Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 06:44:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5njt_3656/04_2023/5njt_3656.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5njt_3656/04_2023/5njt_3656.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5njt_3656/04_2023/5njt_3656.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5njt_3656/04_2023/5njt_3656.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5njt_3656/04_2023/5njt_3656.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5njt_3656/04_2023/5njt_3656.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.128 sd= 2.386 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: 5 Type Number sf(0) Gaussians P 4579 5.49 5 S 90 5.16 5 C 64432 2.51 5 N 25265 2.21 5 O 38731 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "W ARG 63": "NH1" <-> "NH2" Residue "W ARG 221": "NH1" <-> "NH2" Residue "Z ARG 92": "NH1" <-> "NH2" Residue "a ARG 172": "NH1" <-> "NH2" Residue "b GLU 107": "OE1" <-> "OE2" Residue "h ARG 11": "NH1" <-> "NH2" Residue "i ARG 42": "NH1" <-> "NH2" Residue "k ARG 89": "NH1" <-> "NH2" Residue "l ARG 86": "NH1" <-> "NH2" Residue "o ARG 28": "NH1" <-> "NH2" Residue "x ARG 6": "NH1" <-> "NH2" Residue "x ARG 22": "NH1" <-> "NH2" Residue "x ARG 29": "NH1" <-> "NH2" Residue "x ARG 65": "NH1" <-> "NH2" Residue "x ARG 86": "NH1" <-> "NH2" Residue "x ARG 89": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 133097 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 33115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1544, 33115 Classifications: {'RNA': 1544} Modifications used: {'rna2p_pur': 119, 'rna2p_pyr': 84, 'rna3p_pur': 753, 'rna3p_pyr': 588} Link IDs: {'rna2p': 203, 'rna3p': 1340} Chain: "B" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 896 Classifications: {'peptide': 224} Incomplete info: {'backbone_only': 210} Link IDs: {'PTRANS': 7, 'TRANS': 216} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 935 Unresolved non-hydrogen angles: 1330 Unresolved non-hydrogen dihedrals: 596 Unresolved non-hydrogen chiralities: 274 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 15, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 8, 'GLU:plan': 20, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 417 Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 840 Classifications: {'peptide': 210} Incomplete info: {'backbone_only': 192} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 204} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 835 Unresolved non-hydrogen angles: 1201 Unresolved non-hydrogen dihedrals: 530 Unresolved non-hydrogen chiralities: 252 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 4, 'TYR:plan': 8, 'ASN:plan1': 7, 'TRP:plan': 3, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 13, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 387 Chain: "D" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 797 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 180} Link IDs: {'CIS': 3, 'PTRANS': 10, 'TRANS': 185} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 839 Unresolved non-hydrogen angles: 1194 Unresolved non-hydrogen dihedrals: 549 Unresolved non-hydrogen chiralities: 234 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 6, 'TYR:plan': 8, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 5, 'ARG%COO:plan': 1, 'PHE:plan': 7, 'GLU:plan': 17, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 404 Chain: "E" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 661 Classifications: {'peptide': 165} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 145} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 156} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 582 Unresolved non-hydrogen angles: 840 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 199 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 5, 'ASN:plan1': 6, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 213 Chain: "F" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 381 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 90} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 92} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 415 Unresolved non-hydrogen angles: 594 Unresolved non-hydrogen dihedrals: 266 Unresolved non-hydrogen chiralities: 116 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'GLU%COO:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 224 Chain: "G" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 613 Classifications: {'peptide': 153} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 143} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 145} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 636 Unresolved non-hydrogen angles: 906 Unresolved non-hydrogen dihedrals: 411 Unresolved non-hydrogen chiralities: 183 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 14, 'TRP%COO:plan': 1} Unresolved non-hydrogen planarities: 291 Chain: "H" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 525 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 120} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 124} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 525 Unresolved non-hydrogen angles: 751 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 162 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 12, 'TRP%COO:plan': 1} Unresolved non-hydrogen planarities: 225 Chain: "I" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 521 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 115} Link IDs: {'CIS': 4, 'PTRANS': 5, 'TRANS': 120} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 500 Unresolved non-hydrogen angles: 716 Unresolved non-hydrogen dihedrals: 312 Unresolved non-hydrogen chiralities: 152 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 3, 'ARG%COO:plan': 1, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 225 Chain: "J" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 409 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 98} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 95} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 423 Unresolved non-hydrogen angles: 604 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 131 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 7, 'TYR:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 166 Chain: "K" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 472 Classifications: {'peptide': 118} Incomplete info: {'backbone_only': 106} Link IDs: {'CIS': 3, 'PTRANS': 6, 'TRANS': 108} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 418 Unresolved non-hydrogen angles: 607 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 138 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 170 Chain: "L" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 549 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 122} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 124} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 531 Unresolved non-hydrogen angles: 757 Unresolved non-hydrogen dihedrals: 338 Unresolved non-hydrogen chiralities: 160 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 9, 'HIS:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 216 Chain: "M" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 444 Classifications: {'peptide': 111} Incomplete info: {'backbone_only': 100} Link IDs: {'CIS': 5, 'PTRANS': 3, 'TRANS': 102} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 447 Unresolved non-hydrogen angles: 635 Unresolved non-hydrogen dihedrals: 272 Unresolved non-hydrogen chiralities: 136 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 202 Chain: "N" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 241 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 56} Link IDs: {'CIS': 3, 'PTRANS': 3, 'TRANS': 53} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 268 Unresolved non-hydrogen angles: 372 Unresolved non-hydrogen dihedrals: 188 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 7, 'TRP%COO:plan': 1} Unresolved non-hydrogen planarities: 116 Chain: "O" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 353 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 83} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 85} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 391 Unresolved non-hydrogen angles: 554 Unresolved non-hydrogen dihedrals: 247 Unresolved non-hydrogen chiralities: 112 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 8, 'HIS:plan': 5, 'ARG%COO:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 192 Chain: "P" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 357 Classifications: {'peptide': 89} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 82} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 4, 'TRANS': 82} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 514 Unresolved non-hydrogen dihedrals: 238 Unresolved non-hydrogen chiralities: 104 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 155 Chain: "Q" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 345 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 82} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 372 Unresolved non-hydrogen angles: 527 Unresolved non-hydrogen dihedrals: 238 Unresolved non-hydrogen chiralities: 110 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 161 Chain: "R" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 285 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 66} Link IDs: {'CIS': 4, 'PTRANS': 2, 'TRANS': 64} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 303 Unresolved non-hydrogen angles: 428 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 87 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'GLU%COO:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 133 Chain: "S" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 320 Classifications: {'peptide': 80} Incomplete info: {'backbone_only': 73} Link IDs: {'CIS': 3, 'PTRANS': 4, 'TRANS': 72} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 345 Unresolved non-hydrogen angles: 491 Unresolved non-hydrogen dihedrals: 236 Unresolved non-hydrogen chiralities: 96 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 5, 'GLU:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 155 Chain: "T" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 345 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 83} Link IDs: {'CIS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 315 Unresolved non-hydrogen angles: 451 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 107 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 7, 'TYR:plan': 1, 'ASN:plan1': 8, 'HIS:plan': 2, 'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 115 Chain: "U" Number of atoms: 62767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2923, 62767 Classifications: {'RNA': 2923} Modifications used: {'rna2p_pur': 278, 'rna2p_pyr': 152, 'rna3p_pur': 1417, 'rna3p_pyr': 1076} Link IDs: {'rna2p': 430, 'rna3p': 2492} Chain: "V" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2395 Classifications: {'RNA': 112} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 53, 'rna3p_pyr': 44} Link IDs: {'rna2p': 15, 'rna3p': 96} Chain: "W" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2111 Classifications: {'peptide': 275} Link IDs: {'CIS': 2, 'PTRANS': 17, 'TRANS': 255} Chain: "X" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1575 Classifications: {'peptide': 207} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 193} Chain: "Y" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1561 Classifications: {'peptide': 205} Link IDs: {'CIS': 3, 'PTRANS': 7, 'TRANS': 194} Chain: "Z" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1404 Classifications: {'peptide': 178} Link IDs: {'CIS': 3, 'PTRANS': 7, 'TRANS': 167} Chain: "a" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1342 Classifications: {'peptide': 175} Link IDs: {'CIS': 4, 'PTRANS': 9, 'TRANS': 161} Chain: "b" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "c" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1123 Classifications: {'peptide': 142} Link IDs: {'CIS': 2, 'PTRANS': 8, 'TRANS': 131} Chain: "d" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 920 Classifications: {'peptide': 122} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 116} Chain: "e" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1081 Classifications: {'peptide': 146} Link IDs: {'CIS': 5, 'PTRANS': 5, 'TRANS': 135} Chain: "f" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1097 Classifications: {'peptide': 138} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 129} Chain: "g" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 953 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "h" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 912 Classifications: {'peptide': 120} Link IDs: {'CIS': 4, 'PTRANS': 1, 'TRANS': 114} Chain: "i" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 936 Classifications: {'peptide': 114} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 107} Chain: "j" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 940 Classifications: {'peptide': 117} Link IDs: {'CIS': 1, 'TRANS': 115} Chain: "k" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 786 Classifications: {'peptide': 101} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 96} Chain: "l" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 103} Chain: "m" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 752 Classifications: {'peptide': 93} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 89} Chain: "n" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 754 Classifications: {'peptide': 100} Link IDs: {'CIS': 5, 'PTRANS': 6, 'TRANS': 88} Chain: "o" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 630 Classifications: {'peptide': 82} Link IDs: {'CIS': 2, 'PTRANS': 2, 'TRANS': 77} Chain: "p" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 426 Classifications: {'peptide': 54} Link IDs: {'CIS': 3, 'PTRANS': 3, 'TRANS': 47} Chain: "q" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 401 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "r" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 367 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "s" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 512 Classifications: {'peptide': 64} Link IDs: {'CIS': 2, 'TRANS': 61} Chain: "t" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 288 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "u" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'CIS': 4, 'PTRANS': 1, 'TRANS': 52} Chain: "v" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 530 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "w" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "y" Number of atoms: 503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 503 Classifications: {'peptide': 64} Link IDs: {'CIS': 3, 'PTRANS': 2, 'TRANS': 58} Chain: "x" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 866 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 2, 'TRANS': 101} Time building chain proxies: 51.15, per 1000 atoms: 0.38 Number of scatterers: 133097 At special positions: 0 Unit cell: (268.832, 274.252, 241.732, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 90 16.00 P 4579 15.00 O 38731 8.00 N 25265 7.00 C 64432 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: 60.02 Conformation dependent library (CDL) restraints added in 5.2 seconds 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5948 Finding SS restraints... Secondary structure from input PDB file: 161 helices and 78 sheets defined 29.1% alpha, 11.2% beta 1557 base pairs and 2396 stacking pairs defined. Time for finding SS restraints: 45.35 Creating SS restraints... Processing helix chain 'B' and resid 10 through 15 removed outlier: 3.597A pdb=" N VAL B 14 " --> pdb=" O GLU B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.733A pdb=" N LYS B 28 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG B 29 " --> pdb=" O LYS B 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 25 through 29' Processing helix chain 'B' and resid 42 through 62 Processing helix chain 'B' and resid 76 through 86 removed outlier: 3.828A pdb=" N VAL B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 104 removed outlier: 3.952A pdb=" N PHE B 104 " --> pdb=" O THR B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 120 Processing helix chain 'B' and resid 130 through 143 removed outlier: 3.697A pdb=" N VAL B 134 " --> pdb=" O PRO B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 149 removed outlier: 3.557A pdb=" N GLY B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 154 removed outlier: 3.665A pdb=" N ASP B 153 " --> pdb=" O GLY B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 179 removed outlier: 3.652A pdb=" N LEU B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 196 removed outlier: 3.959A pdb=" N GLU B 195 " --> pdb=" O ASP B 192 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 196 " --> pdb=" O PRO B 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 192 through 196' Processing helix chain 'B' and resid 206 through 226 removed outlier: 3.547A pdb=" N GLN B 226 " --> pdb=" O LEU B 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 11 Processing helix chain 'C' and resid 27 through 46 removed outlier: 4.041A pdb=" N PHE C 31 " --> pdb=" O ASP C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 77 removed outlier: 3.524A pdb=" N GLY C 77 " --> pdb=" O GLY C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 95 Processing helix chain 'C' and resid 111 through 122 Processing helix chain 'C' and resid 128 through 140 Processing helix chain 'D' and resid 9 through 16 removed outlier: 3.812A pdb=" N GLY D 16 " --> pdb=" O SER D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 60 Processing helix chain 'D' and resid 64 through 77 Processing helix chain 'D' and resid 81 through 90 Processing helix chain 'D' and resid 93 through 100 Processing helix chain 'D' and resid 106 through 115 Processing helix chain 'D' and resid 148 through 157 Processing helix chain 'D' and resid 191 through 197 Processing helix chain 'E' and resid 55 through 68 Processing helix chain 'E' and resid 108 through 115 Processing helix chain 'E' and resid 116 through 118 No H-bonds generated for 'chain 'E' and resid 116 through 118' Processing helix chain 'E' and resid 132 through 145 Processing helix chain 'E' and resid 149 through 157 removed outlier: 3.566A pdb=" N ARG E 157 " --> pdb=" O VAL E 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 32 Processing helix chain 'F' and resid 71 through 78 Processing helix chain 'G' and resid 21 through 29 Processing helix chain 'G' and resid 35 through 52 removed outlier: 3.839A pdb=" N SER G 39 " --> pdb=" O LYS G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 66 Processing helix chain 'G' and resid 92 through 109 Processing helix chain 'G' and resid 115 through 128 Processing helix chain 'G' and resid 133 through 145 Processing helix chain 'H' and resid 5 through 21 removed outlier: 3.507A pdb=" N ARG H 21 " --> pdb=" O ALA H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 43 Processing helix chain 'H' and resid 114 through 122 Processing helix chain 'I' and resid 34 through 39 removed outlier: 3.891A pdb=" N ILE I 39 " --> pdb=" O ILE I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 89 Processing helix chain 'I' and resid 94 through 99 Processing helix chain 'J' and resid 15 through 31 removed outlier: 3.640A pdb=" N ALA J 29 " --> pdb=" O ILE J 25 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ARG J 31 " --> pdb=" O GLU J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 86 Processing helix chain 'J' and resid 87 through 89 No H-bonds generated for 'chain 'J' and resid 87 through 89' Processing helix chain 'K' and resid 56 through 60 removed outlier: 3.518A pdb=" N SER K 60 " --> pdb=" O SER K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 79 Processing helix chain 'K' and resid 94 through 103 Processing helix chain 'K' and resid 104 through 106 No H-bonds generated for 'chain 'K' and resid 104 through 106' Processing helix chain 'M' and resid 14 through 20 Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 54 through 59 Processing helix chain 'M' and resid 65 through 75 Processing helix chain 'N' and resid 3 through 10 Processing helix chain 'N' and resid 40 through 51 Processing helix chain 'O' and resid 4 through 15 Processing helix chain 'O' and resid 25 through 45 Processing helix chain 'O' and resid 49 through 74 Processing helix chain 'O' and resid 74 through 86 Processing helix chain 'P' and resid 55 through 62 Processing helix chain 'P' and resid 67 through 77 Processing helix chain 'P' and resid 79 through 88 Processing helix chain 'R' and resid 32 through 38 Processing helix chain 'R' and resid 53 through 70 removed outlier: 4.137A pdb=" N MET R 70 " --> pdb=" O ARG R 66 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 23 Processing helix chain 'T' and resid 7 through 39 Processing helix chain 'T' and resid 44 through 63 Processing helix chain 'T' and resid 69 through 88 Processing helix chain 'W' and resid 30 through 32 No H-bonds generated for 'chain 'W' and resid 30 through 32' Processing helix chain 'W' and resid 177 through 179 No H-bonds generated for 'chain 'W' and resid 177 through 179' Processing helix chain 'W' and resid 197 through 201 removed outlier: 3.691A pdb=" N HIS W 200 " --> pdb=" O ASN W 197 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLU W 201 " --> pdb=" O GLU W 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 197 through 201' Processing helix chain 'W' and resid 209 through 215 removed outlier: 4.486A pdb=" N GLY W 215 " --> pdb=" O SER W 211 " (cutoff:3.500A) Processing helix chain 'W' and resid 264 through 268 removed outlier: 3.589A pdb=" N ASP W 267 " --> pdb=" O ASN W 264 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS W 268 " --> pdb=" O LYS W 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 264 through 268' Processing helix chain 'X' and resid 57 through 61 removed outlier: 3.505A pdb=" N SER X 61 " --> pdb=" O GLU X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 67 removed outlier: 3.590A pdb=" N GLY X 67 " --> pdb=" O LYS X 63 " (cutoff:3.500A) Processing helix chain 'X' and resid 68 through 70 No H-bonds generated for 'chain 'X' and resid 68 through 70' Processing helix chain 'X' and resid 98 through 102 removed outlier: 4.219A pdb=" N ILE X 101 " --> pdb=" O LYS X 98 " (cutoff:3.500A) Processing helix chain 'X' and resid 121 through 127 removed outlier: 3.530A pdb=" N HIS X 126 " --> pdb=" O ALA X 122 " (cutoff:3.500A) Processing helix chain 'Y' and resid 20 through 25 Processing helix chain 'Y' and resid 29 through 42 removed outlier: 3.874A pdb=" N PHE Y 34 " --> pdb=" O GLU Y 30 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP Y 35 " --> pdb=" O SER Y 31 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA Y 36 " --> pdb=" O VAL Y 32 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU Y 38 " --> pdb=" O PHE Y 34 " (cutoff:3.500A) Processing helix chain 'Y' and resid 102 through 120 removed outlier: 4.267A pdb=" N LEU Y 108 " --> pdb=" O LYS Y 104 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE Y 110 " --> pdb=" O ARG Y 106 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER Y 115 " --> pdb=" O LYS Y 111 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE Y 119 " --> pdb=" O SER Y 115 " (cutoff:3.500A) Processing helix chain 'Y' and resid 135 through 146 removed outlier: 4.231A pdb=" N MET Y 139 " --> pdb=" O LYS Y 135 " (cutoff:3.500A) Processing helix chain 'Y' and resid 160 through 166 removed outlier: 3.735A pdb=" N SER Y 166 " --> pdb=" O ALA Y 162 " (cutoff:3.500A) Processing helix chain 'Y' and resid 182 through 187 Processing helix chain 'Y' and resid 195 through 206 removed outlier: 3.634A pdb=" N VAL Y 199 " --> pdb=" O THR Y 195 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU Y 200 " --> pdb=" O LYS Y 196 " (cutoff:3.500A) Processing helix chain 'Z' and resid 4 through 9 removed outlier: 3.501A pdb=" N TYR Z 8 " --> pdb=" O LEU Z 4 " (cutoff:3.500A) Processing helix chain 'Z' and resid 11 through 20 removed outlier: 3.648A pdb=" N MET Z 17 " --> pdb=" O ALA Z 13 " (cutoff:3.500A) Processing helix chain 'Z' and resid 51 through 58 removed outlier: 4.022A pdb=" N GLU Z 55 " --> pdb=" O ASP Z 51 " (cutoff:3.500A) Processing helix chain 'Z' and resid 92 through 100 removed outlier: 3.885A pdb=" N TYR Z 97 " --> pdb=" O GLY Z 93 " (cutoff:3.500A) Processing helix chain 'Z' and resid 100 through 105 removed outlier: 4.223A pdb=" N SER Z 105 " --> pdb=" O ASP Z 101 " (cutoff:3.500A) Processing helix chain 'Z' and resid 107 through 111 Processing helix chain 'Z' and resid 162 through 174 Processing helix chain 'a' and resid 59 through 77 removed outlier: 3.709A pdb=" N GLY a 67 " --> pdb=" O ARG a 63 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR a 68 " --> pdb=" O ALA a 64 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR a 69 " --> pdb=" O LEU a 65 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG a 70 " --> pdb=" O HIS a 66 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU a 73 " --> pdb=" O THR a 69 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN a 75 " --> pdb=" O SER a 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 78 through 80 No H-bonds generated for 'chain 'a' and resid 78 through 80' Processing helix chain 'a' and resid 138 through 151 removed outlier: 4.459A pdb=" N ALA a 144 " --> pdb=" O GLU a 140 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA a 151 " --> pdb=" O ALA a 147 " (cutoff:3.500A) Processing helix chain 'b' and resid 5 through 14 removed outlier: 3.936A pdb=" N LYS b 9 " --> pdb=" O ILE b 5 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL b 10 " --> pdb=" O GLU b 6 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL b 11 " --> pdb=" O THR b 7 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU b 14 " --> pdb=" O VAL b 10 " (cutoff:3.500A) Processing helix chain 'b' and resid 15 through 20 removed outlier: 3.839A pdb=" N LYS b 20 " --> pdb=" O ALA b 16 " (cutoff:3.500A) Processing helix chain 'b' and resid 33 through 46 removed outlier: 5.436A pdb=" N LYS b 43 " --> pdb=" O THR b 39 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLN b 44 " --> pdb=" O GLU b 40 " (cutoff:3.500A) Processing helix chain 'b' and resid 74 through 78 removed outlier: 3.534A pdb=" N THR b 77 " --> pdb=" O ASP b 74 " (cutoff:3.500A) Processing helix chain 'b' and resid 94 through 98 Processing helix chain 'c' and resid 29 through 39 removed outlier: 4.179A pdb=" N ALA c 35 " --> pdb=" O SER c 31 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE c 36 " --> pdb=" O GLU c 32 " (cutoff:3.500A) Processing helix chain 'c' and resid 90 through 96 Processing helix chain 'c' and resid 98 through 110 removed outlier: 3.680A pdb=" N GLU c 103 " --> pdb=" O GLU c 99 " (cutoff:3.500A) Processing helix chain 'c' and resid 117 through 123 removed outlier: 3.633A pdb=" N LYS c 122 " --> pdb=" O GLN c 118 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU c 123 " --> pdb=" O MET c 119 " (cutoff:3.500A) Processing helix chain 'c' and resid 133 through 137 removed outlier: 3.798A pdb=" N GLN c 136 " --> pdb=" O HIS c 133 " (cutoff:3.500A) Processing helix chain 'd' and resid 105 through 109 Processing helix chain 'd' and resid 111 through 117 removed outlier: 3.603A pdb=" N SER d 116 " --> pdb=" O MET d 112 " (cutoff:3.500A) Processing helix chain 'e' and resid 37 through 41 Processing helix chain 'e' and resid 78 through 85 removed outlier: 3.826A pdb=" N PHE e 85 " --> pdb=" O LEU e 82 " (cutoff:3.500A) Processing helix chain 'e' and resid 92 through 98 removed outlier: 3.805A pdb=" N GLU e 98 " --> pdb=" O GLU e 94 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 140 removed outlier: 3.681A pdb=" N VAL e 136 " --> pdb=" O ALA e 132 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLU e 137 " --> pdb=" O LYS e 133 " (cutoff:3.500A) Processing helix chain 'f' and resid 44 through 56 removed outlier: 3.651A pdb=" N ILE f 52 " --> pdb=" O GLU f 48 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA f 53 " --> pdb=" O ALA f 49 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR f 55 " --> pdb=" O ARG f 51 " (cutoff:3.500A) Processing helix chain 'f' and resid 110 through 115 removed outlier: 3.641A pdb=" N ALA f 114 " --> pdb=" O SER f 110 " (cutoff:3.500A) Processing helix chain 'f' and resid 116 through 121 removed outlier: 4.029A pdb=" N ALA f 121 " --> pdb=" O ALA f 117 " (cutoff:3.500A) Processing helix chain 'g' and resid 11 through 28 removed outlier: 3.630A pdb=" N ASP g 19 " --> pdb=" O ALA g 15 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR g 22 " --> pdb=" O ARG g 18 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE g 25 " --> pdb=" O THR g 21 " (cutoff:3.500A) Processing helix chain 'g' and resid 34 through 38 Processing helix chain 'g' and resid 40 through 54 removed outlier: 4.155A pdb=" N LYS g 46 " --> pdb=" O SER g 42 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR g 49 " --> pdb=" O GLU g 45 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG g 53 " --> pdb=" O THR g 49 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY g 54 " --> pdb=" O LEU g 50 " (cutoff:3.500A) Processing helix chain 'g' and resid 55 through 63 removed outlier: 3.772A pdb=" N ARG g 60 " --> pdb=" O LEU g 56 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 86 removed outlier: 3.540A pdb=" N LEU g 83 " --> pdb=" O ALA g 79 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE g 84 " --> pdb=" O LEU g 80 " (cutoff:3.500A) Processing helix chain 'h' and resid 10 through 20 removed outlier: 3.748A pdb=" N ALA h 16 " --> pdb=" O LEU h 12 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG h 17 " --> pdb=" O LYS h 13 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL h 18 " --> pdb=" O ARG h 14 " (cutoff:3.500A) Processing helix chain 'h' and resid 75 through 89 removed outlier: 4.041A pdb=" N ALA h 82 " --> pdb=" O GLY h 78 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU h 87 " --> pdb=" O LYS h 83 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS h 88 " --> pdb=" O ARG h 84 " (cutoff:3.500A) Processing helix chain 'h' and resid 106 through 115 removed outlier: 3.769A pdb=" N ALA h 110 " --> pdb=" O VAL h 106 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG h 114 " --> pdb=" O ALA h 110 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU h 115 " --> pdb=" O ASP h 111 " (cutoff:3.500A) Processing helix chain 'i' and resid 6 through 12 removed outlier: 3.899A pdb=" N ILE i 11 " --> pdb=" O LEU i 7 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR i 12 " --> pdb=" O ILE i 8 " (cutoff:3.500A) Processing helix chain 'i' and resid 56 through 59 Processing helix chain 'i' and resid 100 through 105 removed outlier: 3.567A pdb=" N LEU i 103 " --> pdb=" O LEU i 100 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG i 104 " --> pdb=" O TYR i 101 " (cutoff:3.500A) Processing helix chain 'i' and resid 108 through 114 Processing helix chain 'j' and resid 8 through 18 removed outlier: 3.676A pdb=" N ARG j 13 " --> pdb=" O VAL j 9 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL j 17 " --> pdb=" O ARG j 13 " (cutoff:3.500A) Processing helix chain 'j' and resid 19 through 22 removed outlier: 3.955A pdb=" N LYS j 22 " --> pdb=" O LYS j 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 19 through 22' Processing helix chain 'j' and resid 25 through 29 removed outlier: 3.523A pdb=" N LYS j 28 " --> pdb=" O PHE j 25 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS j 29 " --> pdb=" O GLY j 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 25 through 29' Processing helix chain 'j' and resid 34 through 50 removed outlier: 3.567A pdb=" N MET j 40 " --> pdb=" O ASN j 36 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA j 46 " --> pdb=" O SER j 42 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG j 48 " --> pdb=" O ASN j 44 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP j 49 " --> pdb=" O TYR j 45 " (cutoff:3.500A) Processing helix chain 'j' and resid 52 through 57 removed outlier: 3.522A pdb=" N PHE j 57 " --> pdb=" O LYS j 53 " (cutoff:3.500A) Processing helix chain 'j' and resid 57 through 62 Processing helix chain 'j' and resid 62 through 70 removed outlier: 4.498A pdb=" N ALA j 68 " --> pdb=" O ARG j 64 " (cutoff:3.500A) Processing helix chain 'j' and resid 75 through 86 removed outlier: 4.228A pdb=" N HIS j 81 " --> pdb=" O SER j 77 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS j 84 " --> pdb=" O MET j 80 " (cutoff:3.500A) Processing helix chain 'j' and resid 94 through 99 Processing helix chain 'j' and resid 104 through 116 removed outlier: 3.795A pdb=" N ALA j 115 " --> pdb=" O ASP j 111 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLN j 116 " --> pdb=" O ALA j 112 " (cutoff:3.500A) Processing helix chain 'l' and resid 14 through 22 removed outlier: 4.106A pdb=" N LEU l 19 " --> pdb=" O ARG l 15 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N VAL l 20 " --> pdb=" O LYS l 16 " (cutoff:3.500A) Processing helix chain 'l' and resid 28 through 31 Processing helix chain 'l' and resid 32 through 37 Processing helix chain 'l' and resid 43 through 61 removed outlier: 3.852A pdb=" N ILE l 47 " --> pdb=" O ALA l 43 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL l 50 " --> pdb=" O ILE l 46 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER l 53 " --> pdb=" O LYS l 49 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N HIS l 60 " --> pdb=" O ALA l 56 " (cutoff:3.500A) Processing helix chain 'l' and resid 65 through 67 No H-bonds generated for 'chain 'l' and resid 65 through 67' Processing helix chain 'l' and resid 88 through 92 removed outlier: 3.705A pdb=" N GLY l 91 " --> pdb=" O ARG l 88 " (cutoff:3.500A) Processing helix chain 'm' and resid 15 through 22 removed outlier: 3.906A pdb=" N ASP m 19 " --> pdb=" O GLU m 15 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET m 21 " --> pdb=" O SER m 17 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR m 22 " --> pdb=" O ALA m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 36 through 46 removed outlier: 3.560A pdb=" N ALA m 42 " --> pdb=" O GLU m 38 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU m 44 " --> pdb=" O LYS m 40 " (cutoff:3.500A) Processing helix chain 'p' and resid 11 through 16 removed outlier: 3.569A pdb=" N ARG p 16 " --> pdb=" O LYS p 12 " (cutoff:3.500A) Processing helix chain 'r' and resid 9 through 16 Processing helix chain 'r' and resid 17 through 22 Processing helix chain 'r' and resid 24 through 37 removed outlier: 3.739A pdb=" N VAL r 30 " --> pdb=" O ASN r 26 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU r 31 " --> pdb=" O GLY r 27 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ARG r 35 " --> pdb=" O LEU r 31 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS r 37 " --> pdb=" O ARG r 33 " (cutoff:3.500A) Processing helix chain 's' and resid 7 through 12 removed outlier: 3.570A pdb=" N ALA s 11 " --> pdb=" O HIS s 7 " (cutoff:3.500A) Processing helix chain 's' and resid 37 through 45 removed outlier: 3.773A pdb=" N LYS s 43 " --> pdb=" O LYS s 39 " (cutoff:3.500A) Processing helix chain 'u' and resid 50 through 55 Processing helix chain 'v' and resid 10 through 33 removed outlier: 3.586A pdb=" N GLU v 15 " --> pdb=" O THR v 11 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLN v 16 " --> pdb=" O ALA v 12 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER v 20 " --> pdb=" O GLN v 16 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN v 27 " --> pdb=" O GLU v 23 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU v 28 " --> pdb=" O GLU v 24 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE v 30 " --> pdb=" O PHE v 26 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN v 31 " --> pdb=" O ASN v 27 " (cutoff:3.500A) Processing helix chain 'v' and resid 41 through 64 removed outlier: 3.997A pdb=" N LYS v 48 " --> pdb=" O ARG v 44 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET v 53 " --> pdb=" O ALA v 49 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR v 55 " --> pdb=" O ALA v 51 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL v 56 " --> pdb=" O ARG v 52 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE v 57 " --> pdb=" O MET v 53 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG v 58 " --> pdb=" O LYS v 54 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE v 62 " --> pdb=" O ARG v 58 " (cutoff:3.500A) Processing helix chain 'w' and resid 17 through 25 removed outlier: 3.941A pdb=" N VAL w 21 " --> pdb=" O GLU w 17 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR w 22 " --> pdb=" O ASP w 18 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL w 23 " --> pdb=" O GLN w 19 " (cutoff:3.500A) Processing helix chain 'w' and resid 40 through 45 Processing helix chain 'x' and resid 13 through 24 removed outlier: 4.222A pdb=" N HIS x 19 " --> pdb=" O ALA x 15 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS x 23 " --> pdb=" O HIS x 19 " (cutoff:3.500A) Processing helix chain 'x' and resid 26 through 31 Processing helix chain 'x' and resid 77 through 93 removed outlier: 4.673A pdb=" N LYS x 83 " --> pdb=" O LEU x 79 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG x 86 " --> pdb=" O ASN x 82 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN x 87 " --> pdb=" O LYS x 83 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS x 92 " --> pdb=" O ILE x 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 34 Processing sheet with id=AA2, first strand: chain 'B' and resid 67 through 70 Processing sheet with id=AA3, first strand: chain 'B' and resid 184 through 185 Processing sheet with id=AA4, first strand: chain 'C' and resid 54 through 58 removed outlier: 3.560A pdb=" N GLU C 55 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 166 through 170 removed outlier: 3.506A pdb=" N TYR C 167 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR C 150 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU C 169 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL C 148 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL C 199 " --> pdb=" O ALA C 184 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA C 184 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP C 182 " --> pdb=" O ILE C 201 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 165 through 166 Processing sheet with id=AA7, first strand: chain 'E' and resid 18 through 19 Processing sheet with id=AA8, first strand: chain 'E' and resid 22 through 23 Processing sheet with id=AA9, first strand: chain 'E' and resid 39 through 40 Processing sheet with id=AB1, first strand: chain 'F' and resid 2 through 4 removed outlier: 3.756A pdb=" N SER F 67 " --> pdb=" O ARG F 2 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 7 through 8 removed outlier: 4.382A pdb=" N MET F 7 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE F 89 " --> pdb=" O MET F 7 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'F' and resid 44 through 46 removed outlier: 3.798A pdb=" N GLY F 44 " --> pdb=" O TYR F 60 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY F 58 " --> pdb=" O ARG F 46 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 75 through 76 Processing sheet with id=AB5, first strand: chain 'H' and resid 24 through 26 Processing sheet with id=AB6, first strand: chain 'H' and resid 111 through 112 removed outlier: 3.632A pdb=" N GLY H 111 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE H 103 " --> pdb=" O TYR H 130 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N TYR H 130 " --> pdb=" O ILE H 103 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ILE H 105 " --> pdb=" O LEU H 128 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 6 through 10 removed outlier: 3.740A pdb=" N GLY I 8 " --> pdb=" O VAL I 19 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL I 19 " --> pdb=" O GLY I 8 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY I 10 " --> pdb=" O ALA I 17 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL I 16 " --> pdb=" O HIS I 68 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS I 68 " --> pdb=" O VAL I 16 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 8 through 11 removed outlier: 3.518A pdb=" N ARG J 9 " --> pdb=" O GLU J 99 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU J 99 " --> pdb=" O ARG J 9 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 45 through 48 removed outlier: 3.606A pdb=" N SER K 45 " --> pdb=" O ILE K 36 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER K 47 " --> pdb=" O VAL K 34 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL K 34 " --> pdb=" O SER K 47 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE K 33 " --> pdb=" O ARG K 26 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR K 87 " --> pdb=" O ALA K 23 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG K 113 " --> pdb=" O VAL K 86 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL K 88 " --> pdb=" O ARG K 113 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 68 through 69 Processing sheet with id=AC2, first strand: chain 'L' and resid 65 through 66 removed outlier: 3.539A pdb=" N ALA L 66 " --> pdb=" O ALA L 78 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'P' and resid 4 through 5 Processing sheet with id=AC4, first strand: chain 'P' and resid 22 through 23 removed outlier: 6.869A pdb=" N VAL P 22 " --> pdb=" O ILE P 34 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 39 through 40 removed outlier: 3.689A pdb=" N THR P 39 " --> pdb=" O LYS P 50 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Q' and resid 27 through 32 removed outlier: 3.730A pdb=" N VAL Q 27 " --> pdb=" O LYS Q 44 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Q' and resid 47 through 49 removed outlier: 6.953A pdb=" N LYS Q 47 " --> pdb=" O LYS Q 73 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE Q 75 " --> pdb=" O LYS Q 47 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ARG Q 74 " --> pdb=" O THR Q 66 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'S' and resid 31 through 32 removed outlier: 6.881A pdb=" N VAL S 31 " --> pdb=" O ALA S 50 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'W' and resid 34 through 35 Processing sheet with id=AD1, first strand: chain 'W' and resid 65 through 66 removed outlier: 4.709A pdb=" N LEU W 105 " --> pdb=" O ASP W 66 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR W 80 " --> pdb=" O LEU W 93 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'W' and resid 129 through 131 removed outlier: 3.591A pdb=" N SER W 191 " --> pdb=" O HIS W 142 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'W' and resid 172 through 175 removed outlier: 3.502A pdb=" N VAL W 174 " --> pdb=" O ARG W 182 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'X' and resid 5 through 14 removed outlier: 3.994A pdb=" N GLY X 11 " --> pdb=" O VAL X 27 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE X 28 " --> pdb=" O LEU X 186 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU X 185 " --> pdb=" O VAL X 179 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL X 179 " --> pdb=" O LEU X 185 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU X 187 " --> pdb=" O VAL X 177 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLU X 175 " --> pdb=" O LYS X 189 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N VAL X 108 " --> pdb=" O ASN X 173 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL X 113 " --> pdb=" O LEU X 199 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU X 199 " --> pdb=" O VAL X 113 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'X' and resid 77 through 81 removed outlier: 6.453A pdb=" N LYS X 77 " --> pdb=" O ASP X 55 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ASP X 55 " --> pdb=" O LYS X 77 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLN X 37 " --> pdb=" O GLN X 50 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY X 52 " --> pdb=" O VAL X 35 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL X 35 " --> pdb=" O GLY X 52 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N ASP X 54 " --> pdb=" O ASN X 33 " (cutoff:3.500A) removed outlier: 10.217A pdb=" N ASN X 33 " --> pdb=" O ASP X 54 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'X' and resid 118 through 120 removed outlier: 3.583A pdb=" N GLY X 118 " --> pdb=" O MET X 164 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Y' and resid 123 through 125 removed outlier: 3.660A pdb=" N ILE Y 124 " --> pdb=" O LEU Y 192 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE Y 194 " --> pdb=" O ILE Y 124 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE Y 154 " --> pdb=" O VAL Y 176 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Z' and resid 66 through 67 Processing sheet with id=AD9, first strand: chain 'a' and resid 9 through 10 Processing sheet with id=AE1, first strand: chain 'a' and resid 24 through 27 removed outlier: 3.514A pdb=" N VAL a 25 " --> pdb=" O ARG a 36 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG a 36 " --> pdb=" O VAL a 25 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'a' and resid 84 through 89 removed outlier: 3.746A pdb=" N VAL a 134 " --> pdb=" O ARG a 86 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'a' and resid 97 through 100 Processing sheet with id=AE4, first strand: chain 'c' and resid 124 through 125 removed outlier: 6.233A pdb=" N LEU c 17 " --> pdb=" O ILE c 56 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE c 58 " --> pdb=" O LEU c 17 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL c 19 " --> pdb=" O ILE c 58 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'c' and resid 74 through 76 Processing sheet with id=AE6, first strand: chain 'd' and resid 7 through 9 removed outlier: 6.261A pdb=" N GLN d 45 " --> pdb=" O ARG d 17 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL d 19 " --> pdb=" O VAL d 43 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL d 43 " --> pdb=" O VAL d 19 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR d 21 " --> pdb=" O CYS d 41 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N CYS d 41 " --> pdb=" O THR d 21 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LYS d 23 " --> pdb=" O ILE d 39 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ILE d 39 " --> pdb=" O LYS d 23 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'd' and resid 68 through 70 removed outlier: 3.693A pdb=" N TYR d 76 " --> pdb=" O THR i 76 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'd' and resid 101 through 103 Processing sheet with id=AE9, first strand: chain 'e' and resid 123 through 125 Processing sheet with id=AF1, first strand: chain 'f' and resid 33 through 36 Processing sheet with id=AF2, first strand: chain 'f' and resid 40 through 43 removed outlier: 3.579A pdb=" N ILE f 42 " --> pdb=" O ALA f 95 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL f 96 " --> pdb=" O PRO f 70 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'f' and resid 64 through 66 removed outlier: 3.530A pdb=" N GLU f 105 " --> pdb=" O TRP f 65 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'f' and resid 75 through 76 Processing sheet with id=AF5, first strand: chain 'g' and resid 29 through 33 removed outlier: 4.651A pdb=" N MET g 114 " --> pdb=" O LEU g 104 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'g' and resid 70 through 72 removed outlier: 6.659A pdb=" N GLN g 77 " --> pdb=" O ALA g 71 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'h' and resid 54 through 57 removed outlier: 4.036A pdb=" N ALA h 54 " --> pdb=" O ILE h 44 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA h 56 " --> pdb=" O ALA h 42 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA h 42 " --> pdb=" O ALA h 56 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE h 34 " --> pdb=" O TYR h 41 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN h 43 " --> pdb=" O ASN h 32 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'i' and resid 41 through 46 removed outlier: 6.714A pdb=" N THR i 28 " --> pdb=" O VAL i 90 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS i 86 " --> pdb=" O HIS i 32 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LYS i 34 " --> pdb=" O ILE i 84 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE i 84 " --> pdb=" O LYS i 34 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'k' and resid 11 through 14 Processing sheet with id=AG1, first strand: chain 'k' and resid 20 through 22 removed outlier: 6.552A pdb=" N LYS k 94 " --> pdb=" O GLU k 63 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N THR k 59 " --> pdb=" O GLU k 98 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'k' and resid 71 through 75 Processing sheet with id=AG3, first strand: chain 'l' and resid 5 through 6 removed outlier: 3.743A pdb=" N ALA l 5 " --> pdb=" O ILE l 105 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL l 106 " --> pdb=" O SER l 72 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'l' and resid 5 through 6 removed outlier: 3.743A pdb=" N ALA l 5 " --> pdb=" O ILE l 105 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'l' and resid 84 through 85 Processing sheet with id=AG6, first strand: chain 'm' and resid 25 through 30 removed outlier: 4.476A pdb=" N ARG m 77 " --> pdb=" O VAL m 30 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LYS m 78 " --> pdb=" O ILE m 56 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ILE m 56 " --> pdb=" O LYS m 78 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE m 80 " --> pdb=" O VAL m 54 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL m 54 " --> pdb=" O ILE m 80 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LYS m 82 " --> pdb=" O ASP m 52 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'm' and resid 63 through 66 Processing sheet with id=AG8, first strand: chain 'n' and resid 20 through 21 removed outlier: 3.507A pdb=" N VAL n 9 " --> pdb=" O GLY n 21 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'n' and resid 26 through 27 Processing sheet with id=AH1, first strand: chain 'n' and resid 40 through 44 Processing sheet with id=AH2, first strand: chain 'n' and resid 81 through 82 Processing sheet with id=AH3, first strand: chain 'o' and resid 30 through 31 removed outlier: 3.921A pdb=" N GLY o 30 " --> pdb=" O ARG o 47 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG o 47 " --> pdb=" O GLY o 30 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER o 43 " --> pdb=" O ALA o 69 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU o 67 " --> pdb=" O LEU o 45 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'o' and resid 54 through 55 removed outlier: 6.735A pdb=" N TYR o 54 " --> pdb=" O VAL o 87 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N VAL o 89 " --> pdb=" O TYR o 54 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'p' and resid 27 through 28 Processing sheet with id=AH6, first strand: chain 'p' and resid 48 through 49 removed outlier: 3.504A pdb=" N TYR p 49 " --> pdb=" O LYS p 52 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'q' and resid 2 through 5 removed outlier: 3.503A pdb=" N SER q 19 " --> pdb=" O ILE q 5 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'q' and resid 31 through 35 Processing sheet with id=AH9, first strand: chain 's' and resid 23 through 25 Processing sheet with id=AI1, first strand: chain 't' and resid 14 through 19 Processing sheet with id=AI2, first strand: chain 'u' and resid 15 through 17 removed outlier: 3.649A pdb=" N SER u 25 " --> pdb=" O ASN u 17 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'u' and resid 34 through 36 removed outlier: 3.859A pdb=" N VAL u 36 " --> pdb=" O VAL u 47 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL u 47 " --> pdb=" O VAL u 36 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'w' and resid 37 through 38 removed outlier: 3.543A pdb=" N HIS w 37 " --> pdb=" O LEU w 4 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'y' and resid 22 through 26 removed outlier: 7.230A pdb=" N VAL y 31 " --> pdb=" O LYS y 11 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N THR y 13 " --> pdb=" O VAL y 31 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL y 33 " --> pdb=" O THR y 13 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LYS y 15 " --> pdb=" O VAL y 33 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'x' and resid 4 through 6 removed outlier: 7.046A pdb=" N ASN x 4 " --> pdb=" O VAL x 39 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N VAL x 41 " --> pdb=" O ASN x 4 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ARG x 6 " --> pdb=" O VAL x 41 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP x 38 " --> pdb=" O THR x 56 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER x 66 " --> pdb=" O VAL x 55 " (cutoff:3.500A) 1191 hydrogen bonds defined for protein. 3306 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3943 hydrogen bonds 6362 hydrogen bond angles 0 basepair planarities 1557 basepair parallelities 2396 stacking parallelities Total time for adding SS restraints: 226.36 Time building geometry restraints manager: 64.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.07 - 1.22: 1118 1.22 - 1.37: 44736 1.37 - 1.52: 75877 1.52 - 1.67: 23295 1.67 - 1.82: 162 Bond restraints: 145188 Sorted by residual: bond pdb=" C VAL C 5 " pdb=" O VAL C 5 " ideal model delta sigma weight residual 1.236 1.075 0.161 1.19e-02 7.06e+03 1.84e+02 bond pdb=" CA ASN C 6 " pdb=" C ASN C 6 " ideal model delta sigma weight residual 1.524 1.661 -0.137 1.26e-02 6.30e+03 1.19e+02 bond pdb=" N ASN C 6 " pdb=" CA ASN C 6 " ideal model delta sigma weight residual 1.457 1.603 -0.146 1.41e-02 5.03e+03 1.07e+02 bond pdb=" N VAL C 5 " pdb=" CA VAL C 5 " ideal model delta sigma weight residual 1.459 1.577 -0.118 1.25e-02 6.40e+03 8.97e+01 bond pdb=" C ASN C 6 " pdb=" O ASN C 6 " ideal model delta sigma weight residual 1.238 1.322 -0.085 1.28e-02 6.10e+03 4.38e+01 ... (remaining 145183 not shown) Histogram of bond angle deviations from ideal: 78.72 - 90.87: 1 90.87 - 103.02: 9165 103.02 - 115.17: 111725 115.17 - 127.33: 86249 127.33 - 139.48: 10722 Bond angle restraints: 217862 Sorted by residual: angle pdb=" C ASN C 6 " pdb=" N PRO C 7 " pdb=" CA PRO C 7 " ideal model delta sigma weight residual 119.84 98.68 21.16 1.25e+00 6.40e-01 2.87e+02 angle pdb=" N VAL C 5 " pdb=" CA VAL C 5 " pdb=" C VAL C 5 " ideal model delta sigma weight residual 109.34 139.48 -30.14 2.08e+00 2.31e-01 2.10e+02 angle pdb=" C ASN k 50 " pdb=" N PRO k 51 " pdb=" CD PRO k 51 " ideal model delta sigma weight residual 125.00 78.72 46.28 4.10e+00 5.95e-02 1.27e+02 angle pdb=" CA VAL C 5 " pdb=" C VAL C 5 " pdb=" N ASN C 6 " ideal model delta sigma weight residual 116.60 132.27 -15.67 1.45e+00 4.76e-01 1.17e+02 angle pdb=" N GLU h 27 " pdb=" CA GLU h 27 " pdb=" C GLU h 27 " ideal model delta sigma weight residual 112.47 99.08 13.39 1.24e+00 6.50e-01 1.17e+02 ... (remaining 217857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 69011 35.99 - 71.98: 3918 71.98 - 107.97: 345 107.97 - 143.96: 38 143.96 - 179.95: 67 Dihedral angle restraints: 73379 sinusoidal: 61811 harmonic: 11568 Sorted by residual: dihedral pdb=" C4' A U 183 " pdb=" C3' A U 183 " pdb=" C2' A U 183 " pdb=" C1' A U 183 " ideal model delta sinusoidal sigma weight residual -35.00 33.46 -68.46 1 8.00e+00 1.56e-02 9.49e+01 dihedral pdb=" C5' A U 183 " pdb=" C4' A U 183 " pdb=" C3' A U 183 " pdb=" O3' A U 183 " ideal model delta sinusoidal sigma weight residual 147.00 79.09 67.91 1 8.00e+00 1.56e-02 9.36e+01 dihedral pdb=" O4' C U1281 " pdb=" C1' C U1281 " pdb=" N1 C U1281 " pdb=" C2 C U1281 " ideal model delta sinusoidal sigma weight residual -160.00 15.39 -175.39 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 73376 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 25258 0.108 - 0.216: 1359 0.216 - 0.324: 108 0.324 - 0.432: 33 0.432 - 0.540: 2 Chirality restraints: 26760 Sorted by residual: chirality pdb=" C3' G U 377 " pdb=" C4' G U 377 " pdb=" O3' G U 377 " pdb=" C2' G U 377 " both_signs ideal model delta sigma weight residual False -2.74 -2.21 -0.54 2.00e-01 2.50e+01 7.28e+00 chirality pdb=" CB ILE x 57 " pdb=" CA ILE x 57 " pdb=" CG1 ILE x 57 " pdb=" CG2 ILE x 57 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.44 2.00e-01 2.50e+01 4.77e+00 chirality pdb=" C3' G U 649 " pdb=" C4' G U 649 " pdb=" O3' G U 649 " pdb=" C2' G U 649 " both_signs ideal model delta sigma weight residual False -2.48 -2.05 -0.42 2.00e-01 2.50e+01 4.51e+00 ... (remaining 26757 not shown) Planarity restraints: 11351 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN k 50 " -0.152 5.00e-02 4.00e+02 2.35e-01 8.87e+01 pdb=" N PRO k 51 " 0.404 5.00e-02 4.00e+02 pdb=" CA PRO k 51 " -0.167 5.00e-02 4.00e+02 pdb=" CD PRO k 51 " -0.086 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U A1330 " 0.073 2.00e-02 2.50e+03 3.80e-02 3.25e+01 pdb=" N1 U A1330 " -0.077 2.00e-02 2.50e+03 pdb=" C2 U A1330 " -0.012 2.00e-02 2.50e+03 pdb=" O2 U A1330 " -0.008 2.00e-02 2.50e+03 pdb=" N3 U A1330 " 0.004 2.00e-02 2.50e+03 pdb=" C4 U A1330 " 0.017 2.00e-02 2.50e+03 pdb=" O4 U A1330 " 0.026 2.00e-02 2.50e+03 pdb=" C5 U A1330 " -0.023 2.00e-02 2.50e+03 pdb=" C6 U A1330 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C U2376 " 0.066 2.00e-02 2.50e+03 3.55e-02 2.83e+01 pdb=" N1 C U2376 " -0.075 2.00e-02 2.50e+03 pdb=" C2 C U2376 " -0.023 2.00e-02 2.50e+03 pdb=" O2 C U2376 " 0.004 2.00e-02 2.50e+03 pdb=" N3 C U2376 " 0.008 2.00e-02 2.50e+03 pdb=" C4 C U2376 " 0.001 2.00e-02 2.50e+03 pdb=" N4 C U2376 " 0.017 2.00e-02 2.50e+03 pdb=" C5 C U2376 " 0.016 2.00e-02 2.50e+03 pdb=" C6 C U2376 " -0.015 2.00e-02 2.50e+03 ... (remaining 11348 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.92: 11 1.92 - 2.67: 9068 2.67 - 3.41: 171725 3.41 - 4.16: 436646 4.16 - 4.90: 576753 Nonbonded interactions: 1194203 Sorted by model distance: nonbonded pdb=" CD1 LEU j 95 " pdb=" CD1 LEU j 98 " model vdw 1.178 3.880 nonbonded pdb=" O2' G A 702 " pdb=" NH1 ARG x 100 " model vdw 1.473 2.520 nonbonded pdb=" CE2 PHE x 31 " pdb=" CD1 ILE x 88 " model vdw 1.593 3.760 nonbonded pdb=" O ASN C 6 " pdb=" C PRO C 7 " model vdw 1.657 3.270 nonbonded pdb=" O MET j 94 " pdb=" CD2 LEU j 98 " model vdw 1.708 3.460 ... (remaining 1194198 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 26.050 Check model and map are aligned: 1.470 Set scattering table: 0.920 Process input model: 471.690 Find NCS groups from input model: 2.600 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 510.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 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 : 0.008 0.161 145188 Z= 0.471 Angle : 1.181 46.282 217862 Z= 0.578 Chirality : 0.056 0.540 26760 Planarity : 0.007 0.235 11351 Dihedral : 17.846 179.951 67431 Min Nonbonded Distance : 1.178 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.56 % Allowed : 14.20 % Favored : 85.24 % Rotamer Outliers : 1.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 1.70 % Twisted Proline : 0.51 % Twisted General : 0.02 % 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: -5.34 (0.08), residues: 5500 helix: -4.10 (0.07), residues: 1433 sheet: -3.34 (0.15), residues: 816 loop : -3.47 (0.09), residues: 3251 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1353 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 1310 time to evaluate : 5.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 10 residues processed: 1334 average time/residue: 1.2903 time to fit residues: 2875.1548 Evaluate side-chains 917 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 907 time to evaluate : 5.430 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.9686 time to fit residues: 23.7040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 995 random chunks: chunk 840 optimal weight: 1.9990 chunk 754 optimal weight: 0.3980 chunk 418 optimal weight: 10.0000 chunk 257 optimal weight: 8.9990 chunk 508 optimal weight: 5.9990 chunk 402 optimal weight: 10.0000 chunk 779 optimal weight: 20.0000 chunk 301 optimal weight: 20.0000 chunk 474 optimal weight: 20.0000 chunk 580 optimal weight: 8.9990 chunk 903 optimal weight: 1.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 86 ASN W 226 ASN ** X 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 189 HIS Z 2 ASN ** Z 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 20 ASN a 23 ASN a 59 GLN ** a 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 57 ASN ** b 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 70 ASN b 73 ASN b 80 ASN c 131 HIS ** d 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 39 ASN e 54 GLN e 78 ASN e 106 ASN ** f 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 27 ASN ** g 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 32 HIS j 36 ASN j 37 GLN j 52 GLN ** k 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 2 GLN ** l 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 37 ASN ** l 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 64 HIS ** o 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 19 HIS p 40 HIS q 26 ASN s 31 HIS t 36 GLN u 20 HIS w 48 ASN y 20 ASN x 70 ASN x 91 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.098 145188 Z= 0.261 Angle : 0.771 17.512 217862 Z= 0.392 Chirality : 0.041 0.379 26760 Planarity : 0.006 0.152 11351 Dihedral : 18.140 179.974 60850 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.64 % Favored : 88.20 % Rotamer Outliers : 5.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 1.70 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -4.02 (0.10), residues: 5500 helix: -1.85 (0.12), residues: 1524 sheet: -2.89 (0.17), residues: 775 loop : -3.15 (0.09), residues: 3201 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1168 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1009 time to evaluate : 5.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 159 outliers final: 102 residues processed: 1070 average time/residue: 1.2346 time to fit residues: 2292.8444 Evaluate side-chains 1000 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 898 time to evaluate : 5.228 Switching outliers to nearest non-outliers outliers start: 102 outliers final: 0 residues processed: 102 average time/residue: 0.9429 time to fit residues: 186.9968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 995 random chunks: chunk 502 optimal weight: 10.0000 chunk 280 optimal weight: 30.0000 chunk 752 optimal weight: 10.0000 chunk 615 optimal weight: 10.0000 chunk 249 optimal weight: 20.0000 chunk 905 optimal weight: 7.9990 chunk 977 optimal weight: 10.0000 chunk 806 optimal weight: 0.8980 chunk 897 optimal weight: 1.9990 chunk 308 optimal weight: 20.0000 chunk 726 optimal weight: 7.9990 overall best weight: 5.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 58 HIS W 95 ASN ** X 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 140 HIS ** Y 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 122 ASN Y 169 ASN Y 188 ASN ** Z 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 4 HIS e 114 ASN ** g 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 75 ASN ** i 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 36 ASN ** j 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 61 ASN ** l 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 67 ASN w 37 HIS ** x 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.100 145188 Z= 0.350 Angle : 0.836 12.632 217862 Z= 0.421 Chirality : 0.043 0.412 26760 Planarity : 0.006 0.143 11351 Dihedral : 18.346 178.723 60850 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 24.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.62 % Favored : 85.27 % Rotamer Outliers : 5.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 1.70 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.46 (0.10), residues: 5500 helix: -0.79 (0.13), residues: 1514 sheet: -2.89 (0.16), residues: 784 loop : -3.04 (0.10), residues: 3202 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1082 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 940 time to evaluate : 5.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 142 outliers final: 80 residues processed: 1010 average time/residue: 1.2153 time to fit residues: 2127.8759 Evaluate side-chains 947 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 867 time to evaluate : 5.482 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 0 residues processed: 80 average time/residue: 0.9703 time to fit residues: 154.5078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 995 random chunks: chunk 894 optimal weight: 1.9990 chunk 680 optimal weight: 9.9990 chunk 469 optimal weight: 9.9990 chunk 100 optimal weight: 20.0000 chunk 432 optimal weight: 10.0000 chunk 607 optimal weight: 10.0000 chunk 908 optimal weight: 3.9990 chunk 961 optimal weight: 1.9990 chunk 474 optimal weight: 20.0000 chunk 860 optimal weight: 3.9990 chunk 259 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 95 ASN ** X 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 37 GLN X 68 HIS ** X 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 172 GLN Y 40 GLN ** Y 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 169 ASN Z 2 ASN Z 37 ASN a 59 GLN ** b 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 39 ASN ** g 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 77 GLN g 81 GLN ** i 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 36 ASN ** j 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 52 GLN ** j 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 101 ASN ** o 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 20 HIS v 39 ASN x 91 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.093 145188 Z= 0.240 Angle : 0.715 12.309 217862 Z= 0.363 Chirality : 0.038 0.385 26760 Planarity : 0.005 0.141 11351 Dihedral : 18.046 179.919 60850 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.04 % Favored : 88.85 % Rotamer Outliers : 5.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 1.70 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -3.04 (0.11), residues: 5500 helix: -0.22 (0.14), residues: 1532 sheet: -2.71 (0.16), residues: 789 loop : -2.89 (0.10), residues: 3179 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 914 time to evaluate : 5.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 139 outliers final: 86 residues processed: 981 average time/residue: 1.1888 time to fit residues: 2024.4805 Evaluate side-chains 939 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 853 time to evaluate : 4.971 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 0 residues processed: 86 average time/residue: 0.8840 time to fit residues: 150.9498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 995 random chunks: chunk 801 optimal weight: 4.9990 chunk 545 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 716 optimal weight: 0.7980 chunk 396 optimal weight: 10.0000 chunk 820 optimal weight: 5.9990 chunk 664 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 491 optimal weight: 30.0000 chunk 863 optimal weight: 10.0000 chunk 242 optimal weight: 4.9990 overall best weight: 5.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 169 ASN ** b 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 37 ASN ** i 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 36 ASN j 52 GLN j 72 ASN ** k 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 81 ASN x 2 ASN x 91 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.098 145188 Z= 0.323 Angle : 0.780 14.086 217862 Z= 0.393 Chirality : 0.041 0.408 26760 Planarity : 0.005 0.145 11351 Dihedral : 18.107 179.732 60850 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 23.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.20 % Favored : 85.69 % Rotamer Outliers : 4.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 1.70 % 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: -3.02 (0.11), residues: 5500 helix: -0.13 (0.14), residues: 1540 sheet: -2.67 (0.17), residues: 775 loop : -2.93 (0.10), residues: 3185 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1017 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 902 time to evaluate : 5.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 115 outliers final: 66 residues processed: 948 average time/residue: 1.2637 time to fit residues: 2082.5157 Evaluate side-chains 914 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 848 time to evaluate : 5.454 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 0 residues processed: 66 average time/residue: 1.0033 time to fit residues: 132.2705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 995 random chunks: chunk 323 optimal weight: 9.9990 chunk 866 optimal weight: 4.9990 chunk 190 optimal weight: 30.0000 chunk 564 optimal weight: 8.9990 chunk 237 optimal weight: 30.0000 chunk 962 optimal weight: 6.9990 chunk 799 optimal weight: 0.9980 chunk 445 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 318 optimal weight: 8.9990 chunk 505 optimal weight: 10.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 59 GLN ** b 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 57 ASN ** g 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 77 GLN ** i 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 36 ASN ** j 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 52 GLN ** o 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 47 GLN x 91 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.104 145188 Z= 0.367 Angle : 0.840 13.303 217862 Z= 0.421 Chirality : 0.044 0.409 26760 Planarity : 0.006 0.151 11351 Dihedral : 18.362 178.818 60850 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 26.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 15.36 % Favored : 84.51 % Rotamer Outliers : 4.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 1.70 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -3.11 (0.11), residues: 5500 helix: -0.21 (0.14), residues: 1549 sheet: -2.71 (0.17), residues: 779 loop : -3.01 (0.10), residues: 3172 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1007 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 878 time to evaluate : 5.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 129 outliers final: 81 residues processed: 937 average time/residue: 1.1924 time to fit residues: 1935.1407 Evaluate side-chains 938 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 857 time to evaluate : 5.047 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 0 residues processed: 81 average time/residue: 0.8496 time to fit residues: 136.8815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 995 random chunks: chunk 928 optimal weight: 0.0030 chunk 108 optimal weight: 10.0000 chunk 548 optimal weight: 10.0000 chunk 703 optimal weight: 0.8980 chunk 544 optimal weight: 10.0000 chunk 810 optimal weight: 5.9990 chunk 537 optimal weight: 10.0000 chunk 959 optimal weight: 0.8980 chunk 600 optimal weight: 30.0000 chunk 584 optimal weight: 7.9990 chunk 442 optimal weight: 6.9990 overall best weight: 2.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 169 ASN a 107 ASN ** b 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 77 GLN ** i 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 91 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.070 145188 Z= 0.209 Angle : 0.702 29.000 217862 Z= 0.355 Chirality : 0.038 0.396 26760 Planarity : 0.005 0.194 11351 Dihedral : 18.011 179.278 60850 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.78 % Favored : 88.11 % Rotamer Outliers : 2.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 1.70 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.11), residues: 5500 helix: 0.28 (0.14), residues: 1522 sheet: -2.45 (0.17), residues: 777 loop : -2.85 (0.10), residues: 3201 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 992 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 914 time to evaluate : 5.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 78 outliers final: 33 residues processed: 951 average time/residue: 1.2594 time to fit residues: 2084.5191 Evaluate side-chains 857 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 824 time to evaluate : 5.446 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.9783 time to fit residues: 67.7415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 995 random chunks: chunk 593 optimal weight: 20.0000 chunk 382 optimal weight: 9.9990 chunk 572 optimal weight: 10.0000 chunk 288 optimal weight: 50.0000 chunk 188 optimal weight: 0.0070 chunk 185 optimal weight: 10.0000 chunk 609 optimal weight: 10.0000 chunk 653 optimal weight: 10.0000 chunk 474 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 753 optimal weight: 6.9990 overall best weight: 7.4010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 169 ASN ** b 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 109 ASN ** e 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 77 GLN h 39 HIS ** i 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 36 ASN ** j 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 101 ASN l 95 GLN u 16 ASN ** x 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 91 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.116 145188 Z= 0.428 Angle : 0.900 23.560 217862 Z= 0.448 Chirality : 0.046 0.443 26760 Planarity : 0.006 0.179 11351 Dihedral : 18.515 179.617 60850 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 29.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 16.93 % Favored : 82.95 % Rotamer Outliers : 4.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 1.70 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.07 (0.11), residues: 5500 helix: -0.08 (0.14), residues: 1535 sheet: -2.67 (0.17), residues: 760 loop : -3.03 (0.10), residues: 3205 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 983 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 867 time to evaluate : 5.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 116 outliers final: 74 residues processed: 910 average time/residue: 1.1974 time to fit residues: 1887.2209 Evaluate side-chains 904 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 830 time to evaluate : 5.123 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 0 residues processed: 74 average time/residue: 0.9212 time to fit residues: 135.3688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 995 random chunks: chunk 872 optimal weight: 0.8980 chunk 918 optimal weight: 0.9980 chunk 838 optimal weight: 4.9990 chunk 893 optimal weight: 0.9990 chunk 537 optimal weight: 10.0000 chunk 389 optimal weight: 10.0000 chunk 701 optimal weight: 5.9990 chunk 274 optimal weight: 0.0670 chunk 807 optimal weight: 0.6980 chunk 845 optimal weight: 2.9990 chunk 890 optimal weight: 2.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 200 HIS ** W 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 46 GLN Y 49 HIS Y 169 ASN ** b 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 5 GLN ** j 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 91 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.096 145188 Z= 0.152 Angle : 0.670 18.385 217862 Z= 0.337 Chirality : 0.035 0.414 26760 Planarity : 0.005 0.161 11351 Dihedral : 17.772 179.811 60850 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.95 % Favored : 90.96 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 1.70 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.11), residues: 5500 helix: 0.48 (0.14), residues: 1525 sheet: -2.29 (0.18), residues: 783 loop : -2.76 (0.10), residues: 3192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 921 time to evaluate : 4.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 14 residues processed: 934 average time/residue: 1.2141 time to fit residues: 1959.2713 Evaluate side-chains 863 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 849 time to evaluate : 5.482 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.9721 time to fit residues: 31.9106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 995 random chunks: chunk 586 optimal weight: 10.0000 chunk 945 optimal weight: 10.0000 chunk 576 optimal weight: 9.9990 chunk 448 optimal weight: 10.0000 chunk 656 optimal weight: 10.0000 chunk 991 optimal weight: 5.9990 chunk 912 optimal weight: 0.8980 chunk 789 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 609 optimal weight: 10.0000 chunk 484 optimal weight: 10.0000 overall best weight: 5.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 169 ASN ** b 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 36 ASN ** j 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 52 GLN ** o 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 16 ASN ** v 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 91 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.098 145188 Z= 0.358 Angle : 0.818 18.293 217862 Z= 0.408 Chirality : 0.042 0.472 26760 Planarity : 0.006 0.165 11351 Dihedral : 18.078 179.666 60850 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 25.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.89 % Favored : 85.00 % Rotamer Outliers : 1.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 1.70 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.11), residues: 5500 helix: 0.37 (0.14), residues: 1528 sheet: -2.59 (0.17), residues: 793 loop : -2.86 (0.10), residues: 3179 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11000 Ramachandran restraints generated. 5500 Oldfield, 0 Emsley, 5500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 853 time to evaluate : 7.611 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: 32 outliers final: 23 residues processed: 861 average time/residue: 1.2314 time to fit residues: 1841.7677 Evaluate side-chains 847 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 824 time to evaluate : 5.518 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.9865 time to fit residues: 48.8287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 995 random chunks: chunk 626 optimal weight: 10.0000 chunk 840 optimal weight: 2.9990 chunk 241 optimal weight: 0.5980 chunk 727 optimal weight: 0.0470 chunk 116 optimal weight: 10.0000 chunk 219 optimal weight: 20.0000 chunk 790 optimal weight: 10.0000 chunk 330 optimal weight: 20.0000 chunk 811 optimal weight: 0.0870 chunk 100 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 overall best weight: 2.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 191 ASN Y 169 ASN ** b 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 103 HIS ** i 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 86 GLN ** o 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 16 ASN ** v 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 40 ASN ** y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.118042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.104116 restraints weight = 436467.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.106290 restraints weight = 159626.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 75)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.107547 restraints weight = 80404.383| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.090 145188 Z= 0.204 Angle : 0.697 16.672 217862 Z= 0.351 Chirality : 0.037 0.438 26760 Planarity : 0.005 0.158 11351 Dihedral : 17.869 179.669 60850 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.18 % Favored : 88.73 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.53 % Cis-general : 1.70 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.11), residues: 5500 helix: 0.53 (0.14), residues: 1546 sheet: -2.41 (0.18), residues: 786 loop : -2.77 (0.10), residues: 3168 =============================================================================== Job complete usr+sys time: 29751.38 seconds wall clock time: 523 minutes 48.39 seconds (31428.39 seconds total)