : 0.004 0.056 9549 Dihedral : 22.281 179.629 31567 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.01 % Favored : 95.84 % Rotamer: Outliers : 2.61 % Allowed : 25.92 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.10 % 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: 0.57 (0.11), residues: 6040 helix: 1.60 (0.11), residues: 2370 sheet: -0.01 (0.19), residues: 832 loop : -0.52 (0.12), residues: 2838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP 5 171 HIS 0.008 0.001 HIS 5 51 PHE 0.032 0.001 PHE D 143 TYR 0.023 0.001 TYR 3 118 ARG 0.005 0.000 ARG t 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13131.12 seconds wall clock time: 235 minutes 35.66 seconds (14135.66 seconds total)