Starting phenix.real_space_refine on Sun Nov 19 08:47:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eup_24410/11_2023/8eup_24410.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eup_24410/11_2023/8eup_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_24410/11_2023/8eup_24410.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eup_24410/11_2023/8eup_24410.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eup_24410/11_2023/8eup_24410.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eup_24410/11_2023/8eup_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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 31.92, 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: 33.45 Conformation dependent library (CDL) restraints added in 6.7 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: 25.79 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: 55.91 Time building geometry restraints manager: 36.01 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: 44518 35.64 - 71.27: 1987 71.27 - 106.91: 169 106.91 - 142.55: 16 142.55 - 178.19: 19 Dihedral angle restraints: 46709 sinusoidal: 28806 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 46706 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: 7.540 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: 0.080 Extract box with map and model: 27.780 Check model and map are aligned: 0.880 Set scattering table: 0.590 Process input model: 222.500 Find NCS groups from input model: 2.090 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:3.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 264.910 ------------------------------------------------------------------------------- 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 : 17.144 178.186 35045 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 *********************** 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 : 4.733 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 367 average time/residue: 0.7687 time to fit residues: 486.5639 Evaluate side-chains 343 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 338 time to evaluate : 4.742 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.6060 time to fit residues: 11.4384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.1980 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: 1.1542 ------------------------------------------------------------------------------- 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 270 GLN E 75 GLN E 186 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 83472 Z= 0.186 Angle : 0.569 7.094 120860 Z= 0.289 Chirality : 0.036 0.275 15092 Planarity : 0.004 0.052 9549 Dihedral : 15.898 179.948 26012 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.31 % Favored : 95.54 % Rotamer: Outliers : 2.42 % Allowed : 22.25 % Favored : 75.33 % 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: 0.14 (0.11), residues: 6040 helix: 1.08 (0.11), residues: 2354 sheet: -0.04 (0.19), residues: 849 loop : -0.66 (0.12), residues: 2837 *********************** 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 457 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 367 time to evaluate : 4.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 37 residues processed: 438 average time/residue: 0.7443 time to fit residues: 566.7251 Evaluate side-chains 368 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 331 time to evaluate : 4.694 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.5899 time to fit residues: 47.2765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 383 optimal weight: 4.9990 chunk 214 optimal weight: 2.9990 chunk 574 optimal weight: 40.0000 chunk 469 optimal weight: 2.9990 chunk 190 optimal weight: 0.9980 chunk 691 optimal weight: 9.9990 chunk 746 optimal weight: 9.9990 chunk 615 optimal weight: 0.8980 chunk 685 optimal weight: 50.0000 chunk 235 optimal weight: 3.9990 chunk 554 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 14 GLN m 230 HIS x 50 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 83472 Z= 0.240 Angle : 0.569 7.849 120860 Z= 0.290 Chirality : 0.037 0.285 15092 Planarity : 0.004 0.051 9549 Dihedral : 15.898 179.606 26012 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.96 % Favored : 94.90 % Rotamer: Outliers : 2.77 % Allowed : 23.29 % Favored : 73.94 % 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: 0.23 (0.11), residues: 6040 helix: 1.21 (0.11), residues: 2358 sheet: -0.01 (0.19), residues: 828 loop : -0.65 (0.12), residues: 2854 *********************** 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 471 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 368 time to evaluate : 4.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 103 outliers final: 56 residues processed: 451 average time/residue: 0.7524 time to fit residues: 590.3296 Evaluate side-chains 387 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 331 time to evaluate : 4.719 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.5807 time to fit residues: 68.2444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 683 optimal weight: 0.0770 chunk 519 optimal weight: 20.0000 chunk 358 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 329 optimal weight: 6.9990 chunk 464 optimal weight: 50.0000 chunk 693 optimal weight: 0.8980 chunk 734 optimal weight: 4.9990 chunk 362 optimal weight: 5.9990 chunk 657 optimal weight: 1.9990 chunk 197 optimal weight: 0.0000 overall best weight: 0.7946 ------------------------------------------------------------------------------- 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** 4 155 ASN 4 195 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 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN D 188 HIS ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN F 173 ASN ** Q 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 152 GLN x 234 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 83472 Z= 0.148 Angle : 0.514 8.337 120860 Z= 0.262 Chirality : 0.035 0.250 15092 Planarity : 0.004 0.051 9549 Dihedral : 15.706 179.696 26012 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.86 % Favored : 95.99 % Rotamer: Outliers : 1.97 % Allowed : 24.11 % Favored : 73.92 % 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: 1.42 (0.11), residues: 2360 sheet: -0.01 (0.19), residues: 829 loop : -0.56 (0.12), residues: 2851 *********************** 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 456 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 383 time to evaluate : 4.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 30 residues processed: 439 average time/residue: 0.7584 time to fit residues: 578.7021 Evaluate side-chains 379 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 349 time to evaluate : 4.770 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.6128 time to fit residues: 40.5388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 611 optimal weight: 1.9990 chunk 417 optimal weight: 40.0000 chunk 10 optimal weight: 5.9990 chunk 546 optimal weight: 1.9990 chunk 303 optimal weight: 3.9990 chunk 626 optimal weight: 5.9990 chunk 507 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 375 optimal weight: 8.9990 chunk 659 optimal weight: 0.1980 chunk 185 optimal weight: 0.9980 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 32 GLN ** 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** 5 233 GLN 5 292 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 ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN O 189 ASN P 54 HIS ** Q 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 152 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 83472 Z= 0.245 Angle : 0.562 9.697 120860 Z= 0.285 Chirality : 0.037 0.294 15092 Planarity : 0.004 0.050 9549 Dihedral : 15.734 179.555 26012 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.71 % Favored : 95.14 % Rotamer: Outliers : 1.89 % Allowed : 24.89 % Favored : 73.22 % 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: 0.38 (0.11), residues: 6040 helix: 1.42 (0.11), residues: 2363 sheet: -0.13 (0.19), residues: 851 loop : -0.59 (0.12), residues: 2826 *********************** 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 431 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 361 time to evaluate : 4.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 37 residues processed: 403 average time/residue: 0.8004 time to fit residues: 563.0071 Evaluate side-chains 376 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 339 time to evaluate : 4.862 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.6295 time to fit residues: 50.4203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 247 optimal weight: 2.9990 chunk 661 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 chunk 431 optimal weight: 30.0000 chunk 181 optimal weight: 0.7980 chunk 735 optimal weight: 9.9990 chunk 610 optimal weight: 2.9990 chunk 340 optimal weight: 0.2980 chunk 61 optimal weight: 20.0000 chunk 243 optimal weight: 8.9990 chunk 386 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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** ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 ASN D 188 HIS D 200 ASN ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 189 ASN Q 44 ASN ** Q 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 19 GLN x 264 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 83472 Z= 0.283 Angle : 0.592 9.808 120860 Z= 0.299 Chirality : 0.038 0.331 15092 Planarity : 0.004 0.049 9549 Dihedral : 15.796 179.091 26012 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.05 % Favored : 94.80 % Rotamer: Outliers : 2.05 % Allowed : 25.45 % Favored : 72.50 % 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: 0.30 (0.11), residues: 6040 helix: 1.34 (0.11), residues: 2372 sheet: -0.21 (0.19), residues: 849 loop : -0.62 (0.12), residues: 2819 *********************** 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 428 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 351 time to evaluate : 4.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 31 residues processed: 410 average time/residue: 0.7777 time to fit residues: 554.2460 Evaluate side-chains 365 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 334 time to evaluate : 4.812 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.6173 time to fit residues: 42.3243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 708 optimal weight: 0.9980 chunk 82 optimal weight: 20.0000 chunk 418 optimal weight: 8.9990 chunk 536 optimal weight: 6.9990 chunk 416 optimal weight: 5.9990 chunk 618 optimal weight: 2.9990 chunk 410 optimal weight: 0.6980 chunk 732 optimal weight: 8.9990 chunk 458 optimal weight: 20.0000 chunk 446 optimal weight: 4.9990 chunk 338 optimal weight: 30.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 195 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** 5 233 GLN ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 ASN ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS D 200 ASN ** D 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 189 ASN ** Q 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 87 HIS Y 41 GLN e 85 HIS m 252 GLN v 6 GLN x 50 ASN x 264 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 83472 Z= 0.387 Angle : 0.672 10.407 120860 Z= 0.338 Chirality : 0.041 0.345 15092 Planarity : 0.005 0.132 9549 Dihedral : 15.970 179.949 26012 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.68 % Favored : 94.15 % Rotamer: Outliers : 1.81 % Allowed : 26.19 % Favored : 72.00 % 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: 0.14 (0.11), residues: 6040 helix: 1.24 (0.11), residues: 2365 sheet: -0.20 (0.19), residues: 834 loop : -0.77 (0.12), residues: 2841 *********************** 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 420 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 352 time to evaluate : 4.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 38 residues processed: 399 average time/residue: 0.7490 time to fit residues: 521.4432 Evaluate side-chains 370 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 332 time to evaluate : 4.759 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.5895 time to fit residues: 48.2545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 453 optimal weight: 20.0000 chunk 292 optimal weight: 1.9990 chunk 437 optimal weight: 7.9990 chunk 220 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 141 optimal weight: 50.0000 chunk 465 optimal weight: 8.9990 chunk 499 optimal weight: 0.6980 chunk 362 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 575 optimal weight: 30.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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** ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS D 200 ASN 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** Q 127 GLN x 50 ASN x 264 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 83472 Z= 0.296 Angle : 0.603 9.907 120860 Z= 0.306 Chirality : 0.039 0.303 15092 Planarity : 0.005 0.073 9549 Dihedral : 15.839 179.660 26012 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.00 % Favored : 94.85 % Rotamer: Outliers : 1.17 % Allowed : 26.88 % Favored : 71.95 % 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: 1.28 (0.11), residues: 2370 sheet: -0.20 (0.19), residues: 824 loop : -0.71 (0.12), residues: 2846 *********************** 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 387 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 343 time to evaluate : 4.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 20 residues processed: 377 average time/residue: 0.7643 time to fit residues: 503.4797 Evaluate side-chains 350 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 330 time to evaluate : 4.726 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.6561 time to fit residues: 29.7619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 640 optimal weight: 0.9980 chunk 682 optimal weight: 50.0000 chunk 410 optimal weight: 0.7980 chunk 297 optimal weight: 0.6980 chunk 536 optimal weight: 6.9990 chunk 209 optimal weight: 6.9990 chunk 616 optimal weight: 0.5980 chunk 645 optimal weight: 2.9990 chunk 680 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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** 5 127 HIS ** A 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 ASN ** 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** ** Q 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 152 GLN x 50 ASN x 264 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 83472 Z= 0.157 Angle : 0.522 10.696 120860 Z= 0.266 Chirality : 0.035 0.245 15092 Planarity : 0.004 0.051 9549 Dihedral : 15.555 179.461 26012 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.19 % Favored : 95.66 % Rotamer: Outliers : 0.56 % Allowed : 27.28 % Favored : 72.16 % 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: 0.44 (0.11), residues: 6040 helix: 1.50 (0.11), residues: 2377 sheet: -0.20 (0.19), residues: 852 loop : -0.56 (0.12), residues: 2811 *********************** 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 396 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 375 time to evaluate : 4.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 386 average time/residue: 0.7700 time to fit residues: 515.5785 Evaluate side-chains 353 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 343 time to evaluate : 4.703 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.6393 time to fit residues: 17.7338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 440 optimal weight: 8.9990 chunk 342 optimal weight: 8.9990 chunk 501 optimal weight: 0.0970 chunk 757 optimal weight: 9.9990 chunk 696 optimal weight: 1.9990 chunk 602 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 465 optimal weight: 9.9990 chunk 369 optimal weight: 10.0000 overall best weight: 3.4186 ------------------------------------------------------------------------------- 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** ** 5 187 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** ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS D 200 ASN ** 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** m 230 HIS v 152 GLN ** v 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 50 ASN x 264 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 83472 Z= 0.414 Angle : 0.683 12.513 120860 Z= 0.342 Chirality : 0.042 0.346 15092 Planarity : 0.005 0.078 9549 Dihedral : 15.805 179.429 26012 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.59 % Favored : 94.25 % Rotamer: Outliers : 0.45 % Allowed : 27.79 % Favored : 71.76 % 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: 0.19 (0.11), residues: 6040 helix: 1.29 (0.11), residues: 2372 sheet: -0.20 (0.19), residues: 831 loop : -0.74 (0.12), residues: 2837 ********************** 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 352 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 335 time to evaluate : 4.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 348 average time/residue: 0.7976 time to fit residues: 482.1578 Evaluate side-chains 338 residues out of total 5330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 329 time to evaluate : 4.670 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.7098 time to fit residues: 16.9446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 760 random chunks: chunk 478 optimal weight: 0.0060 chunk 642 optimal weight: 0.8980 chunk 184 optimal weight: 0.6980 chunk 555 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 167 optimal weight: 0.5980 chunk 603 optimal weight: 50.0000 chunk 252 optimal weight: 5.9990 chunk 620 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 111 optimal weight: 30.0000 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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** ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 331 ASN ** 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** m 230 HIS v 152 GLN ** v 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 50 ASN x 264 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.154555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.138538 restraints weight = 233900.563| |-----------------------------------------------------------------------------| r_work (start): 0.4329 rms_B_bonded: 1.42 r_work: 0.4023 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4010 r_free = 0.4010 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4010 r_free = 0.4010 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.4010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.2752 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= 0.148 Angle : 0.527 12.831 120860 Z= 0.269 Chirality : 0.035 0.244 15092 Planarity : 0.004 0.053 9549 Dihedral : 15.496 179.852 26012 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.11 % Favored : 95.74 % Rotamer: Outliers : 0.27 % Allowed : 27.92 % Favored : 71.81 % 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: 0.45 (0.11), residues: 6040 helix: 1.52 (0.11), residues: 2366 sheet: -0.12 (0.19), residues: 832 loop : -0.57 (0.12), residues: 2842 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12439.73 seconds wall clock time: 223 minutes 48.39 seconds (13428.39 seconds total)