Starting phenix.real_space_refine on Sun Mar 17 04:27:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9w_6306/03_2024/3j9w_6306.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9w_6306/03_2024/3j9w_6306.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9w_6306/03_2024/3j9w_6306.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9w_6306/03_2024/3j9w_6306.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9w_6306/03_2024/3j9w_6306.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9w_6306/03_2024/3j9w_6306.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 4675 5.49 5 S 94 5.16 5 C 65516 2.51 5 N 25691 2.21 5 O 39449 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B5 TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B7 TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BD ARG 63": "NH1" <-> "NH2" Residue "BD ARG 221": "NH1" <-> "NH2" Residue "BE TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BF TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BF TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BG PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BG ARG 92": "NH1" <-> "NH2" Residue "BH ARG 172": "NH1" <-> "NH2" Residue "BM TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BO PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BP TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BQ TYR 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BR ARG 11": "NH1" <-> "NH2" Residue "BS ARG 42": "NH1" <-> "NH2" Residue "BU TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BU ARG 89": "NH1" <-> "NH2" Residue "BV PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BV ARG 86": "NH1" <-> "NH2" Residue "BZ ARG 28": "NH1" <-> "NH2" Residue "BZ PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 135425 Number of models: 1 Model: "" Number of chains: 54 Chain: "AA" 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': 85, 'rna3p_pur': 753, 'rna3p_pyr': 587} Link IDs: {'rna2p': 204, 'rna3p': 1339} Chain: "AB" 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: "AC" 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': 2, 'PTRANS': 4, 'TRANS': 203} 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: "AD" 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: "AE" 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: "AF" 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: "AG" 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: "AH" 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: "AI" 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: "AJ" 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: "AK" 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: "AL" 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: "AM" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 476 Classifications: {'peptide': 119} Incomplete info: {'backbone_only': 108} Link IDs: {'CIS': 7, 'PTRANS': 3, 'TRANS': 108} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 482 Unresolved non-hydrogen angles: 683 Unresolved non-hydrogen dihedrals: 294 Unresolved non-hydrogen chiralities: 146 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 216 Chain: "AN" 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: "AO" 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: "AP" 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: "AQ" 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: "AR" 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: "AS" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 336 Classifications: {'peptide': 84} Incomplete info: {'backbone_only': 77} Link IDs: {'CIS': 3, 'PTRANS': 4, 'TRANS': 76} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 356 Unresolved non-hydrogen angles: 508 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 100 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': 6} Unresolved non-hydrogen planarities: 163 Chain: "AT" 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: "AX" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1643 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 8, 'rna3p_pur': 32, 'rna3p_pyr': 31} Link IDs: {'rna2p': 13, 'rna3p': 63} Chain: "AY" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 415 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 12, 'rna3p_pyr': 3} Link IDs: {'rna2p': 3, 'rna3p': 15} Chain: "AZ" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 107 Classifications: {'peptide': 24} Incomplete info: {'backbone_only': 1, 'n_c_alpha_c_only': 17} Link IDs: {'CIS': 2, 'PCIS': 1, 'TRANS': 20} Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "B0" 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: "B1" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 530 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "B2" 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: "B3" 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: "B4" 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: "B5" 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: "B6" 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: "B7" 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: "B8" 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: "BA" Number of atoms: 62767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2923, 62767 Classifications: {'RNA': 2923} Modifications used: {'rna2p_pur': 272, 'rna2p_pyr': 147, 'rna3p_pur': 1423, 'rna3p_pyr': 1081} Link IDs: {'rna2p': 419, 'rna3p': 2503} Chain: "BB" 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': 7, 'rna3p_pur': 53, 'rna3p_pyr': 45} Link IDs: {'rna2p': 14, 'rna3p': 97} Chain: "BD" 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: "BE" 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: "BF" 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: "BG" 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: "BH" 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: "BJ" 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: "BK" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 981 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 10, 'TRANS': 122} Chain: "BM" 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: "BN" 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: "BO" 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: "BP" 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: "BQ" 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: "BR" 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: "BS" 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: "BT" 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: "BU" 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: "BV" 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: "BW" 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: "BX" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 754 Classifications: {'peptide': 100} Link IDs: {'CIS': 6, 'PTRANS': 6, 'TRANS': 87} Chain: "BZ" 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} Time building chain proxies: 52.44, per 1000 atoms: 0.39 Number of scatterers: 135425 At special positions: 0 Unit cell: (269.244, 274.784, 240.436, 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 94 16.00 P 4675 15.00 O 39449 8.00 N 25691 7.00 C 65516 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: 57.89 Conformation dependent library (CDL) restraints added in 6.4 seconds 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6000 Finding SS restraints... Secondary structure from input PDB file: 171 helices and 70 sheets defined 34.4% alpha, 13.9% beta 1651 base pairs and 2638 stacking pairs defined. Time for finding SS restraints: 51.05 Creating SS restraints... Processing helix chain 'AB' and resid 8 through 13 Processing helix chain 'AB' and resid 24 through 28 Processing helix chain 'AB' and resid 42 through 64 removed outlier: 3.968A pdb=" N ALAAB 62 " --> pdb=" O LYSAB 58 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLUAB 63 " --> pdb=" O ASNAB 59 " (cutoff:3.500A) Processing helix chain 'AB' and resid 76 through 88 removed outlier: 3.836A pdb=" N VALAB 80 " --> pdb=" O ALAAB 76 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYSAB 81 " --> pdb=" O GLNAB 77 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLUAB 82 " --> pdb=" O ASPAB 78 " (cutoff:3.500A) Processing helix chain 'AB' and resid 104 through 121 Processing helix chain 'AB' and resid 130 through 149 removed outlier: 4.105A pdb=" N LYSAB 146 " --> pdb=" O GLUAB 142 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHEAB 147 " --> pdb=" O ARGAB 143 " (cutoff:3.500A) Processing helix chain 'AB' and resid 150 through 154 removed outlier: 3.537A pdb=" N ASPAB 153 " --> pdb=" O GLYAB 150 " (cutoff:3.500A) Processing helix chain 'AB' and resid 169 through 179 Processing helix chain 'AB' and resid 192 through 196 removed outlier: 3.556A pdb=" N GLUAB 195 " --> pdb=" O ASPAB 192 " (cutoff:3.500A) Processing helix chain 'AB' and resid 206 through 225 removed outlier: 3.756A pdb=" N LEUAB 213 " --> pdb=" O ALAAB 209 " (cutoff:3.500A) Processing helix chain 'AC' and resid 7 through 12 removed outlier: 3.967A pdb=" N ILEAC 12 " --> pdb=" O VALAC 8 " (cutoff:3.500A) Processing helix chain 'AC' and resid 27 through 46 removed outlier: 3.611A pdb=" N PHEAC 31 " --> pdb=" O ASPAC 27 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEUAC 32 " --> pdb=" O TYRAC 28 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYSAC 44 " --> pdb=" O GLUAC 40 " (cutoff:3.500A) Processing helix chain 'AC' and resid 72 through 77 Processing helix chain 'AC' and resid 80 through 95 removed outlier: 3.513A pdb=" N GLUAC 84 " --> pdb=" O GLYAC 80 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEUAC 93 " --> pdb=" O ALAAC 89 " (cutoff:3.500A) Processing helix chain 'AC' and resid 107 through 110 Processing helix chain 'AC' and resid 111 through 125 Processing helix chain 'AC' and resid 128 through 144 Processing helix chain 'AD' and resid 8 through 16 Processing helix chain 'AD' and resid 45 through 62 removed outlier: 4.450A pdb=" N METAD 60 " --> pdb=" O LYSAD 56 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TYRAD 61 " --> pdb=" O LEUAD 57 " (cutoff:3.500A) Processing helix chain 'AD' and resid 64 through 78 Processing helix chain 'AD' and resid 81 through 91 Processing helix chain 'AD' and resid 93 through 101 Processing helix chain 'AD' and resid 106 through 117 Processing helix chain 'AD' and resid 142 through 146 removed outlier: 3.577A pdb=" N ARGAD 146 " --> pdb=" O GLUAD 143 " (cutoff:3.500A) Processing helix chain 'AD' and resid 148 through 157 removed outlier: 4.027A pdb=" N VALAD 157 " --> pdb=" O GLUAD 153 " (cutoff:3.500A) Processing helix chain 'AD' and resid 190 through 198 removed outlier: 3.771A pdb=" N ILEAD 194 " --> pdb=" O ASNAD 190 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TYRAD 198 " --> pdb=" O ILEAD 194 " (cutoff:3.500A) Processing helix chain 'AE' and resid 55 through 70 removed outlier: 3.837A pdb=" N ASNAE 70 " --> pdb=" O ASPAE 66 " (cutoff:3.500A) Processing helix chain 'AE' and resid 108 through 119 Processing helix chain 'AE' and resid 132 through 147 Processing helix chain 'AE' and resid 149 through 157 Processing helix chain 'AF' and resid 15 through 33 Processing helix chain 'AF' and resid 70 through 82 removed outlier: 3.968A pdb=" N GLUAF 74 " --> pdb=" O ALAAF 70 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ARGAF 77 " --> pdb=" O GLNAF 73 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SERAF 82 " --> pdb=" O LEUAF 78 " (cutoff:3.500A) Processing helix chain 'AG' and resid 20 through 31 removed outlier: 3.908A pdb=" N SERAG 24 " --> pdb=" O SERAG 20 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N METAG 31 " --> pdb=" O ILEAG 27 " (cutoff:3.500A) Processing helix chain 'AG' and resid 35 through 53 Processing helix chain 'AG' and resid 57 through 69 Processing helix chain 'AG' and resid 92 through 110 removed outlier: 3.551A pdb=" N LEUAG 110 " --> pdb=" O ASNAG 106 " (cutoff:3.500A) Processing helix chain 'AG' and resid 115 through 129 Processing helix chain 'AG' and resid 131 through 145 removed outlier: 4.016A pdb=" N VALAG 135 " --> pdb=" O THRAG 131 " (cutoff:3.500A) Processing helix chain 'AG' and resid 149 through 153 Processing helix chain 'AH' and resid 5 through 21 Processing helix chain 'AH' and resid 30 through 44 removed outlier: 3.612A pdb=" N ILEAH 36 " --> pdb=" O LEUAH 32 " (cutoff:3.500A) Processing helix chain 'AH' and resid 115 through 122 Processing helix chain 'AI' and resid 35 through 39 removed outlier: 3.703A pdb=" N ILEAI 39 " --> pdb=" O ILEAI 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'AI' and resid 35 through 39' Processing helix chain 'AI' and resid 43 through 55 removed outlier: 3.560A pdb=" N ASPAI 47 " --> pdb=" O ALAAI 43 " (cutoff:3.500A) Proline residue: AI 51 - end of helix Processing helix chain 'AI' and resid 71 through 91 removed outlier: 3.973A pdb=" N ASPAI 91 " --> pdb=" O LEUAI 87 " (cutoff:3.500A) Processing helix chain 'AI' and resid 94 through 102 removed outlier: 3.812A pdb=" N ARGAI 100 " --> pdb=" O THRAI 96 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 14 through 31 removed outlier: 3.576A pdb=" N LEUAJ 18 " --> pdb=" O ASPAJ 14 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THRAJ 28 " --> pdb=" O LYSAJ 24 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALAAJ 29 " --> pdb=" O ILEAJ 25 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 80 through 88 removed outlier: 3.517A pdb=" N METAJ 88 " --> pdb=" O VALAJ 84 " (cutoff:3.500A) Processing helix chain 'AK' and resid 48 through 52 Processing helix chain 'AK' and resid 55 through 59 removed outlier: 4.041A pdb=" N ARGAK 58 " --> pdb=" O ARGAK 55 " (cutoff:3.500A) Processing helix chain 'AK' and resid 61 through 80 removed outlier: 3.591A pdb=" N ALAAK 65 " --> pdb=" O THRAK 61 " (cutoff:3.500A) Processing helix chain 'AK' and resid 93 through 105 removed outlier: 3.888A pdb=" N ARGAK 100 " --> pdb=" O GLUAK 96 " (cutoff:3.500A) Processing helix chain 'AL' and resid 3 through 11 removed outlier: 3.760A pdb=" N LEUAL 7 " --> pdb=" O THRAL 3 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILEAL 8 " --> pdb=" O ILEAL 4 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARGAL 9 " --> pdb=" O ASNAL 5 " (cutoff:3.500A) Processing helix chain 'AM' and resid 14 through 21 Processing helix chain 'AM' and resid 26 through 38 Processing helix chain 'AM' and resid 51 through 63 removed outlier: 3.539A pdb=" N LEUAM 63 " --> pdb=" O ILEAM 59 " (cutoff:3.500A) Processing helix chain 'AM' and resid 65 through 83 Processing helix chain 'AM' and resid 86 through 94 removed outlier: 3.899A pdb=" N GLYAM 94 " --> pdb=" O ARGAM 90 " (cutoff:3.500A) Processing helix chain 'AM' and resid 106 through 111 removed outlier: 4.024A pdb=" N LYSAM 110 " --> pdb=" O ALAAM 106 " (cutoff:3.500A) Processing helix chain 'AN' and resid 3 through 12 Processing helix chain 'AN' and resid 16 through 20 removed outlier: 3.646A pdb=" N GLUAN 20 " --> pdb=" O LYSAN 17 " (cutoff:3.500A) Processing helix chain 'AN' and resid 40 through 51 Processing helix chain 'AO' and resid 4 through 16 removed outlier: 3.550A pdb=" N ASNAO 13 " --> pdb=" O ASNAO 9 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLUAO 14 " --> pdb=" O GLNAO 10 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHEAO 15 " --> pdb=" O LEUAO 11 " (cutoff:3.500A) Processing helix chain 'AO' and resid 23 through 46 removed outlier: 4.024A pdb=" N VALAO 27 " --> pdb=" O GLYAO 23 " (cutoff:3.500A) Processing helix chain 'AO' and resid 49 through 74 Processing helix chain 'AO' and resid 74 through 86 Processing helix chain 'AP' and resid 54 through 63 Processing helix chain 'AP' and resid 67 through 77 Processing helix chain 'AP' and resid 79 through 88 removed outlier: 3.811A pdb=" N PHEAP 83 " --> pdb=" O ILEAP 79 " (cutoff:3.500A) Processing helix chain 'AR' and resid 18 through 22 Processing helix chain 'AR' and resid 31 through 38 Processing helix chain 'AR' and resid 46 through 51 Processing helix chain 'AR' and resid 53 through 70 Processing helix chain 'AS' and resid 13 through 25 Processing helix chain 'AS' and resid 41 through 45 Processing helix chain 'AT' and resid 7 through 41 Processing helix chain 'AT' and resid 45 through 63 removed outlier: 3.838A pdb=" N LYSAT 63 " --> pdb=" O ASPAT 59 " (cutoff:3.500A) Processing helix chain 'AT' and resid 69 through 88 removed outlier: 4.365A pdb=" N ALAAT 73 " --> pdb=" O LYSAT 69 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SERAT 87 " --> pdb=" O VALAT 83 " (cutoff:3.500A) Processing helix chain 'B0' and resid 50 through 55 removed outlier: 3.613A pdb=" N LYSB0 55 " --> pdb=" O ALAB0 51 " (cutoff:3.500A) Processing helix chain 'B1' and resid 2 through 8 removed outlier: 3.587A pdb=" N ASPB1 8 " --> pdb=" O ASNB1 4 " (cutoff:3.500A) Processing helix chain 'B1' and resid 10 through 35 removed outlier: 3.515A pdb=" N PHEB1 26 " --> pdb=" O LYSB1 22 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASNB1 27 " --> pdb=" O GLUB1 23 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHEB1 30 " --> pdb=" O PHEB1 26 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLNB1 31 " --> pdb=" O ASNB1 27 " (cutoff:3.500A) Processing helix chain 'B1' and resid 39 through 65 removed outlier: 3.687A pdb=" N ARGB1 47 " --> pdb=" O ILEB1 43 " (cutoff:3.500A) Processing helix chain 'B2' and resid 16 through 27 Processing helix chain 'B2' and resid 40 through 50 removed outlier: 3.759A pdb=" N METB2 46 " --> pdb=" O ALAB2 42 " (cutoff:3.500A) Processing helix chain 'B4' and resid 9 through 18 Processing helix chain 'B6' and resid 8 through 17 Processing helix chain 'B6' and resid 17 through 23 Processing helix chain 'B6' and resid 24 through 37 removed outlier: 3.582A pdb=" N LYSB6 37 " --> pdb=" O ARGB6 33 " (cutoff:3.500A) Processing helix chain 'B7' and resid 7 through 14 Processing helix chain 'B7' and resid 37 through 46 removed outlier: 4.006A pdb=" N LYSB7 46 " --> pdb=" O ARGB7 42 " (cutoff:3.500A) Processing helix chain 'B7' and resid 51 through 59 removed outlier: 4.074A pdb=" N ARGB7 57 " --> pdb=" O GLYB7 53 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILEB7 58 " --> pdb=" O ASPB7 54 " (cutoff:3.500A) Processing helix chain 'B8' and resid 29 through 33 Processing helix chain 'BD' and resid 30 through 32 No H-bonds generated for 'chain 'BD' and resid 30 through 32' Processing helix chain 'BD' and resid 133 through 135 No H-bonds generated for 'chain 'BD' and resid 133 through 135' Processing helix chain 'BD' and resid 177 through 179 No H-bonds generated for 'chain 'BD' and resid 177 through 179' Processing helix chain 'BD' and resid 197 through 203 removed outlier: 3.862A pdb=" N GLUBD 201 " --> pdb=" O GLUBD 198 " (cutoff:3.500A) Processing helix chain 'BD' and resid 207 through 214 removed outlier: 4.007A pdb=" N SERBD 211 " --> pdb=" O LYSBD 207 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TRPBD 213 " --> pdb=" O GLYBD 209 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYSBD 214 " --> pdb=" O ARGBD 210 " (cutoff:3.500A) Processing helix chain 'BD' and resid 264 through 268 removed outlier: 4.018A pdb=" N LYSBD 268 " --> pdb=" O LYSBD 265 " (cutoff:3.500A) Processing helix chain 'BE' and resid 57 through 61 Processing helix chain 'BE' and resid 62 through 69 Processing helix chain 'BE' and resid 121 through 127 Processing helix chain 'BF' and resid 29 through 42 removed outlier: 3.933A pdb=" N PHEBF 34 " --> pdb=" O GLUBF 30 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASPBF 35 " --> pdb=" O SERBF 31 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALABF 36 " --> pdb=" O VALBF 32 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N METBF 39 " --> pdb=" O ASPBF 35 " (cutoff:3.500A) Processing helix chain 'BF' and resid 102 through 121 removed outlier: 3.641A pdb=" N ILEBF 110 " --> pdb=" O ARGBF 106 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VALBF 118 " --> pdb=" O LEUBF 114 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILEBF 119 " --> pdb=" O SERBF 115 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASPBF 120 " --> pdb=" O SERBF 116 " (cutoff:3.500A) Processing helix chain 'BF' and resid 136 through 146 removed outlier: 3.523A pdb=" N LYSBF 144 " --> pdb=" O ALABF 140 " (cutoff:3.500A) Processing helix chain 'BF' and resid 160 through 166 Processing helix chain 'BF' and resid 177 through 181 removed outlier: 3.873A pdb=" N ILEBF 181 " --> pdb=" O ALABF 178 " (cutoff:3.500A) Processing helix chain 'BF' and resid 182 through 189 removed outlier: 3.792A pdb=" N HISBF 189 " --> pdb=" O ASPBF 185 " (cutoff:3.500A) Processing helix chain 'BF' and resid 195 through 206 removed outlier: 3.742A pdb=" N GLUBF 200 " --> pdb=" O LYSBF 196 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYSBF 201 " --> pdb=" O ALABF 197 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLUBF 203 " --> pdb=" O VALBF 199 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLUBF 204 " --> pdb=" O GLUBF 200 " (cutoff:3.500A) Processing helix chain 'BG' and resid 3 through 8 removed outlier: 3.742A pdb=" N TYRBG 8 " --> pdb=" O LEUBG 4 " (cutoff:3.500A) Processing helix chain 'BG' and resid 11 through 20 removed outlier: 3.598A pdb=" N ALABG 15 " --> pdb=" O GLUBG 11 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THRBG 18 " --> pdb=" O PROBG 14 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHEBG 20 " --> pdb=" O LEUBG 16 " (cutoff:3.500A) Processing helix chain 'BG' and resid 49 through 61 removed outlier: 4.121A pdb=" N ALABG 53 " --> pdb=" O ALABG 49 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLUBG 56 " --> pdb=" O SERBG 52 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEUBG 57 " --> pdb=" O ALABG 53 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THRBG 58 " --> pdb=" O VALBG 54 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHEBG 59 " --> pdb=" O GLUBG 55 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILEBG 60 " --> pdb=" O GLUBG 56 " (cutoff:3.500A) Processing helix chain 'BG' and resid 93 through 106 removed outlier: 4.172A pdb=" N TYRBG 97 " --> pdb=" O GLYBG 93 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYSBG 102 " --> pdb=" O ASPBG 98 " (cutoff:3.500A) Processing helix chain 'BG' and resid 106 through 111 removed outlier: 3.877A pdb=" N VALBG 111 " --> pdb=" O SERBG 107 " (cutoff:3.500A) Processing helix chain 'BG' and resid 162 through 174 removed outlier: 3.699A pdb=" N GLUBG 168 " --> pdb=" O GLUBG 164 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEUBG 170 " --> pdb=" O ALABG 166 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLNBG 172 " --> pdb=" O GLUBG 168 " (cutoff:3.500A) Processing helix chain 'BH' and resid 59 through 81 removed outlier: 3.921A pdb=" N GLYBH 67 " --> pdb=" O ARGBH 63 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THRBH 68 " --> pdb=" O ALABH 64 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARGBH 70 " --> pdb=" O HISBH 66 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SERBH 71 " --> pdb=" O GLYBH 67 " (cutoff:3.500A) Processing helix chain 'BH' and resid 138 through 152 removed outlier: 3.742A pdb=" N VALBH 152 " --> pdb=" O ASNBH 148 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 5 through 20 removed outlier: 3.553A pdb=" N LYSBJ 9 " --> pdb=" O ILEBJ 5 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLUBJ 13 " --> pdb=" O LYSBJ 9 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLUBJ 14 " --> pdb=" O VALBJ 10 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SERBJ 17 " --> pdb=" O GLUBJ 13 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYSBJ 20 " --> pdb=" O ALABJ 16 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 33 through 48 removed outlier: 3.609A pdb=" N GLUBJ 40 " --> pdb=" O SERBJ 36 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYSBJ 43 " --> pdb=" O THRBJ 39 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 62 through 67 removed outlier: 3.647A pdb=" N GLNBJ 66 " --> pdb=" O ARGBJ 62 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 73 through 78 removed outlier: 4.353A pdb=" N THRBJ 77 " --> pdb=" O ASNBJ 73 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 93 through 105 removed outlier: 3.870A pdb=" N ASNBJ 97 " --> pdb=" O ALABJ 93 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHEBJ 99 " --> pdb=" O VALBJ 95 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALABJ 100 " --> pdb=" O LEUBJ 96 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLUBJ 104 " --> pdb=" O ALABJ 100 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALABJ 105 " --> pdb=" O LYSBJ 101 " (cutoff:3.500A) Processing helix chain 'BK' and resid 25 through 30 Processing helix chain 'BK' and resid 34 through 46 removed outlier: 3.643A pdb=" N PHEBK 38 " --> pdb=" O ASNBK 34 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LYSBK 40 " --> pdb=" O METBK 36 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLUBK 41 " --> pdb=" O GLYBK 37 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARGBK 45 " --> pdb=" O GLUBK 41 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THRBK 46 " --> pdb=" O PHEBK 42 " (cutoff:3.500A) Processing helix chain 'BK' and resid 47 through 50 removed outlier: 3.557A pdb=" N ALABK 50 " --> pdb=" O ALABK 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'BK' and resid 47 through 50' Processing helix chain 'BK' and resid 76 through 84 removed outlier: 3.670A pdb=" N LYSBK 80 " --> pdb=" O ALABK 76 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYSBK 81 " --> pdb=" O VALBK 77 " (cutoff:3.500A) Processing helix chain 'BK' and resid 101 through 112 removed outlier: 3.585A pdb=" N GLUBK 107 " --> pdb=" O ASPBK 103 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THRBK 111 " --> pdb=" O GLUBK 107 " (cutoff:3.500A) Processing helix chain 'BK' and resid 120 through 133 removed outlier: 3.575A pdb=" N ARGBK 126 " --> pdb=" O GLUBK 122 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THRBK 131 " --> pdb=" O METBK 127 " (cutoff:3.500A) Processing helix chain 'BM' and resid 28 through 39 removed outlier: 3.535A pdb=" N ALABM 34 " --> pdb=" O SERBM 30 " (cutoff:3.500A) Processing helix chain 'BM' and resid 59 through 63 removed outlier: 3.669A pdb=" N ILEBM 63 " --> pdb=" O ALABM 60 " (cutoff:3.500A) Processing helix chain 'BM' and resid 68 through 73 Processing helix chain 'BM' and resid 90 through 96 Processing helix chain 'BM' and resid 98 through 110 removed outlier: 3.755A pdb=" N LEUBM 102 " --> pdb=" O PROBM 98 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALABM 105 " --> pdb=" O METBM 101 " (cutoff:3.500A) Processing helix chain 'BM' and resid 113 through 123 removed outlier: 3.933A pdb=" N PHEBM 120 " --> pdb=" O GLYBM 116 " (cutoff:3.500A) Processing helix chain 'BM' and resid 133 through 137 Processing helix chain 'BN' and resid 104 through 109 removed outlier: 3.977A pdb=" N GLUBN 108 " --> pdb=" O ARGBN 104 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASNBN 109 " --> pdb=" O GLUBN 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'BN' and resid 104 through 109' Processing helix chain 'BN' and resid 111 through 117 removed outlier: 3.743A pdb=" N VALBN 115 " --> pdb=" O PHEBN 111 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEUBN 117 " --> pdb=" O LYSBN 113 " (cutoff:3.500A) Processing helix chain 'BO' and resid 2 through 6 removed outlier: 3.835A pdb=" N LEUBO 6 " --> pdb=" O LEUBO 3 " (cutoff:3.500A) Processing helix chain 'BO' and resid 56 through 61 Processing helix chain 'BO' and resid 78 through 85 removed outlier: 3.808A pdb=" N GLYBO 84 " --> pdb=" O LYSBO 81 " (cutoff:3.500A) Processing helix chain 'BO' and resid 92 through 97 Processing helix chain 'BO' and resid 129 through 138 removed outlier: 3.596A pdb=" N LYSBO 133 " --> pdb=" O SERBO 129 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLUBO 134 " --> pdb=" O ALABO 130 " (cutoff:3.500A) Processing helix chain 'BP' and resid 44 through 59 removed outlier: 3.635A pdb=" N ALABP 53 " --> pdb=" O ALABP 49 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARGBP 56 " --> pdb=" O ILEBP 52 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYRBP 57 " --> pdb=" O ALABP 53 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYSBP 59 " --> pdb=" O THRBP 55 " (cutoff:3.500A) Processing helix chain 'BP' and resid 110 through 125 removed outlier: 3.502A pdb=" N ARGBP 115 " --> pdb=" O GLUBP 111 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLUBP 116 " --> pdb=" O GLUBP 112 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARGBP 119 " --> pdb=" O ARGBP 115 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALABP 121 " --> pdb=" O ALABP 117 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HISBP 123 " --> pdb=" O ARGBP 119 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYSBP 124 " --> pdb=" O LEUBP 120 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 9 through 28 removed outlier: 3.624A pdb=" N LYSBQ 14 " --> pdb=" O SERBQ 10 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALABQ 15 " --> pdb=" O ALABQ 11 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEUBQ 20 " --> pdb=" O METBQ 16 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILEBQ 25 " --> pdb=" O THRBQ 21 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILEBQ 26 " --> pdb=" O THRBQ 22 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 34 through 54 removed outlier: 4.371A pdb=" N SERBQ 42 " --> pdb=" O LYSBQ 38 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VALBQ 43 " --> pdb=" O GLUBQ 39 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYSBQ 46 " --> pdb=" O SERBQ 42 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYSBQ 52 " --> pdb=" O ILEBQ 48 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARGBQ 53 " --> pdb=" O THRBQ 49 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLYBQ 54 " --> pdb=" O LEUBQ 50 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 55 through 66 removed outlier: 3.501A pdb=" N ARGBQ 60 " --> pdb=" O LEUBQ 56 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALABQ 64 " --> pdb=" O ARGBQ 60 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYRBQ 65 " --> pdb=" O GLNBQ 61 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 78 through 86 removed outlier: 4.225A pdb=" N LEUBQ 83 " --> pdb=" O ALABQ 79 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHEBQ 84 " --> pdb=" O LEUBQ 80 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 86 through 91 Processing helix chain 'BR' and resid 8 through 22 removed outlier: 3.506A pdb=" N LYSBR 13 " --> pdb=" O ALABR 9 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VALBR 18 " --> pdb=" O ARGBR 14 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALABR 20 " --> pdb=" O ALABR 16 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYSBR 21 " --> pdb=" O ARGBR 17 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEUBR 22 " --> pdb=" O VALBR 18 " (cutoff:3.500A) Processing helix chain 'BR' and resid 72 through 89 removed outlier: 3.529A pdb=" N LYSBR 76 " --> pdb=" O SERBR 72 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VALBR 77 " --> pdb=" O ALABR 73 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALABR 82 " --> pdb=" O GLYBR 78 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLUBR 87 " --> pdb=" O LYSBR 83 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYSBR 88 " --> pdb=" O ARGBR 84 " (cutoff:3.500A) Processing helix chain 'BR' and resid 105 through 116 removed outlier: 3.551A pdb=" N LEUBR 109 " --> pdb=" O ARGBR 105 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALABR 113 " --> pdb=" O LEUBR 109 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARGBR 114 " --> pdb=" O ALABR 110 " (cutoff:3.500A) Processing helix chain 'BS' and resid 6 through 13 Processing helix chain 'BS' and resid 14 through 16 No H-bonds generated for 'chain 'BS' and resid 14 through 16' Processing helix chain 'BS' and resid 56 through 59 Processing helix chain 'BS' and resid 100 through 106 removed outlier: 3.727A pdb=" N LEUBS 103 " --> pdb=" O LEUBS 100 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARGBS 104 " --> pdb=" O TYRBS 101 " (cutoff:3.500A) Processing helix chain 'BS' and resid 108 through 114 removed outlier: 3.645A pdb=" N ARGBS 112 " --> pdb=" O GLYBS 108 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYSBS 114 " --> pdb=" O ALABS 110 " (cutoff:3.500A) Processing helix chain 'BT' and resid 6 through 22 removed outlier: 3.585A pdb=" N THRBT 10 " --> pdb=" O GLYBT 6 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARGBT 13 " --> pdb=" O VALBT 9 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYSBT 15 " --> pdb=" O ARGBT 11 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VALBT 17 " --> pdb=" O ARGBT 13 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEUBT 18 " --> pdb=" O ARGBT 14 " (cutoff:3.500A) Processing helix chain 'BT' and resid 26 through 31 removed outlier: 4.214A pdb=" N THRBT 30 " --> pdb=" O GLYBT 26 " (cutoff:3.500A) Processing helix chain 'BT' and resid 31 through 72 removed outlier: 3.962A pdb=" N GLNBT 37 " --> pdb=" O LYSBT 33 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARGBT 50 " --> pdb=" O ALABT 46 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYSBT 54 " --> pdb=" O ARGBT 50 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARGBT 58 " --> pdb=" O LYSBT 54 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYSBT 59 " --> pdb=" O ARGBT 55 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILEBT 62 " --> pdb=" O ARGBT 58 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARGBT 64 " --> pdb=" O LEUBT 60 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALABT 67 " --> pdb=" O THRBT 63 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARGBT 70 " --> pdb=" O ASNBT 66 " (cutoff:3.500A) Processing helix chain 'BT' and resid 75 through 86 removed outlier: 3.612A pdb=" N LEUBT 85 " --> pdb=" O HISBT 81 " (cutoff:3.500A) Processing helix chain 'BT' and resid 92 through 102 removed outlier: 3.615A pdb=" N ASNBT 101 " --> pdb=" O ASPBT 97 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASPBT 102 " --> pdb=" O LEUBT 98 " (cutoff:3.500A) Processing helix chain 'BT' and resid 106 through 117 removed outlier: 3.537A pdb=" N ALABT 110 " --> pdb=" O PHEBT 106 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALABT 113 " --> pdb=" O LEUBT 109 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYSBT 114 " --> pdb=" O ALABT 110 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALABT 115 " --> pdb=" O ASPBT 111 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLNBT 116 " --> pdb=" O ALABT 112 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEUBT 117 " --> pdb=" O ALABT 113 " (cutoff:3.500A) Processing helix chain 'BV' and resid 13 through 25 removed outlier: 3.961A pdb=" N LEUBV 19 " --> pdb=" O ARGBV 15 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VALBV 20 " --> pdb=" O LYSBV 16 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEUBV 23 " --> pdb=" O LEUBV 19 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARGBV 25 " --> pdb=" O METBV 21 " (cutoff:3.500A) Processing helix chain 'BV' and resid 28 through 31 Processing helix chain 'BV' and resid 32 through 39 removed outlier: 3.782A pdb=" N LEUBV 36 " --> pdb=" O ALABV 32 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASNBV 37 " --> pdb=" O VALBV 33 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEUBV 38 " --> pdb=" O SERBV 34 " (cutoff:3.500A) Processing helix chain 'BV' and resid 42 through 60 removed outlier: 4.517A pdb=" N ILEBV 46 " --> pdb=" O ALABV 42 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALABV 58 " --> pdb=" O ALABV 54 " (cutoff:3.500A) Processing helix chain 'BV' and resid 88 through 92 removed outlier: 3.660A pdb=" N ARGBV 92 " --> pdb=" O ALABV 89 " (cutoff:3.500A) Processing helix chain 'BW' and resid 3 through 6 removed outlier: 3.626A pdb=" N ASPBW 6 " --> pdb=" O ASPBW 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'BW' and resid 3 through 6' Processing helix chain 'BW' and resid 14 through 21 removed outlier: 3.631A pdb=" N LEUBW 20 " --> pdb=" O ARGBW 16 " (cutoff:3.500A) Processing helix chain 'BW' and resid 35 through 47 removed outlier: 3.573A pdb=" N ASPBW 41 " --> pdb=" O THRBW 37 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLUBW 44 " --> pdb=" O LYSBW 40 " (cutoff:3.500A) Processing helix chain 'BX' and resid 66 through 68 No H-bonds generated for 'chain 'BX' and resid 66 through 68' Processing sheet with id= A, first strand: chain 'AB' and resid 31 through 34 removed outlier: 6.889A pdb=" N ILEAB 40 " --> pdb=" O PHEAB 32 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'AB' and resid 67 through 69 removed outlier: 6.071A pdb=" N LEUAB 68 " --> pdb=" O PHEAB 162 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'AB' and resid 184 through 187 removed outlier: 3.608A pdb=" N GLYAB 185 " --> pdb=" O VALAB 198 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'AC' and resid 20 through 21 removed outlier: 3.658A pdb=" N LYSAC 53 " --> pdb=" O HISAC 68 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'AC' and resid 164 through 170 removed outlier: 3.684A pdb=" N GLYAC 147 " --> pdb=" O TYRAC 202 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'AD' and resid 124 through 125 removed outlier: 3.764A pdb=" N GLYAD 140 " --> pdb=" O LEUAD 120 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'AE' and resid 15 through 25 removed outlier: 5.418A pdb=" N LEUAE 15 " --> pdb=" O VALAE 38 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VALAE 38 " --> pdb=" O LEUAE 15 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'AE' and resid 85 through 86 Processing sheet with id= I, first strand: chain 'AF' and resid 36 through 47 removed outlier: 6.766A pdb=" N THRAF 38 " --> pdb=" O GLNAF 66 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N GLNAF 66 " --> pdb=" O THRAF 38 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N THRAF 40 " --> pdb=" O ASNAF 64 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASNAF 64 " --> pdb=" O THRAF 40 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ASPAF 42 " --> pdb=" O ILEAF 62 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILEAF 62 " --> pdb=" O ASPAF 42 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARGAF 87 " --> pdb=" O ILEAF 9 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'AG' and resid 73 through 74 Processing sheet with id= K, first strand: chain 'AG' and resid 77 through 78 Processing sheet with id= L, first strand: chain 'AH' and resid 24 through 27 removed outlier: 3.541A pdb=" N ASPAH 48 " --> pdb=" O PHEAH 63 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'AH' and resid 76 through 78 removed outlier: 5.131A pdb=" N VALAH 127 " --> pdb=" O SERAH 107 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SERAH 107 " --> pdb=" O VALAH 127 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VALAH 131 " --> pdb=" O ILEAH 103 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILEAH 103 " --> pdb=" O VALAH 131 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'AI' and resid 6 through 11 removed outlier: 4.046A pdb=" N TYRAI 6 " --> pdb=" O LEUAI 21 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLYAI 8 " --> pdb=" O VALAI 19 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VALAI 19 " --> pdb=" O GLYAI 8 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VALAI 29 " --> pdb=" O VALAI 65 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VALAI 67 " --> pdb=" O VALAI 29 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'AJ' and resid 7 through 12 Processing sheet with id= P, first strand: chain 'AJ' and resid 47 through 52 Processing sheet with id= Q, first strand: chain 'AK' and resid 41 through 47 removed outlier: 3.944A pdb=" N ASNAK 42 " --> pdb=" O ASPAK 38 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ILEAK 36 " --> pdb=" O ILEAK 44 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N TRPAK 46 " --> pdb=" O VALAK 34 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VALAK 34 " --> pdb=" O TRPAK 46 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THRAK 87 " --> pdb=" O ALAAK 23 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'AL' and resid 43 through 53 removed outlier: 6.446A pdb=" N ARGAL 67 " --> pdb=" O THRAL 48 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VALAL 50 " --> pdb=" O TYRAL 65 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TYRAL 65 " --> pdb=" O VALAL 50 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N THRAL 52 " --> pdb=" O ARGAL 63 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ARGAL 63 " --> pdb=" O THRAL 52 " (cutoff:3.500A) removed outlier: 10.140A pdb=" N TYRAL 108 " --> pdb=" O GLUAL 75 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N THRAL 77 " --> pdb=" O TYRAL 108 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ILEAL 110 " --> pdb=" O THRAL 77 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N TYRAL 79 " --> pdb=" O ILEAL 110 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'AP' and resid 3 through 6 Processing sheet with id= T, first strand: chain 'AP' and resid 39 through 41 removed outlier: 3.623A pdb=" N LYSAP 50 " --> pdb=" O THRAP 39 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'AQ' and resid 37 through 49 removed outlier: 4.457A pdb=" N LYSAQ 38 " --> pdb=" O HISAQ 33 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N HISAQ 33 " --> pdb=" O LYSAQ 38 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THRAQ 29 " --> pdb=" O TYRAQ 42 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THRAQ 24 " --> pdb=" O VALAQ 15 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLUAQ 28 " --> pdb=" O GLNAQ 11 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N GLNAQ 11 " --> pdb=" O GLUAQ 28 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N LYSAQ 62 " --> pdb=" O VALAQ 78 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VALAQ 78 " --> pdb=" O LYSAQ 62 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ARGAQ 74 " --> pdb=" O THRAQ 66 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'AS' and resid 31 through 33 Processing sheet with id= W, first strand: chain 'B0' and resid 13 through 17 removed outlier: 3.736A pdb=" N SERB0 25 " --> pdb=" O ASNB0 17 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B2' and resid 34 through 38 Processing sheet with id= Y, first strand: chain 'B3' and resid 22 through 26 removed outlier: 7.230A pdb=" N VALB3 31 " --> pdb=" O LYSB3 11 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N THRB3 13 " --> pdb=" O VALB3 31 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VALB3 33 " --> pdb=" O THRB3 13 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LYSB3 15 " --> pdb=" O VALB3 33 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B4' and resid 48 through 49 Processing sheet with id= AA, first strand: chain 'B5' and resid 17 through 20 removed outlier: 3.630A pdb=" N LYSB5 41 " --> pdb=" O CYSB5 36 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B7' and resid 15 through 16 removed outlier: 4.241A pdb=" N LYSB7 15 " --> pdb=" O LYSB7 23 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYSB7 23 " --> pdb=" O LYSB7 15 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B8' and resid 15 through 19 Processing sheet with id= AD, first strand: chain 'BD' and resid 3 through 5 removed outlier: 4.054A pdb=" N THRBD 18 " --> pdb=" O LYSBD 4 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'BD' and resid 34 through 35 Processing sheet with id= AF, first strand: chain 'BD' and resid 101 through 105 removed outlier: 3.628A pdb=" N ARGBD 102 " --> pdb=" O ILEBD 94 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILEBD 94 " --> pdb=" O ARGBD 102 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THRBD 80 " --> pdb=" O LEUBD 93 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASNBD 95 " --> pdb=" O VALBD 78 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N VALBD 78 " --> pdb=" O ASNBD 95 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'BD' and resid 129 through 131 removed outlier: 3.608A pdb=" N ALABD 190 " --> pdb=" O LEUBD 130 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'BD' and resid 172 through 175 removed outlier: 3.817A pdb=" N VALBD 181 " --> pdb=" O ARGBD 272 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARGBD 272 " --> pdb=" O VALBD 181 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N METBD 183 " --> pdb=" O ILEBD 270 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILEBD 270 " --> pdb=" O METBD 183 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'BE' and resid 12 through 14 removed outlier: 7.095A pdb=" N LEUBE 185 " --> pdb=" O VALBE 179 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VALBE 179 " --> pdb=" O LEUBE 185 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEUBE 187 " --> pdb=" O VALBE 177 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLUBE 175 " --> pdb=" O LYSBE 189 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N THRBE 170 " --> pdb=" O GLYBE 112 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLYBE 112 " --> pdb=" O THRBE 170 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLNBE 172 " --> pdb=" O VALBE 110 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N VALBE 110 " --> pdb=" O GLNBE 172 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'BE' and resid 80 through 81 removed outlier: 4.213A pdb=" N GLNBE 37 " --> pdb=" O GLNBE 50 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N GLYBE 52 " --> pdb=" O VALBE 35 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VALBE 35 " --> pdb=" O GLYBE 52 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'BE' and resid 118 through 120 removed outlier: 3.580A pdb=" N GLYBE 118 " --> pdb=" O METBE 164 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'BF' and resid 6 through 7 removed outlier: 3.621A pdb=" N ILEBF 124 " --> pdb=" O LEUBF 192 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILEBF 194 " --> pdb=" O ILEBF 124 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THRBF 174 " --> pdb=" O ALABF 152 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILEBF 154 " --> pdb=" O THRBF 174 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VALBF 176 " --> pdb=" O ILEBF 154 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'BG' and resid 36 through 37 removed outlier: 3.650A pdb=" N VALBG 89 " --> pdb=" O ILEBG 36 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'BG' and resid 130 through 132 Processing sheet with id= AO, first strand: chain 'BH' and resid 9 through 10 removed outlier: 4.078A pdb=" N GLUBH 43 " --> pdb=" O ALABH 54 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'BH' and resid 16 through 17 removed outlier: 3.782A pdb=" N THRBH 16 " --> pdb=" O LYSBH 28 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VALBH 25 " --> pdb=" O ARGBH 36 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARGBH 36 " --> pdb=" O VALBH 25 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'BH' and resid 96 through 100 removed outlier: 3.870A pdb=" N ARGBH 96 " --> pdb=" O ASNBH 107 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYSBH 103 " --> pdb=" O SERBH 100 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'BH' and resid 122 through 125 removed outlier: 3.647A pdb=" N GLUBH 125 " --> pdb=" O VALBH 133 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VALBH 133 " --> pdb=" O GLUBH 125 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'BK' and resid 56 through 58 removed outlier: 3.675A pdb=" N ILEBK 69 " --> pdb=" O GLUBK 57 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'BK' and resid 99 through 100 Processing sheet with id= AU, first strand: chain 'BM' and resid 124 through 125 removed outlier: 6.110A pdb=" N LEUBM 17 " --> pdb=" O ILEBM 56 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'BM' and resid 74 through 75 removed outlier: 3.731A pdb=" N ARGBM 88 " --> pdb=" O TYRBM 75 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'BN' and resid 7 through 9 removed outlier: 6.334A pdb=" N ALABN 16 " --> pdb=" O ALABN 46 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ALABN 46 " --> pdb=" O ALABN 16 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLUBN 18 " --> pdb=" O LYSBN 44 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VALBN 40 " --> pdb=" O ILEBN 22 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VALBN 24 " --> pdb=" O VALBN 38 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N VALBN 38 " --> pdb=" O VALBN 24 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALABN 83 " --> pdb=" O VALBN 63 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'BN' and resid 69 through 70 removed outlier: 3.843A pdb=" N TYRBN 76 " --> pdb=" O THRBS 76 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VALBS 64 " --> pdb=" O ARGBS 75 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THRBS 61 " --> pdb=" O ARGBS 54 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'BN' and resid 102 through 103 removed outlier: 5.930A pdb=" N VALBN 102 " --> pdb=" O ILEBN 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= AY Processing sheet with id= AZ, first strand: chain 'BO' and resid 122 through 125 removed outlier: 3.974A pdb=" N VALBO 123 " --> pdb=" O THRBO 142 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLUBO 144 " --> pdb=" O VALBO 123 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALABO 125 " --> pdb=" O GLUBO 144 " (cutoff:3.500A) No H-bonds generated for sheet with id= AZ Processing sheet with id= BA, first strand: chain 'BP' and resid 35 through 36 removed outlier: 3.718A pdb=" N GLNBP 35 " --> pdb=" O LYSBP 130 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'BP' and resid 42 through 43 removed outlier: 4.057A pdb=" N ILEBP 42 " --> pdb=" O ALABP 95 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALABP 76 " --> pdb=" O PROBP 90 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLYBP 92 " --> pdb=" O TYRBP 74 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYRBP 74 " --> pdb=" O GLYBP 92 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'BQ' and resid 29 through 33 Processing sheet with id= BD, first strand: chain 'BQ' and resid 29 through 33 Processing sheet with id= BE, first strand: chain 'BR' and resid 51 through 57 removed outlier: 6.354A pdb=" N THRBR 52 " --> pdb=" O ASPBR 46 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASPBR 46 " --> pdb=" O THRBR 52 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALABR 54 " --> pdb=" O ILEBR 44 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHEBR 34 " --> pdb=" O TYRBR 41 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLNBR 43 " --> pdb=" O ASNBR 32 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILEBR 45 " --> pdb=" O ARGBR 30 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARGBR 30 " --> pdb=" O ILEBR 45 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'BS' and resid 41 through 47 removed outlier: 3.920A pdb=" N VALBS 33 " --> pdb=" O GLNBS 44 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHEBS 46 " --> pdb=" O VALBS 31 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VALBS 31 " --> pdb=" O PHEBS 46 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THRBS 28 " --> pdb=" O VALBS 90 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLUBS 88 " --> pdb=" O ARGBS 30 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LYSBS 86 " --> pdb=" O HISBS 32 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LYSBS 34 " --> pdb=" O ILEBS 84 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ILEBS 84 " --> pdb=" O LYSBS 34 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'BU' and resid 3 through 6 Processing sheet with id= BH, first strand: chain 'BU' and resid 60 through 67 removed outlier: 7.227A pdb=" N LYSBU 94 " --> pdb=" O GLUBU 63 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N GLNBU 65 " --> pdb=" O TYRBU 92 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TYRBU 92 " --> pdb=" O GLNBU 65 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'BU' and resid 71 through 74 Processing sheet with id= BJ, first strand: chain 'BV' and resid 3 through 6 Processing sheet with id= BK, first strand: chain 'BV' and resid 3 through 6 Processing sheet with id= BL, first strand: chain 'BV' and resid 82 through 86 Processing sheet with id= BM, first strand: chain 'BW' and resid 8 through 11 removed outlier: 4.498A pdb=" N ARGBW 10 " --> pdb=" O GLUBW 29 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VALBW 81 " --> pdb=" O TYRBW 26 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYSBW 53 " --> pdb=" O LYSBW 82 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'BX' and resid 8 through 10 removed outlier: 4.081A pdb=" N ALABX 25 " --> pdb=" O LEUBX 34 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'BX' and resid 81 through 82 Processing sheet with id= BP, first strand: chain 'BZ' and resid 30 through 31 removed outlier: 4.209A pdb=" N GLYBZ 30 " --> pdb=" O ARGBZ 47 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARGBZ 47 " --> pdb=" O GLYBZ 30 " (cutoff:3.500A) No H-bonds generated for sheet with id= BP Processing sheet with id= BQ, first strand: chain 'BZ' and resid 38 through 39 removed outlier: 3.652A pdb=" N VALBZ 39 " --> pdb=" O GLYBZ 73 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLYBZ 73 " --> pdb=" O VALBZ 39 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'BZ' and resid 59 through 61 removed outlier: 4.022A pdb=" N PHEBZ 68 " --> pdb=" O GLYBZ 60 " (cutoff:3.500A) 1475 hydrogen bonds defined for protein. 4119 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4145 hydrogen bonds 6464 hydrogen bond angles 0 basepair planarities 1651 basepair parallelities 2638 stacking parallelities Total time for adding SS restraints: 224.30 Time building geometry restraints manager: 62.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 21430 1.33 - 1.45: 63335 1.45 - 1.57: 53480 1.57 - 1.69: 9345 1.69 - 1.81: 169 Bond restraints: 147759 Sorted by residual: bond pdb=" CA GLNBV 95 " pdb=" C GLNBV 95 " ideal model delta sigma weight residual 1.523 1.446 0.077 1.24e-02 6.50e+03 3.90e+01 bond pdb=" N ASPBE 150 " pdb=" CA ASPBE 150 " ideal model delta sigma weight residual 1.461 1.505 -0.044 9.20e-03 1.18e+04 2.29e+01 bond pdb=" N ILEBV 96 " pdb=" CA ILEBV 96 " ideal model delta sigma weight residual 1.459 1.405 0.054 1.15e-02 7.56e+03 2.20e+01 bond pdb=" CA ASPBE 150 " pdb=" C ASPBE 150 " ideal model delta sigma weight residual 1.520 1.572 -0.052 1.23e-02 6.61e+03 1.77e+01 bond pdb=" N PROB0 44 " pdb=" CD PROB0 44 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.71e+01 ... (remaining 147754 not shown) Histogram of bond angle deviations from ideal: 82.76 - 94.38: 2 94.38 - 106.01: 22359 106.01 - 117.63: 112836 117.63 - 129.25: 82573 129.25 - 140.88: 4026 Bond angle restraints: 221796 Sorted by residual: angle pdb=" C4' GBA 589 " pdb=" C3' GBA 589 " pdb=" O3' GBA 589 " ideal model delta sigma weight residual 109.40 140.88 -31.48 1.50e+00 4.44e-01 4.40e+02 angle pdb=" C4' GBA 83 " pdb=" C3' GBA 83 " pdb=" O3' GBA 83 " ideal model delta sigma weight residual 109.40 82.76 26.64 1.50e+00 4.44e-01 3.15e+02 angle pdb=" C4' GBA 82 " pdb=" C3' GBA 82 " pdb=" O3' GBA 82 " ideal model delta sigma weight residual 113.00 90.05 22.95 1.50e+00 4.44e-01 2.34e+02 angle pdb=" C4' UBA2487 " pdb=" C3' UBA2487 " pdb=" O3' UBA2487 " ideal model delta sigma weight residual 109.40 131.47 -22.07 1.50e+00 4.44e-01 2.16e+02 angle pdb=" C4' ABA 366 " pdb=" C3' ABA 366 " pdb=" O3' ABA 366 " ideal model delta sigma weight residual 109.40 128.03 -18.63 1.50e+00 4.44e-01 1.54e+02 ... (remaining 221791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 79016 36.00 - 72.00: 11003 72.00 - 108.00: 1350 108.00 - 143.99: 51 143.99 - 179.99: 90 Dihedral angle restraints: 91510 sinusoidal: 79829 harmonic: 11681 Sorted by residual: dihedral pdb=" C5' ABA1092 " pdb=" C4' ABA1092 " pdb=" C3' ABA1092 " pdb=" O3' ABA1092 " ideal model delta sinusoidal sigma weight residual 147.00 76.00 71.00 1 8.00e+00 1.56e-02 1.01e+02 dihedral pdb=" C4' ABA2779 " pdb=" C3' ABA2779 " pdb=" C2' ABA2779 " pdb=" C1' ABA2779 " ideal model delta sinusoidal sigma weight residual -35.00 35.48 -70.48 1 8.00e+00 1.56e-02 9.99e+01 dihedral pdb=" C4' ABA2295 " pdb=" C3' ABA2295 " pdb=" C2' ABA2295 " pdb=" C1' ABA2295 " ideal model delta sinusoidal sigma weight residual -35.00 35.48 -70.48 1 8.00e+00 1.56e-02 9.99e+01 ... (remaining 91507 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.181: 27191 0.181 - 0.361: 78 0.361 - 0.542: 2 0.542 - 0.723: 3 0.723 - 0.903: 1 Chirality restraints: 27275 Sorted by residual: chirality pdb=" C3' GBA 589 " pdb=" C4' GBA 589 " pdb=" O3' GBA 589 " pdb=" C2' GBA 589 " both_signs ideal model delta sigma weight residual False -2.74 -1.84 -0.90 2.00e-01 2.50e+01 2.04e+01 chirality pdb=" C4' ABA1173 " pdb=" C5' ABA1173 " pdb=" O4' ABA1173 " pdb=" C3' ABA1173 " both_signs ideal model delta sigma weight residual False -2.50 -1.80 -0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" C1' ABA1173 " pdb=" O4' ABA1173 " pdb=" C2' ABA1173 " pdb=" N9 ABA1173 " both_signs ideal model delta sigma weight residual False 2.44 1.80 0.64 2.00e-01 2.50e+01 1.01e+01 ... (remaining 27272 not shown) Planarity restraints: 11493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ABA 366 " -0.138 2.00e-02 2.50e+03 9.83e-02 2.66e+02 pdb=" N9 ABA 366 " 0.037 2.00e-02 2.50e+03 pdb=" C8 ABA 366 " 0.031 2.00e-02 2.50e+03 pdb=" N7 ABA 366 " 0.081 2.00e-02 2.50e+03 pdb=" C5 ABA 366 " 0.065 2.00e-02 2.50e+03 pdb=" C6 ABA 366 " 0.100 2.00e-02 2.50e+03 pdb=" N6 ABA 366 " -0.242 2.00e-02 2.50e+03 pdb=" N1 ABA 366 " 0.070 2.00e-02 2.50e+03 pdb=" C2 ABA 366 " 0.011 2.00e-02 2.50e+03 pdb=" N3 ABA 366 " -0.025 2.00e-02 2.50e+03 pdb=" C4 ABA 366 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ABA 841 " -0.093 2.00e-02 2.50e+03 9.36e-02 2.41e+02 pdb=" N9 ABA 841 " -0.020 2.00e-02 2.50e+03 pdb=" C8 ABA 841 " 0.030 2.00e-02 2.50e+03 pdb=" N7 ABA 841 " 0.087 2.00e-02 2.50e+03 pdb=" C5 ABA 841 " 0.069 2.00e-02 2.50e+03 pdb=" C6 ABA 841 " 0.108 2.00e-02 2.50e+03 pdb=" N6 ABA 841 " -0.236 2.00e-02 2.50e+03 pdb=" N1 ABA 841 " 0.075 2.00e-02 2.50e+03 pdb=" C2 ABA 841 " 0.009 2.00e-02 2.50e+03 pdb=" N3 ABA 841 " -0.032 2.00e-02 2.50e+03 pdb=" C4 ABA 841 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ABA1661 " 0.089 2.00e-02 2.50e+03 9.29e-02 2.37e+02 pdb=" N9 ABA1661 " 0.027 2.00e-02 2.50e+03 pdb=" C8 ABA1661 " -0.030 2.00e-02 2.50e+03 pdb=" N7 ABA1661 " -0.087 2.00e-02 2.50e+03 pdb=" C5 ABA1661 " -0.070 2.00e-02 2.50e+03 pdb=" C6 ABA1661 " -0.107 2.00e-02 2.50e+03 pdb=" N6 ABA1661 " 0.235 2.00e-02 2.50e+03 pdb=" N1 ABA1661 " -0.074 2.00e-02 2.50e+03 pdb=" C2 ABA1661 " -0.009 2.00e-02 2.50e+03 pdb=" N3 ABA1661 " 0.030 2.00e-02 2.50e+03 pdb=" C4 ABA1661 " -0.005 2.00e-02 2.50e+03 ... (remaining 11490 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.13: 5 2.13 - 2.82: 38675 2.82 - 3.51: 174654 3.51 - 4.21: 436895 4.21 - 4.90: 553250 Nonbonded interactions: 1203479 Sorted by model distance: nonbonded pdb=" O3' AAX 76 " pdb=" C ASPAZ 89 " model vdw 1.433 3.270 nonbonded pdb=" NH2 ARGB0 18 " pdb=" SD METB0 22 " model vdw 1.858 2.880 nonbonded pdb=" CA ILEAZ 74 " pdb=" CE2 PHEBV 85 " model vdw 1.985 3.770 nonbonded pdb=" O2' UAY 10 " pdb=" OP1 GAY 11 " model vdw 2.074 2.440 nonbonded pdb=" O2' GAY 11 " pdb=" OP2 AAY 12 " model vdw 2.109 2.440 ... (remaining 1203474 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: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 16.060 Check model and map are aligned: 1.460 Set scattering table: 0.950 Process input model: 480.600 Find NCS groups from input model: 2.890 Set up NCS constraints: 0.390 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: 0.030 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 507.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 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 : 0.010 0.077 147759 Z= 0.563 Angle : 1.503 31.479 221796 Z= 0.625 Chirality : 0.032 0.903 27275 Planarity : 0.016 0.392 11493 Dihedral : 24.070 179.992 85510 Min Nonbonded Distance : 1.433 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 2.00 % Allowed : 6.04 % Favored : 91.96 % Rotamer: Outliers : 0.26 % Allowed : 1.28 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 1.79 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.11), residues: 5563 helix: -2.94 (0.07), residues: 1603 sheet: -2.68 (0.15), residues: 820 loop : 0.65 (0.12), residues: 3140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPBT 61 HIS 0.006 0.001 HISBV 60 PHE 0.012 0.001 PHEBZ 80 TYR 0.015 0.001 TYRBQ 91 ARG 0.005 0.000 ARGBV 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1581 residues out of total 4740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1574 time to evaluate : 5.504 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: B0 38 ILE cc_start: 0.6047 (mt) cc_final: 0.5807 (mt) REVERT: B1 18 VAL cc_start: 0.7298 (t) cc_final: 0.6961 (t) REVERT: B2 11 SER cc_start: 0.8592 (t) cc_final: 0.8247 (p) REVERT: B2 36 VAL cc_start: 0.8537 (t) cc_final: 0.8185 (p) REVERT: B4 5 PHE cc_start: 0.7519 (t80) cc_final: 0.7214 (t80) REVERT: B4 10 LYS cc_start: 0.7652 (mtpt) cc_final: 0.7315 (mtpp) REVERT: B5 5 ILE cc_start: 0.7760 (mt) cc_final: 0.7467 (mt) REVERT: B5 44 LEU cc_start: 0.8455 (mt) cc_final: 0.8229 (mp) REVERT: BE 168 GLN cc_start: 0.8094 (tt0) cc_final: 0.7060 (tt0) REVERT: BE 176 ILE cc_start: 0.7709 (mt) cc_final: 0.7495 (tp) REVERT: BF 37 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8475 (mt) REVERT: BF 130 THR cc_start: 0.7403 (p) cc_final: 0.7170 (p) REVERT: BG 12 ILE cc_start: 0.6994 (mp) cc_final: 0.6752 (mt) REVERT: BG 57 LEU cc_start: 0.8559 (tp) cc_final: 0.8329 (tp) REVERT: BG 90 THR cc_start: 0.7941 (p) cc_final: 0.7686 (p) REVERT: BG 91 LEU cc_start: 0.5918 (pp) cc_final: 0.5626 (pp) REVERT: BH 13 SER cc_start: 0.6243 (m) cc_final: 0.5612 (p) REVERT: BM 50 ASP cc_start: 0.4403 (t70) cc_final: 0.4021 (t0) REVERT: BM 75 TYR cc_start: 0.8173 (m-80) cc_final: 0.7663 (m-10) REVERT: BO 6 LEU cc_start: 0.7525 (tp) cc_final: 0.7300 (tp) REVERT: BO 79 LEU cc_start: 0.7982 (tp) cc_final: 0.7761 (tp) REVERT: BO 122 THR cc_start: 0.6330 (p) cc_final: 0.5943 (p) REVERT: BP 79 LEU cc_start: 0.8330 (pp) cc_final: 0.8110 (mp) REVERT: BR 83 LYS cc_start: 0.8322 (mttt) cc_final: 0.6696 (mtpp) REVERT: BS 10 ASP cc_start: 0.7117 (m-30) cc_final: 0.6779 (m-30) REVERT: BT 27 SER cc_start: 0.8652 (m) cc_final: 0.8395 (p) REVERT: BT 62 ILE cc_start: 0.8043 (mt) cc_final: 0.7694 (mt) REVERT: BV 53 SER cc_start: 0.8766 (t) cc_final: 0.8476 (t) REVERT: BV 100 THR cc_start: 0.8834 (m) cc_final: 0.8473 (p) REVERT: BW 1 MET cc_start: 0.3292 (mmm) cc_final: 0.2660 (ptm) REVERT: BW 49 VAL cc_start: 0.7831 (t) cc_final: 0.7508 (t) REVERT: BW 69 TYR cc_start: 0.6244 (m-10) cc_final: 0.5971 (m-10) REVERT: BX 9 VAL cc_start: 0.8324 (t) cc_final: 0.8020 (t) REVERT: BZ 23 ASP cc_start: 0.7600 (t0) cc_final: 0.7392 (t0) REVERT: BZ 32 LYS cc_start: 0.8881 (mmtm) cc_final: 0.8594 (mmtt) outliers start: 7 outliers final: 2 residues processed: 1575 average time/residue: 1.3116 time to fit residues: 3415.2626 Evaluate side-chains 950 residues out of total 4740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 947 time to evaluate : 4.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AZ residue 86 ASP Chi-restraints excluded: chain BF residue 37 ILE Chi-restraints excluded: chain BF residue 66 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 851 optimal weight: 20.0000 chunk 764 optimal weight: 0.9990 chunk 423 optimal weight: 8.9990 chunk 260 optimal weight: 50.0000 chunk 515 optimal weight: 8.9990 chunk 408 optimal weight: 8.9990 chunk 790 optimal weight: 5.9990 chunk 305 optimal weight: 0.0170 chunk 480 optimal weight: 8.9990 chunk 588 optimal weight: 10.0000 chunk 915 optimal weight: 10.0000 overall best weight: 5.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1 27 ASN B3 20 ASN B3 47 GLN B4 19 HIS B4 40 HIS ** B5 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B6 8 ASN B7 60 GLN B7 64 ASN B8 32 HIS ** B8 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 199 GLN ** BD 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BE 14 GLN ** BE 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 67 GLN BF 160 ASN ** BG 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BH 107 ASN ** BJ 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BK 93 ASN BM 59 ASN BN 3 GLN BO 4 HIS ** BP 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BP 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 61 GLN BQ 77 GLN BR 103 HIS BS 5 GLN BS 32 HIS BS 39 ASN BT 37 GLN BT 52 GLN ** BU 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BU 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 60 HIS BV 61 ASN BV 95 GLN BX 2 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 147759 Z= 0.259 Angle : 0.697 12.856 221796 Z= 0.359 Chirality : 0.037 0.458 27275 Planarity : 0.005 0.059 11493 Dihedral : 24.500 179.838 78911 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.90 % Allowed : 5.03 % Favored : 94.07 % Rotamer: Outliers : 6.06 % Allowed : 17.53 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 1.79 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.11), residues: 5563 helix: -0.21 (0.11), residues: 1688 sheet: -2.12 (0.15), residues: 904 loop : -0.10 (0.12), residues: 2971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRPBP 65 HIS 0.016 0.002 HISBV 102 PHE 0.050 0.003 PHEBG 177 TYR 0.033 0.003 TYRBG 128 ARG 0.022 0.001 ARGBG 125 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1241 residues out of total 4740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1075 time to evaluate : 5.508 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: B0 10 LYS cc_start: 0.7752 (mtpp) cc_final: 0.7509 (mttm) REVERT: B1 19 LYS cc_start: 0.8417 (tttp) cc_final: 0.8025 (mtpp) REVERT: B2 30 LYS cc_start: 0.8819 (mtpp) cc_final: 0.7727 (mtmm) REVERT: B3 1 MET cc_start: 0.5805 (tpp) cc_final: 0.5360 (mmm) REVERT: B3 22 PHE cc_start: 0.4790 (m-80) cc_final: 0.4018 (m-80) REVERT: B4 5 PHE cc_start: 0.8074 (t80) cc_final: 0.7748 (t80) REVERT: B4 54 ILE cc_start: 0.8408 (tp) cc_final: 0.8120 (pt) REVERT: B5 31 GLU cc_start: 0.6124 (tm-30) cc_final: 0.5815 (tm-30) REVERT: BD 128 ASN cc_start: 0.6753 (m-40) cc_final: 0.6191 (t0) REVERT: BD 236 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6571 (mm-30) REVERT: BD 264 ASN cc_start: 0.8541 (m110) cc_final: 0.8027 (m110) REVERT: BE 12 MET cc_start: 0.6776 (mmt) cc_final: 0.6515 (mmm) REVERT: BE 168 GLN cc_start: 0.7620 (tt0) cc_final: 0.7227 (tt0) REVERT: BF 67 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8064 (tt0) REVERT: BF 179 ASN cc_start: 0.7558 (m-40) cc_final: 0.7333 (t0) REVERT: BG 12 ILE cc_start: 0.7195 (OUTLIER) cc_final: 0.6982 (mt) REVERT: BG 38 MET cc_start: 0.6603 (mmm) cc_final: 0.6244 (mmm) REVERT: BG 59 PHE cc_start: 0.6186 (m-80) cc_final: 0.5727 (m-80) REVERT: BG 96 MET cc_start: 0.6945 (tpp) cc_final: 0.6566 (tpp) REVERT: BG 141 ILE cc_start: 0.6658 (mp) cc_final: 0.6430 (mm) REVERT: BG 153 ASP cc_start: 0.7231 (m-30) cc_final: 0.6966 (m-30) REVERT: BH 13 SER cc_start: 0.6411 (m) cc_final: 0.6145 (p) REVERT: BH 34 LEU cc_start: 0.7258 (mp) cc_final: 0.6966 (mp) REVERT: BH 41 ASP cc_start: 0.7461 (t0) cc_final: 0.7242 (t0) REVERT: BH 63 ARG cc_start: 0.7785 (mmt90) cc_final: 0.7178 (ttm110) REVERT: BJ 114 GLU cc_start: 0.0051 (OUTLIER) cc_final: -0.0495 (mt-10) REVERT: BM 89 THR cc_start: 0.8752 (t) cc_final: 0.8137 (t) REVERT: BO 38 GLN cc_start: 0.8106 (tp40) cc_final: 0.7651 (tt0) REVERT: BO 94 GLU cc_start: 0.6412 (mm-30) cc_final: 0.6190 (mm-30) REVERT: BP 34 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7450 (tt) REVERT: BP 66 ILE cc_start: 0.8114 (mp) cc_final: 0.7705 (pt) REVERT: BP 79 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8759 (pp) REVERT: BR 111 ASP cc_start: 0.7836 (t70) cc_final: 0.7351 (t0) REVERT: BS 52 LYS cc_start: 0.8246 (mtpt) cc_final: 0.8012 (mtmt) REVERT: BT 108 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7649 (mm-40) REVERT: BT 118 ASN cc_start: 0.7404 (m110) cc_final: 0.6951 (m-40) REVERT: BV 53 SER cc_start: 0.8800 (t) cc_final: 0.8557 (t) REVERT: BV 61 ASN cc_start: 0.7320 (m110) cc_final: 0.6784 (m-40) REVERT: BV 100 THR cc_start: 0.8898 (m) cc_final: 0.8601 (p) REVERT: BW 1 MET cc_start: 0.3531 (mmm) cc_final: 0.3108 (ptm) REVERT: BW 74 SER cc_start: 0.8845 (t) cc_final: 0.8601 (t) REVERT: BZ 23 ASP cc_start: 0.7910 (t0) cc_final: 0.7496 (t0) REVERT: BZ 32 LYS cc_start: 0.9200 (mmtm) cc_final: 0.8728 (mmtt) outliers start: 166 outliers final: 106 residues processed: 1149 average time/residue: 1.1878 time to fit residues: 2354.6415 Evaluate side-chains 1047 residues out of total 4740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 936 time to evaluate : 5.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AZ residue 86 ASP Chi-restraints excluded: chain B0 residue 49 VAL Chi-restraints excluded: chain B1 residue 2 LYS Chi-restraints excluded: chain B1 residue 4 ASN Chi-restraints excluded: chain B1 residue 21 LEU Chi-restraints excluded: chain B1 residue 40 THR Chi-restraints excluded: chain B1 residue 56 VAL Chi-restraints excluded: chain B2 residue 35 VAL Chi-restraints excluded: chain B2 residue 40 ASN Chi-restraints excluded: chain B4 residue 46 CYS Chi-restraints excluded: chain B8 residue 3 VAL Chi-restraints excluded: chain BD residue 10 SER Chi-restraints excluded: chain BD residue 229 ASP Chi-restraints excluded: chain BD residue 255 LEU Chi-restraints excluded: chain BE residue 5 ILE Chi-restraints excluded: chain BE residue 6 LEU Chi-restraints excluded: chain BE residue 40 THR Chi-restraints excluded: chain BE residue 61 SER Chi-restraints excluded: chain BE residue 98 LYS Chi-restraints excluded: chain BE residue 160 LEU Chi-restraints excluded: chain BE residue 187 LEU Chi-restraints excluded: chain BF residue 37 ILE Chi-restraints excluded: chain BF residue 67 GLN Chi-restraints excluded: chain BF residue 80 SER Chi-restraints excluded: chain BF residue 120 ASP Chi-restraints excluded: chain BF residue 124 ILE Chi-restraints excluded: chain BF residue 174 THR Chi-restraints excluded: chain BG residue 12 ILE Chi-restraints excluded: chain BG residue 44 VAL Chi-restraints excluded: chain BG residue 71 LYS Chi-restraints excluded: chain BG residue 132 ILE Chi-restraints excluded: chain BG residue 148 LYS Chi-restraints excluded: chain BH residue 19 LEU Chi-restraints excluded: chain BH residue 24 THR Chi-restraints excluded: chain BH residue 44 ILE Chi-restraints excluded: chain BH residue 51 LEU Chi-restraints excluded: chain BH residue 69 THR Chi-restraints excluded: chain BH residue 70 ARG Chi-restraints excluded: chain BH residue 108 VAL Chi-restraints excluded: chain BH residue 145 ILE Chi-restraints excluded: chain BJ residue 114 GLU Chi-restraints excluded: chain BK residue 56 VAL Chi-restraints excluded: chain BK residue 135 MET Chi-restraints excluded: chain BM residue 37 LEU Chi-restraints excluded: chain BM residue 44 THR Chi-restraints excluded: chain BM residue 91 LEU Chi-restraints excluded: chain BN residue 34 ASN Chi-restraints excluded: chain BN residue 38 VAL Chi-restraints excluded: chain BN residue 65 THR Chi-restraints excluded: chain BN residue 72 SER Chi-restraints excluded: chain BO residue 6 LEU Chi-restraints excluded: chain BO residue 12 SER Chi-restraints excluded: chain BO residue 25 SER Chi-restraints excluded: chain BO residue 27 ASN Chi-restraints excluded: chain BO residue 57 LEU Chi-restraints excluded: chain BO residue 67 THR Chi-restraints excluded: chain BO residue 89 THR Chi-restraints excluded: chain BO residue 92 THR Chi-restraints excluded: chain BO residue 101 VAL Chi-restraints excluded: chain BP residue 3 LEU Chi-restraints excluded: chain BP residue 27 VAL Chi-restraints excluded: chain BP residue 32 PHE Chi-restraints excluded: chain BP residue 34 ILE Chi-restraints excluded: chain BP residue 47 ILE Chi-restraints excluded: chain BP residue 79 LEU Chi-restraints excluded: chain BP residue 85 SER Chi-restraints excluded: chain BP residue 102 VAL Chi-restraints excluded: chain BP residue 132 VAL Chi-restraints excluded: chain BQ residue 5 LYS Chi-restraints excluded: chain BQ residue 21 THR Chi-restraints excluded: chain BQ residue 22 THR Chi-restraints excluded: chain BQ residue 57 HIS Chi-restraints excluded: chain BQ residue 70 VAL Chi-restraints excluded: chain BQ residue 76 ASN Chi-restraints excluded: chain BQ residue 89 THR Chi-restraints excluded: chain BR residue 5 THR Chi-restraints excluded: chain BR residue 40 ILE Chi-restraints excluded: chain BR residue 47 ASP Chi-restraints excluded: chain BR residue 62 ASP Chi-restraints excluded: chain BR residue 63 LEU Chi-restraints excluded: chain BR residue 94 VAL Chi-restraints excluded: chain BR residue 103 HIS Chi-restraints excluded: chain BR residue 105 ARG Chi-restraints excluded: chain BR residue 106 VAL Chi-restraints excluded: chain BR residue 115 GLU Chi-restraints excluded: chain BS residue 27 ASP Chi-restraints excluded: chain BS residue 33 VAL Chi-restraints excluded: chain BS residue 36 VAL Chi-restraints excluded: chain BS residue 61 THR Chi-restraints excluded: chain BS residue 76 THR Chi-restraints excluded: chain BS residue 116 ILE Chi-restraints excluded: chain BT residue 63 THR Chi-restraints excluded: chain BT residue 83 LEU Chi-restraints excluded: chain BT residue 104 THR Chi-restraints excluded: chain BU residue 22 ILE Chi-restraints excluded: chain BU residue 33 VAL Chi-restraints excluded: chain BV residue 20 VAL Chi-restraints excluded: chain BV residue 33 VAL Chi-restraints excluded: chain BV residue 55 ILE Chi-restraints excluded: chain BV residue 70 VAL Chi-restraints excluded: chain BV residue 72 SER Chi-restraints excluded: chain BV residue 106 VAL Chi-restraints excluded: chain BW residue 56 ILE Chi-restraints excluded: chain BW residue 63 SER Chi-restraints excluded: chain BW residue 81 VAL Chi-restraints excluded: chain BX residue 33 VAL Chi-restraints excluded: chain BX residue 81 VAL Chi-restraints excluded: chain BX residue 93 VAL Chi-restraints excluded: chain BZ residue 20 ASN Chi-restraints excluded: chain BZ residue 40 THR Chi-restraints excluded: chain BZ residue 88 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 508 optimal weight: 10.0000 chunk 284 optimal weight: 4.9990 chunk 761 optimal weight: 4.9990 chunk 623 optimal weight: 20.0000 chunk 252 optimal weight: 20.0000 chunk 917 optimal weight: 9.9990 chunk 990 optimal weight: 20.0000 chunk 816 optimal weight: 7.9990 chunk 909 optimal weight: 10.0000 chunk 312 optimal weight: 5.9990 chunk 735 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 37 HIS ** B3 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3 20 ASN B3 47 GLN B4 19 HIS ** B5 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 45 HIS B7 35 ASN B7 38 GLN B7 64 ASN ** B8 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B8 36 GLN BD 11 ASN ** BD 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 199 GLN BD 200 HIS ** BD 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BE 14 GLN ** BE 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 189 HIS ** BG 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 49 ASN ** BH 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BH 107 ASN BJ 66 GLN ** BJ 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BM 59 ASN ** BM 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BM 96 ASN ** BN 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BO 35 HIS ** BP 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BQ 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BR 64 ASN BR 103 HIS BS 5 GLN BS 15 GLN BS 39 ASN BT 52 GLN ** BU 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 147759 Z= 0.304 Angle : 0.715 16.434 221796 Z= 0.367 Chirality : 0.038 0.575 27275 Planarity : 0.005 0.065 11493 Dihedral : 24.620 179.569 78907 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.79 % Allowed : 6.00 % Favored : 93.21 % Rotamer: Outliers : 7.67 % Allowed : 19.69 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 1.79 % 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: -0.48 (0.11), residues: 5563 helix: 0.98 (0.12), residues: 1701 sheet: -1.91 (0.16), residues: 896 loop : -0.49 (0.12), residues: 2966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.004 TRPBD 250 HIS 0.028 0.003 HISBR 103 PHE 0.033 0.003 PHEBG 99 TYR 0.025 0.003 TYRBT 76 ARG 0.010 0.001 ARGBN 97 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1248 residues out of total 4740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1038 time to evaluate : 5.453 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: B0 10 LYS cc_start: 0.8282 (mtpp) cc_final: 0.7975 (mtpp) REVERT: B1 19 LYS cc_start: 0.8563 (tttp) cc_final: 0.8144 (mtpp) REVERT: B1 39 ASN cc_start: 0.7474 (m-40) cc_final: 0.7260 (m110) REVERT: B2 9 LYS cc_start: 0.7867 (ptmt) cc_final: 0.7338 (pttp) REVERT: B2 37 HIS cc_start: 0.8605 (OUTLIER) cc_final: 0.8278 (m-70) REVERT: B3 1 MET cc_start: 0.6397 (tpp) cc_final: 0.5493 (mmm) REVERT: B4 54 ILE cc_start: 0.8385 (tp) cc_final: 0.8134 (pt) REVERT: B6 18 PHE cc_start: 0.8963 (t80) cc_final: 0.8297 (t80) REVERT: B6 29 LEU cc_start: 0.9502 (mp) cc_final: 0.9234 (tp) REVERT: BD 128 ASN cc_start: 0.7174 (m-40) cc_final: 0.6474 (t0) REVERT: BD 236 GLU cc_start: 0.7547 (mm-30) cc_final: 0.6782 (mm-30) REVERT: BD 243 ARG cc_start: 0.8176 (ptm-80) cc_final: 0.7870 (ptm-80) REVERT: BE 133 MET cc_start: 0.8340 (mmm) cc_final: 0.8121 (mmt) REVERT: BE 140 HIS cc_start: 0.8367 (OUTLIER) cc_final: 0.7681 (p-80) REVERT: BE 168 GLN cc_start: 0.7896 (tt0) cc_final: 0.7492 (tt0) REVERT: BF 67 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8204 (tt0) REVERT: BG 12 ILE cc_start: 0.6954 (OUTLIER) cc_final: 0.6737 (mt) REVERT: BG 57 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8396 (tp) REVERT: BG 123 ASP cc_start: 0.5630 (OUTLIER) cc_final: 0.5379 (m-30) REVERT: BH 63 ARG cc_start: 0.7531 (mmt90) cc_final: 0.7127 (ttm110) REVERT: BH 115 GLU cc_start: 0.7144 (pm20) cc_final: 0.6920 (pt0) REVERT: BO 73 GLU cc_start: 0.6338 (mt-10) cc_final: 0.6101 (mt-10) REVERT: BQ 61 GLN cc_start: 0.8766 (mt0) cc_final: 0.8531 (mt0) REVERT: BR 105 ARG cc_start: 0.6863 (OUTLIER) cc_final: 0.5270 (ptp-170) REVERT: BR 111 ASP cc_start: 0.7761 (t0) cc_final: 0.6674 (t0) REVERT: BT 40 MET cc_start: 0.9135 (tpp) cc_final: 0.8914 (ttm) REVERT: BU 18 GLN cc_start: 0.6926 (pt0) cc_final: 0.6547 (pt0) REVERT: BV 21 MET cc_start: 0.8376 (mmm) cc_final: 0.8031 (tpp) REVERT: BV 63 GLU cc_start: 0.6667 (mp0) cc_final: 0.6303 (pm20) REVERT: BW 1 MET cc_start: 0.4110 (mmm) cc_final: 0.3029 (ptm) REVERT: BW 9 LYS cc_start: 0.8706 (mttt) cc_final: 0.8477 (mtmt) REVERT: BW 38 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7987 (mm-30) REVERT: BZ 23 ASP cc_start: 0.8245 (t0) cc_final: 0.7976 (t0) outliers start: 210 outliers final: 148 residues processed: 1134 average time/residue: 1.2461 time to fit residues: 2462.9717 Evaluate side-chains 1079 residues out of total 4740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 924 time to evaluate : 5.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AZ residue 86 ASP Chi-restraints excluded: chain B0 residue 13 THR Chi-restraints excluded: chain B0 residue 22 MET Chi-restraints excluded: chain B0 residue 38 ILE Chi-restraints excluded: chain B0 residue 40 VAL Chi-restraints excluded: chain B1 residue 4 ASN Chi-restraints excluded: chain B1 residue 8 ASP Chi-restraints excluded: chain B1 residue 40 THR Chi-restraints excluded: chain B1 residue 56 VAL Chi-restraints excluded: chain B1 residue 62 ILE Chi-restraints excluded: chain B2 residue 35 VAL Chi-restraints excluded: chain B2 residue 36 VAL Chi-restraints excluded: chain B2 residue 37 HIS Chi-restraints excluded: chain B4 residue 24 VAL Chi-restraints excluded: chain B4 residue 27 MET Chi-restraints excluded: chain B4 residue 46 CYS Chi-restraints excluded: chain B5 residue 5 ILE Chi-restraints excluded: chain B5 residue 18 ILE Chi-restraints excluded: chain B6 residue 4 THR Chi-restraints excluded: chain B6 residue 30 VAL Chi-restraints excluded: chain B6 residue 43 SER Chi-restraints excluded: chain B7 residue 30 SER Chi-restraints excluded: chain B7 residue 54 ASP Chi-restraints excluded: chain B7 residue 59 LYS Chi-restraints excluded: chain B8 residue 3 VAL Chi-restraints excluded: chain B8 residue 7 VAL Chi-restraints excluded: chain BD residue 10 SER Chi-restraints excluded: chain BD residue 26 THR Chi-restraints excluded: chain BD residue 49 LEU Chi-restraints excluded: chain BD residue 223 SER Chi-restraints excluded: chain BD residue 229 ASP Chi-restraints excluded: chain BD residue 254 THR Chi-restraints excluded: chain BD residue 255 LEU Chi-restraints excluded: chain BE residue 5 ILE Chi-restraints excluded: chain BE residue 6 LEU Chi-restraints excluded: chain BE residue 16 PHE Chi-restraints excluded: chain BE residue 40 THR Chi-restraints excluded: chain BE residue 61 SER Chi-restraints excluded: chain BE residue 86 VAL Chi-restraints excluded: chain BE residue 98 LYS Chi-restraints excluded: chain BE residue 134 SER Chi-restraints excluded: chain BE residue 140 HIS Chi-restraints excluded: chain BE residue 187 LEU Chi-restraints excluded: chain BE residue 199 LEU Chi-restraints excluded: chain BF residue 37 ILE Chi-restraints excluded: chain BF residue 67 GLN Chi-restraints excluded: chain BF residue 80 SER Chi-restraints excluded: chain BF residue 124 ILE Chi-restraints excluded: chain BF residue 174 THR Chi-restraints excluded: chain BF residue 192 LEU Chi-restraints excluded: chain BG residue 12 ILE Chi-restraints excluded: chain BG residue 44 VAL Chi-restraints excluded: chain BG residue 57 LEU Chi-restraints excluded: chain BG residue 68 THR Chi-restraints excluded: chain BG residue 71 LYS Chi-restraints excluded: chain BG residue 90 THR Chi-restraints excluded: chain BG residue 108 LEU Chi-restraints excluded: chain BG residue 123 ASP Chi-restraints excluded: chain BG residue 148 LYS Chi-restraints excluded: chain BG residue 155 VAL Chi-restraints excluded: chain BH residue 19 LEU Chi-restraints excluded: chain BH residue 24 THR Chi-restraints excluded: chain BH residue 51 LEU Chi-restraints excluded: chain BH residue 69 THR Chi-restraints excluded: chain BH residue 70 ARG Chi-restraints excluded: chain BH residue 88 LEU Chi-restraints excluded: chain BH residue 93 VAL Chi-restraints excluded: chain BH residue 105 VAL Chi-restraints excluded: chain BH residue 108 VAL Chi-restraints excluded: chain BH residue 145 ILE Chi-restraints excluded: chain BJ residue 89 VAL Chi-restraints excluded: chain BK residue 56 VAL Chi-restraints excluded: chain BM residue 19 VAL Chi-restraints excluded: chain BM residue 46 THR Chi-restraints excluded: chain BM residue 53 ASP Chi-restraints excluded: chain BM residue 65 LEU Chi-restraints excluded: chain BM residue 91 LEU Chi-restraints excluded: chain BN residue 10 VAL Chi-restraints excluded: chain BN residue 34 ASN Chi-restraints excluded: chain BN residue 38 VAL Chi-restraints excluded: chain BN residue 47 THR Chi-restraints excluded: chain BN residue 51 VAL Chi-restraints excluded: chain BN residue 61 VAL Chi-restraints excluded: chain BN residue 65 THR Chi-restraints excluded: chain BN residue 114 ILE Chi-restraints excluded: chain BO residue 12 SER Chi-restraints excluded: chain BO residue 25 SER Chi-restraints excluded: chain BO residue 27 ASN Chi-restraints excluded: chain BO residue 57 LEU Chi-restraints excluded: chain BO residue 61 LEU Chi-restraints excluded: chain BO residue 67 THR Chi-restraints excluded: chain BO residue 80 ASP Chi-restraints excluded: chain BO residue 89 THR Chi-restraints excluded: chain BO residue 92 THR Chi-restraints excluded: chain BO residue 101 VAL Chi-restraints excluded: chain BO residue 105 LEU Chi-restraints excluded: chain BP residue 25 THR Chi-restraints excluded: chain BP residue 27 VAL Chi-restraints excluded: chain BP residue 32 PHE Chi-restraints excluded: chain BP residue 34 ILE Chi-restraints excluded: chain BP residue 47 ILE Chi-restraints excluded: chain BP residue 54 MET Chi-restraints excluded: chain BP residue 71 SER Chi-restraints excluded: chain BP residue 85 SER Chi-restraints excluded: chain BP residue 102 VAL Chi-restraints excluded: chain BQ residue 5 LYS Chi-restraints excluded: chain BQ residue 9 THR Chi-restraints excluded: chain BQ residue 21 THR Chi-restraints excluded: chain BQ residue 33 THR Chi-restraints excluded: chain BQ residue 49 THR Chi-restraints excluded: chain BQ residue 55 ASP Chi-restraints excluded: chain BQ residue 70 VAL Chi-restraints excluded: chain BQ residue 76 ASN Chi-restraints excluded: chain BQ residue 89 THR Chi-restraints excluded: chain BQ residue 120 VAL Chi-restraints excluded: chain BR residue 40 ILE Chi-restraints excluded: chain BR residue 47 ASP Chi-restraints excluded: chain BR residue 62 ASP Chi-restraints excluded: chain BR residue 63 LEU Chi-restraints excluded: chain BR residue 77 VAL Chi-restraints excluded: chain BR residue 80 LEU Chi-restraints excluded: chain BR residue 94 VAL Chi-restraints excluded: chain BR residue 103 HIS Chi-restraints excluded: chain BR residue 105 ARG Chi-restraints excluded: chain BS residue 27 ASP Chi-restraints excluded: chain BS residue 29 LEU Chi-restraints excluded: chain BS residue 33 VAL Chi-restraints excluded: chain BS residue 36 VAL Chi-restraints excluded: chain BS residue 116 ILE Chi-restraints excluded: chain BT residue 31 LEU Chi-restraints excluded: chain BT residue 49 ASP Chi-restraints excluded: chain BT residue 63 THR Chi-restraints excluded: chain BT residue 83 LEU Chi-restraints excluded: chain BT residue 94 MET Chi-restraints excluded: chain BT residue 104 THR Chi-restraints excluded: chain BU residue 22 ILE Chi-restraints excluded: chain BU residue 33 VAL Chi-restraints excluded: chain BV residue 24 ILE Chi-restraints excluded: chain BV residue 33 VAL Chi-restraints excluded: chain BV residue 35 ILE Chi-restraints excluded: chain BV residue 67 ASN Chi-restraints excluded: chain BV residue 70 VAL Chi-restraints excluded: chain BV residue 104 THR Chi-restraints excluded: chain BV residue 106 VAL Chi-restraints excluded: chain BW residue 20 LEU Chi-restraints excluded: chain BW residue 57 MET Chi-restraints excluded: chain BW residue 63 SER Chi-restraints excluded: chain BW residue 81 VAL Chi-restraints excluded: chain BX residue 33 VAL Chi-restraints excluded: chain BX residue 56 ILE Chi-restraints excluded: chain BX residue 81 VAL Chi-restraints excluded: chain BX residue 93 VAL Chi-restraints excluded: chain BZ residue 17 SER Chi-restraints excluded: chain BZ residue 40 THR Chi-restraints excluded: chain BZ residue 88 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 906 optimal weight: 10.0000 chunk 689 optimal weight: 10.0000 chunk 475 optimal weight: 10.0000 chunk 101 optimal weight: 30.0000 chunk 437 optimal weight: 10.0000 chunk 615 optimal weight: 10.0000 chunk 920 optimal weight: 5.9990 chunk 974 optimal weight: 0.3980 chunk 480 optimal weight: 10.0000 chunk 872 optimal weight: 4.9990 chunk 262 optimal weight: 9.9990 overall best weight: 6.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B0 23 ASN ** B1 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 37 HIS ** B3 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B4 19 HIS B5 16 ASN ** B5 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 199 GLN ** BD 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BG 37 ASN ** BG 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 49 ASN ** BH 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BH 107 ASN BM 54 HIS BM 59 ASN BM 96 ASN BM 124 ASN ** BN 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BO 78 ASN BO 106 ASN ** BP 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 27 ASN ** BQ 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BR 103 HIS BS 5 GLN BS 39 ASN BT 52 GLN ** BT 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BU 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BU 81 ASN BV 61 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 147759 Z= 0.280 Angle : 0.693 13.253 221796 Z= 0.356 Chirality : 0.037 0.343 27275 Planarity : 0.005 0.074 11493 Dihedral : 24.736 179.589 78907 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.79 % Allowed : 5.59 % Favored : 93.62 % Rotamer: Outliers : 8.84 % Allowed : 21.95 % Favored : 69.21 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 1.79 % 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: -0.37 (0.11), residues: 5563 helix: 1.37 (0.13), residues: 1729 sheet: -1.63 (0.16), residues: 910 loop : -0.72 (0.12), residues: 2924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRPB0 29 HIS 0.027 0.002 HISB2 37 PHE 0.029 0.003 PHEBF 34 TYR 0.023 0.002 TYRB5 35 ARG 0.027 0.001 ARGBN 88 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1231 residues out of total 4740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 989 time to evaluate : 4.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: AZ 80 MET cc_start: 0.7467 (tpp) cc_final: 0.7189 (tpt) REVERT: B0 33 LEU cc_start: 0.9425 (mp) cc_final: 0.9221 (mp) REVERT: B1 19 LYS cc_start: 0.8442 (tttp) cc_final: 0.8164 (mtpp) REVERT: B2 9 LYS cc_start: 0.7976 (ptmt) cc_final: 0.7480 (pttp) REVERT: B8 35 LYS cc_start: 0.8628 (ttmt) cc_final: 0.8424 (ttmt) REVERT: BD 24 ILE cc_start: 0.8985 (mm) cc_final: 0.8510 (tp) REVERT: BD 101 LYS cc_start: 0.9069 (mttt) cc_final: 0.8243 (mtmm) REVERT: BD 128 ASN cc_start: 0.7387 (m-40) cc_final: 0.6669 (t0) REVERT: BD 236 GLU cc_start: 0.7417 (mm-30) cc_final: 0.6802 (mm-30) REVERT: BD 243 ARG cc_start: 0.8349 (ptm-80) cc_final: 0.7822 (ptm-80) REVERT: BE 37 GLN cc_start: 0.8606 (tm-30) cc_final: 0.8043 (tm-30) REVERT: BE 140 HIS cc_start: 0.8494 (OUTLIER) cc_final: 0.7972 (p-80) REVERT: BF 75 GLN cc_start: 0.7635 (mm-40) cc_final: 0.7425 (mm-40) REVERT: BG 81 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.6152 (mm-30) REVERT: BG 123 ASP cc_start: 0.5488 (OUTLIER) cc_final: 0.5279 (m-30) REVERT: BG 141 ILE cc_start: 0.7171 (mp) cc_final: 0.6858 (mm) REVERT: BH 49 ASN cc_start: 0.7561 (m-40) cc_final: 0.7311 (m110) REVERT: BH 172 ARG cc_start: 0.7946 (mmm160) cc_final: 0.7656 (mmp80) REVERT: BM 18 VAL cc_start: 0.8511 (OUTLIER) cc_final: 0.8124 (p) REVERT: BM 54 HIS cc_start: 0.8949 (OUTLIER) cc_final: 0.8748 (p90) REVERT: BN 115 VAL cc_start: 0.9387 (t) cc_final: 0.9186 (p) REVERT: BO 9 SER cc_start: 0.9315 (t) cc_final: 0.9090 (p) REVERT: BP 34 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.7883 (tt) REVERT: BP 45 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7151 (mpp80) REVERT: BP 56 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7593 (mmm160) REVERT: BQ 14 LYS cc_start: 0.8299 (tttp) cc_final: 0.8005 (tttm) REVERT: BQ 61 GLN cc_start: 0.8765 (mt0) cc_final: 0.8546 (mt0) REVERT: BR 105 ARG cc_start: 0.6624 (OUTLIER) cc_final: 0.4792 (ptp-110) REVERT: BR 111 ASP cc_start: 0.8024 (t70) cc_final: 0.7212 (t0) REVERT: BS 102 TYR cc_start: 0.8401 (p90) cc_final: 0.8098 (p90) REVERT: BV 21 MET cc_start: 0.8483 (mmm) cc_final: 0.8202 (tpp) REVERT: BV 77 ASP cc_start: 0.7785 (m-30) cc_final: 0.7565 (m-30) REVERT: BW 10 ARG cc_start: 0.8906 (ptp90) cc_final: 0.8703 (ptp-170) REVERT: BW 38 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7992 (mm-30) REVERT: BZ 23 ASP cc_start: 0.8373 (t0) cc_final: 0.8123 (t0) REVERT: BZ 66 THR cc_start: 0.9241 (p) cc_final: 0.9020 (p) outliers start: 242 outliers final: 158 residues processed: 1104 average time/residue: 1.1615 time to fit residues: 2234.3982 Evaluate side-chains 1082 residues out of total 4740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 915 time to evaluate : 5.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AZ residue 81 ASN Chi-restraints excluded: chain AZ residue 86 ASP Chi-restraints excluded: chain B0 residue 7 ILE Chi-restraints excluded: chain B0 residue 13 THR Chi-restraints excluded: chain B0 residue 50 SER Chi-restraints excluded: chain B1 residue 6 ILE Chi-restraints excluded: chain B1 residue 56 VAL Chi-restraints excluded: chain B1 residue 62 ILE Chi-restraints excluded: chain B2 residue 4 LEU Chi-restraints excluded: chain B2 residue 5 GLU Chi-restraints excluded: chain B2 residue 35 VAL Chi-restraints excluded: chain B3 residue 60 ASN Chi-restraints excluded: chain B4 residue 27 MET Chi-restraints excluded: chain B4 residue 46 CYS Chi-restraints excluded: chain B5 residue 5 ILE Chi-restraints excluded: chain B5 residue 18 ILE Chi-restraints excluded: chain B5 residue 28 ASP Chi-restraints excluded: chain B6 residue 4 THR Chi-restraints excluded: chain B6 residue 30 VAL Chi-restraints excluded: chain B6 residue 43 SER Chi-restraints excluded: chain B7 residue 17 THR Chi-restraints excluded: chain B7 residue 49 VAL Chi-restraints excluded: chain B8 residue 3 VAL Chi-restraints excluded: chain B8 residue 16 VAL Chi-restraints excluded: chain BD residue 10 SER Chi-restraints excluded: chain BD residue 26 THR Chi-restraints excluded: chain BD residue 49 LEU Chi-restraints excluded: chain BD residue 64 VAL Chi-restraints excluded: chain BD residue 78 VAL Chi-restraints excluded: chain BD residue 223 SER Chi-restraints excluded: chain BD residue 229 ASP Chi-restraints excluded: chain BD residue 254 THR Chi-restraints excluded: chain BD residue 255 LEU Chi-restraints excluded: chain BE residue 15 VAL Chi-restraints excluded: chain BE residue 16 PHE Chi-restraints excluded: chain BE residue 23 ILE Chi-restraints excluded: chain BE residue 26 THR Chi-restraints excluded: chain BE residue 40 THR Chi-restraints excluded: chain BE residue 61 SER Chi-restraints excluded: chain BE residue 91 TYR Chi-restraints excluded: chain BE residue 98 LYS Chi-restraints excluded: chain BE residue 111 THR Chi-restraints excluded: chain BE residue 134 SER Chi-restraints excluded: chain BE residue 140 HIS Chi-restraints excluded: chain BE residue 177 VAL Chi-restraints excluded: chain BE residue 187 LEU Chi-restraints excluded: chain BE residue 188 ILE Chi-restraints excluded: chain BE residue 199 LEU Chi-restraints excluded: chain BF residue 17 ILE Chi-restraints excluded: chain BF residue 37 ILE Chi-restraints excluded: chain BF residue 80 SER Chi-restraints excluded: chain BF residue 110 ILE Chi-restraints excluded: chain BF residue 123 ILE Chi-restraints excluded: chain BF residue 126 LEU Chi-restraints excluded: chain BF residue 173 VAL Chi-restraints excluded: chain BF residue 174 THR Chi-restraints excluded: chain BG residue 44 VAL Chi-restraints excluded: chain BG residue 71 LYS Chi-restraints excluded: chain BG residue 81 GLU Chi-restraints excluded: chain BG residue 100 LEU Chi-restraints excluded: chain BG residue 108 LEU Chi-restraints excluded: chain BG residue 123 ASP Chi-restraints excluded: chain BG residue 148 LYS Chi-restraints excluded: chain BG residue 155 VAL Chi-restraints excluded: chain BH residue 24 THR Chi-restraints excluded: chain BH residue 35 THR Chi-restraints excluded: chain BH residue 51 LEU Chi-restraints excluded: chain BH residue 69 THR Chi-restraints excluded: chain BH residue 70 ARG Chi-restraints excluded: chain BH residue 88 LEU Chi-restraints excluded: chain BH residue 93 VAL Chi-restraints excluded: chain BH residue 108 VAL Chi-restraints excluded: chain BH residue 145 ILE Chi-restraints excluded: chain BJ residue 89 VAL Chi-restraints excluded: chain BK residue 56 VAL Chi-restraints excluded: chain BM residue 18 VAL Chi-restraints excluded: chain BM residue 19 VAL Chi-restraints excluded: chain BM residue 44 THR Chi-restraints excluded: chain BM residue 53 ASP Chi-restraints excluded: chain BM residue 54 HIS Chi-restraints excluded: chain BM residue 55 VAL Chi-restraints excluded: chain BM residue 65 LEU Chi-restraints excluded: chain BM residue 87 SER Chi-restraints excluded: chain BM residue 89 THR Chi-restraints excluded: chain BM residue 91 LEU Chi-restraints excluded: chain BN residue 10 VAL Chi-restraints excluded: chain BN residue 21 THR Chi-restraints excluded: chain BN residue 34 ASN Chi-restraints excluded: chain BN residue 38 VAL Chi-restraints excluded: chain BN residue 51 VAL Chi-restraints excluded: chain BN residue 57 VAL Chi-restraints excluded: chain BN residue 61 VAL Chi-restraints excluded: chain BN residue 65 THR Chi-restraints excluded: chain BN residue 72 SER Chi-restraints excluded: chain BN residue 96 THR Chi-restraints excluded: chain BN residue 116 SER Chi-restraints excluded: chain BO residue 12 SER Chi-restraints excluded: chain BO residue 25 SER Chi-restraints excluded: chain BO residue 27 ASN Chi-restraints excluded: chain BO residue 30 THR Chi-restraints excluded: chain BO residue 57 LEU Chi-restraints excluded: chain BO residue 67 THR Chi-restraints excluded: chain BO residue 79 LEU Chi-restraints excluded: chain BO residue 80 ASP Chi-restraints excluded: chain BO residue 101 VAL Chi-restraints excluded: chain BP residue 27 VAL Chi-restraints excluded: chain BP residue 29 PHE Chi-restraints excluded: chain BP residue 32 PHE Chi-restraints excluded: chain BP residue 34 ILE Chi-restraints excluded: chain BP residue 45 ARG Chi-restraints excluded: chain BP residue 47 ILE Chi-restraints excluded: chain BP residue 54 MET Chi-restraints excluded: chain BP residue 55 THR Chi-restraints excluded: chain BP residue 56 ARG Chi-restraints excluded: chain BP residue 71 SER Chi-restraints excluded: chain BP residue 75 THR Chi-restraints excluded: chain BP residue 85 SER Chi-restraints excluded: chain BP residue 102 VAL Chi-restraints excluded: chain BP residue 127 ILE Chi-restraints excluded: chain BQ residue 21 THR Chi-restraints excluded: chain BQ residue 22 THR Chi-restraints excluded: chain BQ residue 49 THR Chi-restraints excluded: chain BQ residue 55 ASP Chi-restraints excluded: chain BQ residue 56 LEU Chi-restraints excluded: chain BQ residue 76 ASN Chi-restraints excluded: chain BQ residue 95 GLN Chi-restraints excluded: chain BR residue 5 THR Chi-restraints excluded: chain BR residue 17 ARG Chi-restraints excluded: chain BR residue 40 ILE Chi-restraints excluded: chain BR residue 47 ASP Chi-restraints excluded: chain BR residue 63 LEU Chi-restraints excluded: chain BR residue 77 VAL Chi-restraints excluded: chain BR residue 103 HIS Chi-restraints excluded: chain BR residue 105 ARG Chi-restraints excluded: chain BS residue 19 ASP Chi-restraints excluded: chain BS residue 20 LEU Chi-restraints excluded: chain BS residue 27 ASP Chi-restraints excluded: chain BS residue 29 LEU Chi-restraints excluded: chain BS residue 33 VAL Chi-restraints excluded: chain BS residue 49 VAL Chi-restraints excluded: chain BS residue 50 VAL Chi-restraints excluded: chain BS residue 61 THR Chi-restraints excluded: chain BS residue 76 THR Chi-restraints excluded: chain BS residue 116 ILE Chi-restraints excluded: chain BT residue 31 LEU Chi-restraints excluded: chain BT residue 42 SER Chi-restraints excluded: chain BT residue 63 THR Chi-restraints excluded: chain BT residue 94 MET Chi-restraints excluded: chain BT residue 104 THR Chi-restraints excluded: chain BU residue 33 VAL Chi-restraints excluded: chain BV residue 24 ILE Chi-restraints excluded: chain BV residue 33 VAL Chi-restraints excluded: chain BV residue 35 ILE Chi-restraints excluded: chain BV residue 70 VAL Chi-restraints excluded: chain BV residue 104 THR Chi-restraints excluded: chain BV residue 106 VAL Chi-restraints excluded: chain BW residue 12 VAL Chi-restraints excluded: chain BW residue 58 ASN Chi-restraints excluded: chain BW residue 63 SER Chi-restraints excluded: chain BW residue 81 VAL Chi-restraints excluded: chain BX residue 33 VAL Chi-restraints excluded: chain BX residue 79 THR Chi-restraints excluded: chain BX residue 81 VAL Chi-restraints excluded: chain BX residue 93 VAL Chi-restraints excluded: chain BZ residue 17 SER Chi-restraints excluded: chain BZ residue 40 THR Chi-restraints excluded: chain BZ residue 88 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 811 optimal weight: 0.3980 chunk 553 optimal weight: 10.0000 chunk 14 optimal weight: 30.0000 chunk 725 optimal weight: 20.0000 chunk 402 optimal weight: 0.6980 chunk 831 optimal weight: 10.0000 chunk 673 optimal weight: 10.0000 chunk 1 optimal weight: 30.0000 chunk 497 optimal weight: 10.0000 chunk 874 optimal weight: 0.8980 chunk 245 optimal weight: 20.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 199 GLN ** BD 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 50 GLN ** BE 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BN 45 GLN ** BQ 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 81 GLN BR 103 HIS BS 5 GLN BS 15 GLN BS 39 ASN BT 52 GLN ** BT 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BU 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BU 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 59 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 147759 Z= 0.213 Angle : 0.645 12.871 221796 Z= 0.330 Chirality : 0.035 0.361 27275 Planarity : 0.004 0.083 11493 Dihedral : 24.734 179.183 78907 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.65 % Allowed : 6.00 % Favored : 93.35 % Rotamer: Outliers : 8.18 % Allowed : 24.73 % Favored : 67.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 1.79 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.11), residues: 5563 helix: 1.55 (0.13), residues: 1744 sheet: -1.46 (0.16), residues: 906 loop : -0.78 (0.12), residues: 2913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPBD 213 HIS 0.033 0.002 HISBM 54 PHE 0.032 0.002 PHEB3 42 TYR 0.022 0.002 TYRB5 35 ARG 0.011 0.001 ARGBO 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1183 residues out of total 4740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 959 time to evaluate : 5.623 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: B1 19 LYS cc_start: 0.8310 (tttp) cc_final: 0.8077 (mtpp) REVERT: B2 9 LYS cc_start: 0.8003 (ptmt) cc_final: 0.7488 (pttp) REVERT: B2 18 ASP cc_start: 0.8042 (p0) cc_final: 0.7630 (p0) REVERT: B4 36 MET cc_start: 0.8453 (tmm) cc_final: 0.7891 (tmm) REVERT: B4 54 ILE cc_start: 0.8782 (pt) cc_final: 0.8578 (pt) REVERT: B8 35 LYS cc_start: 0.8608 (ttmt) cc_final: 0.8390 (ttmt) REVERT: BD 24 ILE cc_start: 0.8989 (mm) cc_final: 0.8558 (tp) REVERT: BD 101 LYS cc_start: 0.9108 (mttt) cc_final: 0.8013 (mtmm) REVERT: BD 128 ASN cc_start: 0.7449 (m-40) cc_final: 0.6984 (m-40) REVERT: BD 236 GLU cc_start: 0.7317 (mm-30) cc_final: 0.6766 (mm-30) REVERT: BD 243 ARG cc_start: 0.7981 (ptm-80) cc_final: 0.7675 (ptm-80) REVERT: BE 37 GLN cc_start: 0.8527 (tm-30) cc_final: 0.7912 (tm-30) REVERT: BE 120 GLN cc_start: 0.8479 (mt0) cc_final: 0.7101 (mt0) REVERT: BE 140 HIS cc_start: 0.8496 (OUTLIER) cc_final: 0.8052 (p-80) REVERT: BF 37 ILE cc_start: 0.9515 (OUTLIER) cc_final: 0.9238 (tp) REVERT: BG 32 GLU cc_start: 0.7248 (tp30) cc_final: 0.6890 (tp30) REVERT: BG 37 ASN cc_start: 0.7340 (m110) cc_final: 0.7037 (t0) REVERT: BG 97 TYR cc_start: 0.6575 (m-80) cc_final: 0.6025 (m-80) REVERT: BG 123 ASP cc_start: 0.5306 (OUTLIER) cc_final: 0.5053 (m-30) REVERT: BG 129 THR cc_start: 0.7328 (m) cc_final: 0.7099 (p) REVERT: BM 18 VAL cc_start: 0.8593 (t) cc_final: 0.8242 (p) REVERT: BM 104 LEU cc_start: 0.8661 (tp) cc_final: 0.8414 (tp) REVERT: BN 34 ASN cc_start: 0.8810 (OUTLIER) cc_final: 0.8577 (p0) REVERT: BN 38 VAL cc_start: 0.9247 (OUTLIER) cc_final: 0.9043 (p) REVERT: BN 76 TYR cc_start: 0.7896 (m-80) cc_final: 0.7616 (m-80) REVERT: BN 115 VAL cc_start: 0.9422 (t) cc_final: 0.9216 (p) REVERT: BO 95 LEU cc_start: 0.8019 (tp) cc_final: 0.7772 (tp) REVERT: BP 34 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.7954 (tt) REVERT: BP 45 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7033 (mpp80) REVERT: BP 106 ILE cc_start: 0.8468 (tp) cc_final: 0.8076 (tt) REVERT: BQ 14 LYS cc_start: 0.8324 (tttp) cc_final: 0.8077 (tttm) REVERT: BR 105 ARG cc_start: 0.6515 (OUTLIER) cc_final: 0.4590 (ptp-110) REVERT: BR 111 ASP cc_start: 0.7900 (t70) cc_final: 0.7682 (t0) REVERT: BZ 23 ASP cc_start: 0.8355 (t0) cc_final: 0.8144 (t0) outliers start: 224 outliers final: 164 residues processed: 1064 average time/residue: 1.1197 time to fit residues: 2090.1678 Evaluate side-chains 1086 residues out of total 4740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 914 time to evaluate : 5.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AZ residue 86 ASP Chi-restraints excluded: chain B0 residue 13 THR Chi-restraints excluded: chain B0 residue 50 SER Chi-restraints excluded: chain B1 residue 6 ILE Chi-restraints excluded: chain B1 residue 56 VAL Chi-restraints excluded: chain B1 residue 62 ILE Chi-restraints excluded: chain B2 residue 28 LEU Chi-restraints excluded: chain B2 residue 35 VAL Chi-restraints excluded: chain B3 residue 33 VAL Chi-restraints excluded: chain B3 residue 60 ASN Chi-restraints excluded: chain B4 residue 24 VAL Chi-restraints excluded: chain B4 residue 53 ASP Chi-restraints excluded: chain B5 residue 18 ILE Chi-restraints excluded: chain B5 residue 28 ASP Chi-restraints excluded: chain B6 residue 4 THR Chi-restraints excluded: chain B6 residue 30 VAL Chi-restraints excluded: chain B6 residue 43 SER Chi-restraints excluded: chain B7 residue 17 THR Chi-restraints excluded: chain B7 residue 30 SER Chi-restraints excluded: chain B7 residue 49 VAL Chi-restraints excluded: chain B7 residue 59 LYS Chi-restraints excluded: chain B8 residue 3 VAL Chi-restraints excluded: chain B8 residue 7 VAL Chi-restraints excluded: chain B8 residue 16 VAL Chi-restraints excluded: chain BD residue 10 SER Chi-restraints excluded: chain BD residue 49 LEU Chi-restraints excluded: chain BD residue 78 VAL Chi-restraints excluded: chain BD residue 104 ILE Chi-restraints excluded: chain BD residue 223 SER Chi-restraints excluded: chain BD residue 229 ASP Chi-restraints excluded: chain BD residue 255 LEU Chi-restraints excluded: chain BE residue 6 LEU Chi-restraints excluded: chain BE residue 13 THR Chi-restraints excluded: chain BE residue 15 VAL Chi-restraints excluded: chain BE residue 16 PHE Chi-restraints excluded: chain BE residue 23 ILE Chi-restraints excluded: chain BE residue 26 THR Chi-restraints excluded: chain BE residue 40 THR Chi-restraints excluded: chain BE residue 50 GLN Chi-restraints excluded: chain BE residue 61 SER Chi-restraints excluded: chain BE residue 91 TYR Chi-restraints excluded: chain BE residue 98 LYS Chi-restraints excluded: chain BE residue 106 GLU Chi-restraints excluded: chain BE residue 111 THR Chi-restraints excluded: chain BE residue 134 SER Chi-restraints excluded: chain BE residue 140 HIS Chi-restraints excluded: chain BE residue 187 LEU Chi-restraints excluded: chain BE residue 188 ILE Chi-restraints excluded: chain BF residue 37 ILE Chi-restraints excluded: chain BF residue 77 SER Chi-restraints excluded: chain BF residue 123 ILE Chi-restraints excluded: chain BF residue 124 ILE Chi-restraints excluded: chain BF residue 125 VAL Chi-restraints excluded: chain BF residue 129 LEU Chi-restraints excluded: chain BF residue 132 ASP Chi-restraints excluded: chain BF residue 154 ILE Chi-restraints excluded: chain BF residue 174 THR Chi-restraints excluded: chain BG residue 44 VAL Chi-restraints excluded: chain BG residue 71 LYS Chi-restraints excluded: chain BG residue 77 PHE Chi-restraints excluded: chain BG residue 100 LEU Chi-restraints excluded: chain BG residue 123 ASP Chi-restraints excluded: chain BG residue 132 ILE Chi-restraints excluded: chain BG residue 148 LYS Chi-restraints excluded: chain BG residue 155 VAL Chi-restraints excluded: chain BH residue 24 THR Chi-restraints excluded: chain BH residue 35 THR Chi-restraints excluded: chain BH residue 51 LEU Chi-restraints excluded: chain BH residue 70 ARG Chi-restraints excluded: chain BH residue 88 LEU Chi-restraints excluded: chain BH residue 93 VAL Chi-restraints excluded: chain BH residue 103 LYS Chi-restraints excluded: chain BH residue 108 VAL Chi-restraints excluded: chain BH residue 145 ILE Chi-restraints excluded: chain BJ residue 43 LYS Chi-restraints excluded: chain BJ residue 89 VAL Chi-restraints excluded: chain BK residue 56 VAL Chi-restraints excluded: chain BM residue 12 ILE Chi-restraints excluded: chain BM residue 19 VAL Chi-restraints excluded: chain BM residue 46 THR Chi-restraints excluded: chain BM residue 55 VAL Chi-restraints excluded: chain BM residue 65 LEU Chi-restraints excluded: chain BM residue 89 THR Chi-restraints excluded: chain BM residue 91 LEU Chi-restraints excluded: chain BN residue 2 ILE Chi-restraints excluded: chain BN residue 10 VAL Chi-restraints excluded: chain BN residue 34 ASN Chi-restraints excluded: chain BN residue 38 VAL Chi-restraints excluded: chain BN residue 45 GLN Chi-restraints excluded: chain BN residue 51 VAL Chi-restraints excluded: chain BN residue 57 VAL Chi-restraints excluded: chain BN residue 61 VAL Chi-restraints excluded: chain BN residue 65 THR Chi-restraints excluded: chain BN residue 72 SER Chi-restraints excluded: chain BN residue 114 ILE Chi-restraints excluded: chain BN residue 116 SER Chi-restraints excluded: chain BO residue 12 SER Chi-restraints excluded: chain BO residue 25 SER Chi-restraints excluded: chain BO residue 27 ASN Chi-restraints excluded: chain BO residue 57 LEU Chi-restraints excluded: chain BO residue 67 THR Chi-restraints excluded: chain BO residue 69 ILE Chi-restraints excluded: chain BO residue 80 ASP Chi-restraints excluded: chain BO residue 89 THR Chi-restraints excluded: chain BO residue 94 GLU Chi-restraints excluded: chain BO residue 105 LEU Chi-restraints excluded: chain BO residue 117 LEU Chi-restraints excluded: chain BP residue 27 VAL Chi-restraints excluded: chain BP residue 29 PHE Chi-restraints excluded: chain BP residue 32 PHE Chi-restraints excluded: chain BP residue 34 ILE Chi-restraints excluded: chain BP residue 45 ARG Chi-restraints excluded: chain BP residue 47 ILE Chi-restraints excluded: chain BP residue 54 MET Chi-restraints excluded: chain BP residue 55 THR Chi-restraints excluded: chain BP residue 71 SER Chi-restraints excluded: chain BP residue 75 THR Chi-restraints excluded: chain BP residue 102 VAL Chi-restraints excluded: chain BP residue 125 LEU Chi-restraints excluded: chain BP residue 127 ILE Chi-restraints excluded: chain BQ residue 17 LEU Chi-restraints excluded: chain BQ residue 21 THR Chi-restraints excluded: chain BQ residue 33 THR Chi-restraints excluded: chain BQ residue 49 THR Chi-restraints excluded: chain BQ residue 56 LEU Chi-restraints excluded: chain BQ residue 76 ASN Chi-restraints excluded: chain BQ residue 89 THR Chi-restraints excluded: chain BQ residue 101 ILE Chi-restraints excluded: chain BR residue 17 ARG Chi-restraints excluded: chain BR residue 40 ILE Chi-restraints excluded: chain BR residue 47 ASP Chi-restraints excluded: chain BR residue 63 LEU Chi-restraints excluded: chain BR residue 77 VAL Chi-restraints excluded: chain BR residue 101 LEU Chi-restraints excluded: chain BR residue 103 HIS Chi-restraints excluded: chain BR residue 105 ARG Chi-restraints excluded: chain BR residue 115 GLU Chi-restraints excluded: chain BS residue 20 LEU Chi-restraints excluded: chain BS residue 29 LEU Chi-restraints excluded: chain BS residue 33 VAL Chi-restraints excluded: chain BS residue 36 VAL Chi-restraints excluded: chain BS residue 50 VAL Chi-restraints excluded: chain BS residue 76 THR Chi-restraints excluded: chain BS residue 116 ILE Chi-restraints excluded: chain BT residue 31 LEU Chi-restraints excluded: chain BT residue 49 ASP Chi-restraints excluded: chain BT residue 63 THR Chi-restraints excluded: chain BT residue 77 SER Chi-restraints excluded: chain BT residue 83 LEU Chi-restraints excluded: chain BT residue 94 MET Chi-restraints excluded: chain BT residue 104 THR Chi-restraints excluded: chain BU residue 33 VAL Chi-restraints excluded: chain BV residue 12 ILE Chi-restraints excluded: chain BV residue 24 ILE Chi-restraints excluded: chain BV residue 33 VAL Chi-restraints excluded: chain BV residue 35 ILE Chi-restraints excluded: chain BV residue 67 ASN Chi-restraints excluded: chain BV residue 70 VAL Chi-restraints excluded: chain BV residue 101 SER Chi-restraints excluded: chain BV residue 104 THR Chi-restraints excluded: chain BV residue 106 VAL Chi-restraints excluded: chain BW residue 12 VAL Chi-restraints excluded: chain BW residue 58 ASN Chi-restraints excluded: chain BW residue 63 SER Chi-restraints excluded: chain BW residue 81 VAL Chi-restraints excluded: chain BX residue 33 VAL Chi-restraints excluded: chain BX residue 59 GLN Chi-restraints excluded: chain BX residue 81 VAL Chi-restraints excluded: chain BX residue 93 VAL Chi-restraints excluded: chain BZ residue 18 THR Chi-restraints excluded: chain BZ residue 40 THR Chi-restraints excluded: chain BZ residue 88 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 327 optimal weight: 9.9990 chunk 877 optimal weight: 1.9990 chunk 192 optimal weight: 50.0000 chunk 572 optimal weight: 10.0000 chunk 240 optimal weight: 20.0000 chunk 975 optimal weight: 0.9990 chunk 809 optimal weight: 6.9990 chunk 451 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 322 optimal weight: 50.0000 chunk 512 optimal weight: 10.0000 overall best weight: 5.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B5 16 ASN ** B5 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B8 36 GLN BD 11 ASN BD 58 HIS ** BD 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 19 ASN ** BE 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 49 ASN ** BN 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BO 54 GLN ** BO 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BP 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 57 HIS BQ 81 GLN ** BS 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 15 GLN ** BT 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BU 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BU 45 ASN ** BU 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BZ 48 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 147759 Z= 0.266 Angle : 0.683 12.979 221796 Z= 0.348 Chirality : 0.037 0.313 27275 Planarity : 0.005 0.117 11493 Dihedral : 24.768 179.638 78907 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.67 % Allowed : 6.24 % Favored : 93.10 % Rotamer: Outliers : 8.77 % Allowed : 25.05 % Favored : 66.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 1.79 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.12), residues: 5563 helix: 1.60 (0.13), residues: 1750 sheet: -1.45 (0.16), residues: 894 loop : -0.88 (0.12), residues: 2919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPBD 213 HIS 0.018 0.002 HISBR 103 PHE 0.032 0.002 PHEBE 53 TYR 0.019 0.002 TYRBP 74 ARG 0.009 0.001 ARGBT 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1178 residues out of total 4740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 938 time to evaluate : 5.537 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: B2 9 LYS cc_start: 0.7992 (ptmt) cc_final: 0.7513 (pttp) REVERT: B4 20 PHE cc_start: 0.8865 (t80) cc_final: 0.8515 (t80) REVERT: B4 54 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8565 (pt) REVERT: B8 4 ARG cc_start: 0.8295 (mtm110) cc_final: 0.8078 (mtm110) REVERT: BD 24 ILE cc_start: 0.9024 (mm) cc_final: 0.8599 (tp) REVERT: BD 100 GLU cc_start: 0.7740 (tp30) cc_final: 0.7440 (tp30) REVERT: BD 101 LYS cc_start: 0.8960 (mttt) cc_final: 0.7967 (mtmm) REVERT: BD 128 ASN cc_start: 0.7516 (m-40) cc_final: 0.6881 (t0) REVERT: BD 236 GLU cc_start: 0.7417 (mm-30) cc_final: 0.6852 (mm-30) REVERT: BE 37 GLN cc_start: 0.8677 (tm-30) cc_final: 0.8127 (tm-30) REVERT: BE 140 HIS cc_start: 0.8597 (OUTLIER) cc_final: 0.8179 (p-80) REVERT: BG 81 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.6417 (mm-30) REVERT: BG 129 THR cc_start: 0.7378 (m) cc_final: 0.7170 (p) REVERT: BM 6 MET cc_start: 0.6930 (pmm) cc_final: 0.6577 (pmm) REVERT: BM 97 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.7405 (p90) REVERT: BN 34 ASN cc_start: 0.8819 (OUTLIER) cc_final: 0.8591 (p0) REVERT: BN 38 VAL cc_start: 0.9257 (OUTLIER) cc_final: 0.9056 (p) REVERT: BN 76 TYR cc_start: 0.7981 (m-80) cc_final: 0.7643 (m-80) REVERT: BP 34 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.7841 (tt) REVERT: BP 45 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.7251 (mpp80) REVERT: BP 56 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7366 (tpt90) REVERT: BP 106 ILE cc_start: 0.8555 (tp) cc_final: 0.8245 (tt) REVERT: BQ 14 LYS cc_start: 0.8361 (tttp) cc_final: 0.8123 (tttm) REVERT: BQ 47 MET cc_start: 0.8947 (tpp) cc_final: 0.8557 (tpp) REVERT: BR 111 ASP cc_start: 0.7827 (t70) cc_final: 0.7611 (t0) REVERT: BV 21 MET cc_start: 0.8379 (tpp) cc_final: 0.7947 (tpp) REVERT: BX 40 MET cc_start: 0.7704 (tpt) cc_final: 0.7235 (tpt) REVERT: BZ 85 LYS cc_start: 0.9258 (mtpt) cc_final: 0.8901 (mtpp) outliers start: 240 outliers final: 185 residues processed: 1052 average time/residue: 1.2570 time to fit residues: 2344.1506 Evaluate side-chains 1092 residues out of total 4740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 898 time to evaluate : 4.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AZ residue 81 ASN Chi-restraints excluded: chain AZ residue 86 ASP Chi-restraints excluded: chain B0 residue 7 ILE Chi-restraints excluded: chain B0 residue 13 THR Chi-restraints excluded: chain B0 residue 50 SER Chi-restraints excluded: chain B1 residue 10 THR Chi-restraints excluded: chain B1 residue 43 ILE Chi-restraints excluded: chain B1 residue 56 VAL Chi-restraints excluded: chain B1 residue 62 ILE Chi-restraints excluded: chain B2 residue 4 LEU Chi-restraints excluded: chain B2 residue 35 VAL Chi-restraints excluded: chain B3 residue 24 THR Chi-restraints excluded: chain B3 residue 33 VAL Chi-restraints excluded: chain B3 residue 60 ASN Chi-restraints excluded: chain B4 residue 24 VAL Chi-restraints excluded: chain B4 residue 46 CYS Chi-restraints excluded: chain B4 residue 54 ILE Chi-restraints excluded: chain B5 residue 16 ASN Chi-restraints excluded: chain B5 residue 18 ILE Chi-restraints excluded: chain B5 residue 28 ASP Chi-restraints excluded: chain B6 residue 4 THR Chi-restraints excluded: chain B6 residue 30 VAL Chi-restraints excluded: chain B6 residue 43 SER Chi-restraints excluded: chain B7 residue 17 THR Chi-restraints excluded: chain B7 residue 30 SER Chi-restraints excluded: chain B7 residue 49 VAL Chi-restraints excluded: chain B7 residue 59 LYS Chi-restraints excluded: chain B8 residue 3 VAL Chi-restraints excluded: chain B8 residue 7 VAL Chi-restraints excluded: chain B8 residue 16 VAL Chi-restraints excluded: chain B8 residue 24 MET Chi-restraints excluded: chain BD residue 10 SER Chi-restraints excluded: chain BD residue 49 LEU Chi-restraints excluded: chain BD residue 64 VAL Chi-restraints excluded: chain BD residue 78 VAL Chi-restraints excluded: chain BD residue 80 THR Chi-restraints excluded: chain BD residue 98 ASP Chi-restraints excluded: chain BD residue 104 ILE Chi-restraints excluded: chain BD residue 229 ASP Chi-restraints excluded: chain BD residue 255 LEU Chi-restraints excluded: chain BD residue 265 LYS Chi-restraints excluded: chain BE residue 16 PHE Chi-restraints excluded: chain BE residue 23 ILE Chi-restraints excluded: chain BE residue 26 THR Chi-restraints excluded: chain BE residue 40 THR Chi-restraints excluded: chain BE residue 91 TYR Chi-restraints excluded: chain BE residue 98 LYS Chi-restraints excluded: chain BE residue 106 GLU Chi-restraints excluded: chain BE residue 108 VAL Chi-restraints excluded: chain BE residue 111 THR Chi-restraints excluded: chain BE residue 134 SER Chi-restraints excluded: chain BE residue 140 HIS Chi-restraints excluded: chain BE residue 187 LEU Chi-restraints excluded: chain BE residue 188 ILE Chi-restraints excluded: chain BE residue 192 VAL Chi-restraints excluded: chain BF residue 110 ILE Chi-restraints excluded: chain BF residue 119 ILE Chi-restraints excluded: chain BF residue 123 ILE Chi-restraints excluded: chain BF residue 124 ILE Chi-restraints excluded: chain BF residue 125 VAL Chi-restraints excluded: chain BF residue 129 LEU Chi-restraints excluded: chain BF residue 132 ASP Chi-restraints excluded: chain BF residue 154 ILE Chi-restraints excluded: chain BF residue 174 THR Chi-restraints excluded: chain BG residue 17 MET Chi-restraints excluded: chain BG residue 44 VAL Chi-restraints excluded: chain BG residue 68 THR Chi-restraints excluded: chain BG residue 71 LYS Chi-restraints excluded: chain BG residue 77 PHE Chi-restraints excluded: chain BG residue 81 GLU Chi-restraints excluded: chain BG residue 100 LEU Chi-restraints excluded: chain BG residue 108 LEU Chi-restraints excluded: chain BG residue 125 ARG Chi-restraints excluded: chain BG residue 148 LYS Chi-restraints excluded: chain BG residue 155 VAL Chi-restraints excluded: chain BH residue 24 THR Chi-restraints excluded: chain BH residue 35 THR Chi-restraints excluded: chain BH residue 51 LEU Chi-restraints excluded: chain BH residue 69 THR Chi-restraints excluded: chain BH residue 88 LEU Chi-restraints excluded: chain BH residue 93 VAL Chi-restraints excluded: chain BH residue 103 LYS Chi-restraints excluded: chain BH residue 145 ILE Chi-restraints excluded: chain BJ residue 43 LYS Chi-restraints excluded: chain BJ residue 89 VAL Chi-restraints excluded: chain BK residue 56 VAL Chi-restraints excluded: chain BM residue 12 ILE Chi-restraints excluded: chain BM residue 19 VAL Chi-restraints excluded: chain BM residue 44 THR Chi-restraints excluded: chain BM residue 46 THR Chi-restraints excluded: chain BM residue 51 THR Chi-restraints excluded: chain BM residue 55 VAL Chi-restraints excluded: chain BM residue 65 LEU Chi-restraints excluded: chain BM residue 89 THR Chi-restraints excluded: chain BM residue 91 LEU Chi-restraints excluded: chain BM residue 97 TYR Chi-restraints excluded: chain BN residue 10 VAL Chi-restraints excluded: chain BN residue 34 ASN Chi-restraints excluded: chain BN residue 38 VAL Chi-restraints excluded: chain BN residue 44 LYS Chi-restraints excluded: chain BN residue 51 VAL Chi-restraints excluded: chain BN residue 57 VAL Chi-restraints excluded: chain BN residue 61 VAL Chi-restraints excluded: chain BN residue 65 THR Chi-restraints excluded: chain BN residue 114 ILE Chi-restraints excluded: chain BN residue 116 SER Chi-restraints excluded: chain BO residue 12 SER Chi-restraints excluded: chain BO residue 25 SER Chi-restraints excluded: chain BO residue 27 ASN Chi-restraints excluded: chain BO residue 57 LEU Chi-restraints excluded: chain BO residue 67 THR Chi-restraints excluded: chain BO residue 69 ILE Chi-restraints excluded: chain BO residue 79 LEU Chi-restraints excluded: chain BO residue 80 ASP Chi-restraints excluded: chain BO residue 89 THR Chi-restraints excluded: chain BO residue 94 GLU Chi-restraints excluded: chain BO residue 105 LEU Chi-restraints excluded: chain BO residue 117 LEU Chi-restraints excluded: chain BP residue 27 VAL Chi-restraints excluded: chain BP residue 29 PHE Chi-restraints excluded: chain BP residue 32 PHE Chi-restraints excluded: chain BP residue 34 ILE Chi-restraints excluded: chain BP residue 45 ARG Chi-restraints excluded: chain BP residue 47 ILE Chi-restraints excluded: chain BP residue 54 MET Chi-restraints excluded: chain BP residue 55 THR Chi-restraints excluded: chain BP residue 56 ARG Chi-restraints excluded: chain BP residue 71 SER Chi-restraints excluded: chain BP residue 75 THR Chi-restraints excluded: chain BP residue 102 VAL Chi-restraints excluded: chain BP residue 125 LEU Chi-restraints excluded: chain BP residue 127 ILE Chi-restraints excluded: chain BQ residue 9 THR Chi-restraints excluded: chain BQ residue 17 LEU Chi-restraints excluded: chain BQ residue 21 THR Chi-restraints excluded: chain BQ residue 33 THR Chi-restraints excluded: chain BQ residue 49 THR Chi-restraints excluded: chain BQ residue 56 LEU Chi-restraints excluded: chain BQ residue 74 GLU Chi-restraints excluded: chain BQ residue 76 ASN Chi-restraints excluded: chain BQ residue 89 THR Chi-restraints excluded: chain BQ residue 101 ILE Chi-restraints excluded: chain BR residue 6 SER Chi-restraints excluded: chain BR residue 17 ARG Chi-restraints excluded: chain BR residue 40 ILE Chi-restraints excluded: chain BR residue 47 ASP Chi-restraints excluded: chain BR residue 48 VAL Chi-restraints excluded: chain BR residue 63 LEU Chi-restraints excluded: chain BR residue 77 VAL Chi-restraints excluded: chain BR residue 101 LEU Chi-restraints excluded: chain BR residue 103 HIS Chi-restraints excluded: chain BR residue 105 ARG Chi-restraints excluded: chain BR residue 115 GLU Chi-restraints excluded: chain BS residue 19 ASP Chi-restraints excluded: chain BS residue 20 LEU Chi-restraints excluded: chain BS residue 29 LEU Chi-restraints excluded: chain BS residue 33 VAL Chi-restraints excluded: chain BS residue 36 VAL Chi-restraints excluded: chain BS residue 49 VAL Chi-restraints excluded: chain BS residue 76 THR Chi-restraints excluded: chain BS residue 116 ILE Chi-restraints excluded: chain BT residue 31 LEU Chi-restraints excluded: chain BT residue 42 SER Chi-restraints excluded: chain BT residue 49 ASP Chi-restraints excluded: chain BT residue 63 THR Chi-restraints excluded: chain BT residue 77 SER Chi-restraints excluded: chain BT residue 83 LEU Chi-restraints excluded: chain BT residue 94 MET Chi-restraints excluded: chain BT residue 104 THR Chi-restraints excluded: chain BT residue 116 GLN Chi-restraints excluded: chain BU residue 33 VAL Chi-restraints excluded: chain BV residue 4 LYS Chi-restraints excluded: chain BV residue 12 ILE Chi-restraints excluded: chain BV residue 24 ILE Chi-restraints excluded: chain BV residue 33 VAL Chi-restraints excluded: chain BV residue 35 ILE Chi-restraints excluded: chain BV residue 50 VAL Chi-restraints excluded: chain BV residue 67 ASN Chi-restraints excluded: chain BV residue 70 VAL Chi-restraints excluded: chain BV residue 77 ASP Chi-restraints excluded: chain BV residue 101 SER Chi-restraints excluded: chain BV residue 104 THR Chi-restraints excluded: chain BV residue 106 VAL Chi-restraints excluded: chain BV residue 107 VAL Chi-restraints excluded: chain BW residue 12 VAL Chi-restraints excluded: chain BW residue 58 ASN Chi-restraints excluded: chain BW residue 63 SER Chi-restraints excluded: chain BW residue 81 VAL Chi-restraints excluded: chain BX residue 33 VAL Chi-restraints excluded: chain BX residue 59 GLN Chi-restraints excluded: chain BX residue 81 VAL Chi-restraints excluded: chain BX residue 93 VAL Chi-restraints excluded: chain BZ residue 40 THR Chi-restraints excluded: chain BZ residue 88 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 940 optimal weight: 10.0000 chunk 109 optimal weight: 30.0000 chunk 555 optimal weight: 20.0000 chunk 712 optimal weight: 10.0000 chunk 551 optimal weight: 10.0000 chunk 820 optimal weight: 6.9990 chunk 544 optimal weight: 50.0000 chunk 971 optimal weight: 0.9980 chunk 608 optimal weight: 10.0000 chunk 592 optimal weight: 20.0000 chunk 448 optimal weight: 20.0000 overall best weight: 7.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B7 38 GLN ** B8 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 86 ASN ** BD 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 19 ASN ** BE 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 50 GLN ** BE 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 49 ASN BH 107 ASN ** BM 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BN 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BP 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 81 GLN ** BS 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BS 15 GLN ** BT 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BU 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BU 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 59 GLN ** BX 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.5387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 147759 Z= 0.320 Angle : 0.735 13.719 221796 Z= 0.373 Chirality : 0.039 0.363 27275 Planarity : 0.005 0.096 11493 Dihedral : 24.894 179.748 78905 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 19.90 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.14 % Favored : 92.20 % Rotamer: Outliers : 9.42 % Allowed : 25.79 % Favored : 64.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 1.79 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.12), residues: 5563 helix: 1.51 (0.13), residues: 1761 sheet: -1.35 (0.17), residues: 903 loop : -1.07 (0.12), residues: 2899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRPB0 29 HIS 0.010 0.002 HISBX 64 PHE 0.020 0.002 PHEB3 22 TYR 0.056 0.002 TYRB5 17 ARG 0.010 0.001 ARGBT 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1173 residues out of total 4740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 915 time to evaluate : 5.705 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: B2 9 LYS cc_start: 0.7972 (ptmt) cc_final: 0.7490 (pttp) REVERT: B2 38 GLU cc_start: 0.8080 (pm20) cc_final: 0.7804 (pm20) REVERT: B4 20 PHE cc_start: 0.8934 (t80) cc_final: 0.8652 (t80) REVERT: B4 36 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8203 (tmm) REVERT: B4 54 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8534 (pt) REVERT: B7 6 THR cc_start: 0.9065 (m) cc_final: 0.8744 (p) REVERT: BD 24 ILE cc_start: 0.9044 (mm) cc_final: 0.8662 (tp) REVERT: BD 100 GLU cc_start: 0.7803 (tp30) cc_final: 0.7524 (tp30) REVERT: BD 101 LYS cc_start: 0.8904 (mttt) cc_final: 0.8536 (mtmm) REVERT: BD 128 ASN cc_start: 0.7624 (m-40) cc_final: 0.6973 (t0) REVERT: BD 236 GLU cc_start: 0.7456 (mm-30) cc_final: 0.6897 (mm-30) REVERT: BE 37 GLN cc_start: 0.8647 (tm-30) cc_final: 0.8398 (tm-30) REVERT: BE 140 HIS cc_start: 0.8454 (OUTLIER) cc_final: 0.7969 (p-80) REVERT: BF 34 PHE cc_start: 0.9027 (t80) cc_final: 0.8725 (t80) REVERT: BF 173 VAL cc_start: 0.8382 (OUTLIER) cc_final: 0.8162 (p) REVERT: BG 26 MET cc_start: 0.6568 (ptm) cc_final: 0.6194 (ppp) REVERT: BM 6 MET cc_start: 0.6951 (pmm) cc_final: 0.6652 (pmm) REVERT: BM 97 TYR cc_start: 0.8395 (OUTLIER) cc_final: 0.7531 (p90) REVERT: BM 136 GLN cc_start: 0.8714 (mp10) cc_final: 0.8449 (mp10) REVERT: BN 34 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8419 (p0) REVERT: BN 38 VAL cc_start: 0.9288 (OUTLIER) cc_final: 0.9064 (p) REVERT: BN 76 TYR cc_start: 0.7791 (m-80) cc_final: 0.7479 (m-80) REVERT: BP 34 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.7900 (tt) REVERT: BP 45 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7304 (mpp80) REVERT: BP 56 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7457 (tpt90) REVERT: BP 79 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8732 (pp) REVERT: BQ 14 LYS cc_start: 0.8440 (tttp) cc_final: 0.8177 (tttm) REVERT: BR 111 ASP cc_start: 0.7872 (t70) cc_final: 0.7630 (t0) REVERT: BS 52 LYS cc_start: 0.8623 (mtmt) cc_final: 0.8344 (mtmt) REVERT: BV 21 MET cc_start: 0.8364 (tpp) cc_final: 0.8119 (tpp) REVERT: BV 108 SER cc_start: 0.7999 (m) cc_final: 0.7633 (p) REVERT: BX 31 ASP cc_start: 0.7482 (t0) cc_final: 0.7269 (t0) REVERT: BZ 85 LYS cc_start: 0.9212 (mtpt) cc_final: 0.8769 (mttt) outliers start: 258 outliers final: 205 residues processed: 1041 average time/residue: 1.1704 time to fit residues: 2142.9243 Evaluate side-chains 1095 residues out of total 4740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 879 time to evaluate : 5.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AZ residue 81 ASN Chi-restraints excluded: chain AZ residue 86 ASP Chi-restraints excluded: chain B0 residue 7 ILE Chi-restraints excluded: chain B0 residue 13 THR Chi-restraints excluded: chain B0 residue 40 VAL Chi-restraints excluded: chain B0 residue 50 SER Chi-restraints excluded: chain B1 residue 6 ILE Chi-restraints excluded: chain B1 residue 10 THR Chi-restraints excluded: chain B1 residue 21 LEU Chi-restraints excluded: chain B1 residue 43 ILE Chi-restraints excluded: chain B1 residue 56 VAL Chi-restraints excluded: chain B1 residue 62 ILE Chi-restraints excluded: chain B2 residue 5 GLU Chi-restraints excluded: chain B2 residue 35 VAL Chi-restraints excluded: chain B3 residue 33 VAL Chi-restraints excluded: chain B3 residue 60 ASN Chi-restraints excluded: chain B4 residue 3 VAL Chi-restraints excluded: chain B4 residue 24 VAL Chi-restraints excluded: chain B4 residue 36 MET Chi-restraints excluded: chain B4 residue 46 CYS Chi-restraints excluded: chain B4 residue 54 ILE Chi-restraints excluded: chain B5 residue 1 MET Chi-restraints excluded: chain B5 residue 28 ASP Chi-restraints excluded: chain B5 residue 43 THR Chi-restraints excluded: chain B6 residue 4 THR Chi-restraints excluded: chain B6 residue 30 VAL Chi-restraints excluded: chain B6 residue 43 SER Chi-restraints excluded: chain B7 residue 17 THR Chi-restraints excluded: chain B7 residue 30 SER Chi-restraints excluded: chain B7 residue 54 ASP Chi-restraints excluded: chain B7 residue 59 LYS Chi-restraints excluded: chain B8 residue 3 VAL Chi-restraints excluded: chain B8 residue 7 VAL Chi-restraints excluded: chain B8 residue 16 VAL Chi-restraints excluded: chain B8 residue 17 ILE Chi-restraints excluded: chain B8 residue 24 MET Chi-restraints excluded: chain BD residue 9 THR Chi-restraints excluded: chain BD residue 10 SER Chi-restraints excluded: chain BD residue 37 LEU Chi-restraints excluded: chain BD residue 49 LEU Chi-restraints excluded: chain BD residue 64 VAL Chi-restraints excluded: chain BD residue 78 VAL Chi-restraints excluded: chain BD residue 80 THR Chi-restraints excluded: chain BD residue 82 GLU Chi-restraints excluded: chain BD residue 104 ILE Chi-restraints excluded: chain BD residue 183 MET Chi-restraints excluded: chain BD residue 223 SER Chi-restraints excluded: chain BD residue 229 ASP Chi-restraints excluded: chain BD residue 255 LEU Chi-restraints excluded: chain BD residue 265 LYS Chi-restraints excluded: chain BE residue 5 ILE Chi-restraints excluded: chain BE residue 13 THR Chi-restraints excluded: chain BE residue 15 VAL Chi-restraints excluded: chain BE residue 16 PHE Chi-restraints excluded: chain BE residue 23 ILE Chi-restraints excluded: chain BE residue 26 THR Chi-restraints excluded: chain BE residue 40 THR Chi-restraints excluded: chain BE residue 91 TYR Chi-restraints excluded: chain BE residue 98 LYS Chi-restraints excluded: chain BE residue 106 GLU Chi-restraints excluded: chain BE residue 108 VAL Chi-restraints excluded: chain BE residue 111 THR Chi-restraints excluded: chain BE residue 124 LYS Chi-restraints excluded: chain BE residue 134 SER Chi-restraints excluded: chain BE residue 140 HIS Chi-restraints excluded: chain BE residue 177 VAL Chi-restraints excluded: chain BE residue 187 LEU Chi-restraints excluded: chain BE residue 188 ILE Chi-restraints excluded: chain BF residue 17 ILE Chi-restraints excluded: chain BF residue 63 LYS Chi-restraints excluded: chain BF residue 110 ILE Chi-restraints excluded: chain BF residue 119 ILE Chi-restraints excluded: chain BF residue 123 ILE Chi-restraints excluded: chain BF residue 124 ILE Chi-restraints excluded: chain BF residue 132 ASP Chi-restraints excluded: chain BF residue 154 ILE Chi-restraints excluded: chain BF residue 156 THR Chi-restraints excluded: chain BF residue 173 VAL Chi-restraints excluded: chain BF residue 174 THR Chi-restraints excluded: chain BG residue 16 LEU Chi-restraints excluded: chain BG residue 17 MET Chi-restraints excluded: chain BG residue 71 LYS Chi-restraints excluded: chain BG residue 74 ILE Chi-restraints excluded: chain BG residue 77 PHE Chi-restraints excluded: chain BG residue 90 THR Chi-restraints excluded: chain BG residue 100 LEU Chi-restraints excluded: chain BG residue 108 LEU Chi-restraints excluded: chain BG residue 148 LYS Chi-restraints excluded: chain BG residue 155 VAL Chi-restraints excluded: chain BH residue 24 THR Chi-restraints excluded: chain BH residue 35 THR Chi-restraints excluded: chain BH residue 44 ILE Chi-restraints excluded: chain BH residue 51 LEU Chi-restraints excluded: chain BH residue 88 LEU Chi-restraints excluded: chain BH residue 90 LEU Chi-restraints excluded: chain BH residue 93 VAL Chi-restraints excluded: chain BH residue 103 LYS Chi-restraints excluded: chain BJ residue 43 LYS Chi-restraints excluded: chain BJ residue 89 VAL Chi-restraints excluded: chain BK residue 56 VAL Chi-restraints excluded: chain BM residue 12 ILE Chi-restraints excluded: chain BM residue 19 VAL Chi-restraints excluded: chain BM residue 44 THR Chi-restraints excluded: chain BM residue 46 THR Chi-restraints excluded: chain BM residue 51 THR Chi-restraints excluded: chain BM residue 55 VAL Chi-restraints excluded: chain BM residue 59 ASN Chi-restraints excluded: chain BM residue 65 LEU Chi-restraints excluded: chain BM residue 89 THR Chi-restraints excluded: chain BM residue 91 LEU Chi-restraints excluded: chain BM residue 97 TYR Chi-restraints excluded: chain BM residue 110 LEU Chi-restraints excluded: chain BN residue 10 VAL Chi-restraints excluded: chain BN residue 34 ASN Chi-restraints excluded: chain BN residue 38 VAL Chi-restraints excluded: chain BN residue 51 VAL Chi-restraints excluded: chain BN residue 57 VAL Chi-restraints excluded: chain BN residue 65 THR Chi-restraints excluded: chain BN residue 114 ILE Chi-restraints excluded: chain BN residue 116 SER Chi-restraints excluded: chain BO residue 12 SER Chi-restraints excluded: chain BO residue 25 SER Chi-restraints excluded: chain BO residue 27 ASN Chi-restraints excluded: chain BO residue 57 LEU Chi-restraints excluded: chain BO residue 67 THR Chi-restraints excluded: chain BO residue 69 ILE Chi-restraints excluded: chain BO residue 79 LEU Chi-restraints excluded: chain BO residue 80 ASP Chi-restraints excluded: chain BO residue 82 LEU Chi-restraints excluded: chain BO residue 89 THR Chi-restraints excluded: chain BO residue 94 GLU Chi-restraints excluded: chain BO residue 95 LEU Chi-restraints excluded: chain BO residue 105 LEU Chi-restraints excluded: chain BO residue 117 LEU Chi-restraints excluded: chain BP residue 27 VAL Chi-restraints excluded: chain BP residue 29 PHE Chi-restraints excluded: chain BP residue 32 PHE Chi-restraints excluded: chain BP residue 34 ILE Chi-restraints excluded: chain BP residue 43 THR Chi-restraints excluded: chain BP residue 45 ARG Chi-restraints excluded: chain BP residue 47 ILE Chi-restraints excluded: chain BP residue 54 MET Chi-restraints excluded: chain BP residue 55 THR Chi-restraints excluded: chain BP residue 56 ARG Chi-restraints excluded: chain BP residue 71 SER Chi-restraints excluded: chain BP residue 75 THR Chi-restraints excluded: chain BP residue 79 LEU Chi-restraints excluded: chain BP residue 102 VAL Chi-restraints excluded: chain BP residue 125 LEU Chi-restraints excluded: chain BQ residue 9 THR Chi-restraints excluded: chain BQ residue 17 LEU Chi-restraints excluded: chain BQ residue 21 THR Chi-restraints excluded: chain BQ residue 23 ASP Chi-restraints excluded: chain BQ residue 32 THR Chi-restraints excluded: chain BQ residue 33 THR Chi-restraints excluded: chain BQ residue 48 ILE Chi-restraints excluded: chain BQ residue 49 THR Chi-restraints excluded: chain BQ residue 56 LEU Chi-restraints excluded: chain BQ residue 74 GLU Chi-restraints excluded: chain BQ residue 76 ASN Chi-restraints excluded: chain BQ residue 89 THR Chi-restraints excluded: chain BQ residue 101 ILE Chi-restraints excluded: chain BQ residue 117 ILE Chi-restraints excluded: chain BR residue 6 SER Chi-restraints excluded: chain BR residue 17 ARG Chi-restraints excluded: chain BR residue 45 ILE Chi-restraints excluded: chain BR residue 47 ASP Chi-restraints excluded: chain BR residue 48 VAL Chi-restraints excluded: chain BR residue 63 LEU Chi-restraints excluded: chain BR residue 77 VAL Chi-restraints excluded: chain BR residue 101 LEU Chi-restraints excluded: chain BR residue 103 HIS Chi-restraints excluded: chain BR residue 105 ARG Chi-restraints excluded: chain BR residue 115 GLU Chi-restraints excluded: chain BS residue 19 ASP Chi-restraints excluded: chain BS residue 20 LEU Chi-restraints excluded: chain BS residue 29 LEU Chi-restraints excluded: chain BS residue 33 VAL Chi-restraints excluded: chain BS residue 36 VAL Chi-restraints excluded: chain BS residue 49 VAL Chi-restraints excluded: chain BS residue 50 VAL Chi-restraints excluded: chain BS residue 61 THR Chi-restraints excluded: chain BS residue 116 ILE Chi-restraints excluded: chain BT residue 31 LEU Chi-restraints excluded: chain BT residue 42 SER Chi-restraints excluded: chain BT residue 49 ASP Chi-restraints excluded: chain BT residue 63 THR Chi-restraints excluded: chain BT residue 77 SER Chi-restraints excluded: chain BT residue 83 LEU Chi-restraints excluded: chain BT residue 94 MET Chi-restraints excluded: chain BT residue 104 THR Chi-restraints excluded: chain BU residue 15 GLU Chi-restraints excluded: chain BU residue 33 VAL Chi-restraints excluded: chain BU residue 48 VAL Chi-restraints excluded: chain BV residue 4 LYS Chi-restraints excluded: chain BV residue 24 ILE Chi-restraints excluded: chain BV residue 33 VAL Chi-restraints excluded: chain BV residue 35 ILE Chi-restraints excluded: chain BV residue 50 VAL Chi-restraints excluded: chain BV residue 64 MET Chi-restraints excluded: chain BV residue 67 ASN Chi-restraints excluded: chain BV residue 70 VAL Chi-restraints excluded: chain BV residue 77 ASP Chi-restraints excluded: chain BV residue 104 THR Chi-restraints excluded: chain BV residue 106 VAL Chi-restraints excluded: chain BV residue 107 VAL Chi-restraints excluded: chain BW residue 12 VAL Chi-restraints excluded: chain BW residue 14 THR Chi-restraints excluded: chain BW residue 58 ASN Chi-restraints excluded: chain BW residue 81 VAL Chi-restraints excluded: chain BX residue 33 VAL Chi-restraints excluded: chain BX residue 56 ILE Chi-restraints excluded: chain BX residue 81 VAL Chi-restraints excluded: chain BX residue 93 VAL Chi-restraints excluded: chain BZ residue 40 THR Chi-restraints excluded: chain BZ residue 88 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 601 optimal weight: 10.0000 chunk 387 optimal weight: 50.0000 chunk 580 optimal weight: 20.0000 chunk 292 optimal weight: 6.9990 chunk 190 optimal weight: 50.0000 chunk 188 optimal weight: 40.0000 chunk 617 optimal weight: 10.0000 chunk 661 optimal weight: 10.0000 chunk 480 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 763 optimal weight: 2.9990 overall best weight: 7.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B5 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 135 HIS ** BF 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 107 ASN ** BM 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BN 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BP 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 27 ASN BQ 68 ASN BR 103 HIS BS 15 GLN BT 52 GLN ** BT 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BU 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BU 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.5844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 147759 Z= 0.333 Angle : 0.760 16.164 221796 Z= 0.384 Chirality : 0.040 0.395 27275 Planarity : 0.005 0.147 11493 Dihedral : 25.014 179.533 78905 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.37 % Favored : 91.95 % Rotamer: Outliers : 8.84 % Allowed : 27.36 % Favored : 63.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 1.79 % 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: -0.64 (0.11), residues: 5563 helix: 1.41 (0.13), residues: 1769 sheet: -1.41 (0.17), residues: 911 loop : -1.27 (0.11), residues: 2883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRPB0 29 HIS 0.014 0.002 HISBD 200 PHE 0.025 0.003 PHEBR 95 TYR 0.030 0.003 TYRBO 74 ARG 0.010 0.001 ARGBT 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1155 residues out of total 4740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 913 time to evaluate : 5.463 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: B2 9 LYS cc_start: 0.7997 (ptmt) cc_final: 0.7512 (pttp) REVERT: B4 20 PHE cc_start: 0.8924 (t80) cc_final: 0.8677 (t80) REVERT: BD 24 ILE cc_start: 0.9004 (mm) cc_final: 0.8645 (tp) REVERT: BD 100 GLU cc_start: 0.7805 (tp30) cc_final: 0.7517 (tp30) REVERT: BD 101 LYS cc_start: 0.8948 (mttt) cc_final: 0.8560 (mtmm) REVERT: BD 128 ASN cc_start: 0.7638 (m-40) cc_final: 0.7004 (t0) REVERT: BD 236 GLU cc_start: 0.7426 (mm-30) cc_final: 0.6919 (mm-30) REVERT: BE 133 MET cc_start: 0.8165 (mmm) cc_final: 0.7954 (tpt) REVERT: BE 140 HIS cc_start: 0.8473 (OUTLIER) cc_final: 0.7973 (p-80) REVERT: BE 159 LEU cc_start: 0.8996 (mt) cc_final: 0.8579 (mp) REVERT: BG 26 MET cc_start: 0.6676 (ptm) cc_final: 0.6433 (ppp) REVERT: BG 165 GLU cc_start: 0.7594 (tt0) cc_final: 0.7291 (tt0) REVERT: BH 58 ASP cc_start: 0.6891 (p0) cc_final: 0.6473 (p0) REVERT: BM 93 MET cc_start: 0.7208 (tpp) cc_final: 0.6518 (tpp) REVERT: BM 97 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.7636 (p90) REVERT: BM 136 GLN cc_start: 0.8572 (mp10) cc_final: 0.8034 (mp10) REVERT: BN 34 ASN cc_start: 0.8812 (OUTLIER) cc_final: 0.8491 (p0) REVERT: BN 76 TYR cc_start: 0.7821 (m-80) cc_final: 0.7533 (m-80) REVERT: BP 45 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7424 (mpp80) REVERT: BP 56 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7543 (tpt90) REVERT: BP 79 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8679 (pp) REVERT: BQ 14 LYS cc_start: 0.8479 (tttp) cc_final: 0.8245 (tttm) REVERT: BR 76 LYS cc_start: 0.7275 (ptpp) cc_final: 0.6948 (ptpp) REVERT: BR 111 ASP cc_start: 0.7857 (t70) cc_final: 0.7613 (t0) REVERT: BT 57 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.7063 (m-80) REVERT: BV 108 SER cc_start: 0.7930 (m) cc_final: 0.7561 (p) REVERT: BX 31 ASP cc_start: 0.7708 (t0) cc_final: 0.7373 (t0) REVERT: BX 83 TYR cc_start: 0.7383 (m-80) cc_final: 0.7013 (m-80) REVERT: BZ 85 LYS cc_start: 0.9138 (mtpt) cc_final: 0.8667 (mttt) outliers start: 242 outliers final: 192 residues processed: 1027 average time/residue: 1.1302 time to fit residues: 2038.6840 Evaluate side-chains 1081 residues out of total 4740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 882 time to evaluate : 7.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AZ residue 81 ASN Chi-restraints excluded: chain AZ residue 86 ASP Chi-restraints excluded: chain B0 residue 7 ILE Chi-restraints excluded: chain B0 residue 13 THR Chi-restraints excluded: chain B0 residue 19 SER Chi-restraints excluded: chain B0 residue 40 VAL Chi-restraints excluded: chain B0 residue 50 SER Chi-restraints excluded: chain B1 residue 10 THR Chi-restraints excluded: chain B1 residue 20 SER Chi-restraints excluded: chain B1 residue 40 THR Chi-restraints excluded: chain B1 residue 56 VAL Chi-restraints excluded: chain B2 residue 5 GLU Chi-restraints excluded: chain B2 residue 28 LEU Chi-restraints excluded: chain B2 residue 35 VAL Chi-restraints excluded: chain B3 residue 24 THR Chi-restraints excluded: chain B3 residue 33 VAL Chi-restraints excluded: chain B4 residue 24 VAL Chi-restraints excluded: chain B4 residue 46 CYS Chi-restraints excluded: chain B5 residue 18 ILE Chi-restraints excluded: chain B5 residue 43 THR Chi-restraints excluded: chain B6 residue 4 THR Chi-restraints excluded: chain B7 residue 10 SER Chi-restraints excluded: chain B7 residue 17 THR Chi-restraints excluded: chain B7 residue 30 SER Chi-restraints excluded: chain B7 residue 54 ASP Chi-restraints excluded: chain B7 residue 59 LYS Chi-restraints excluded: chain B8 residue 3 VAL Chi-restraints excluded: chain B8 residue 7 VAL Chi-restraints excluded: chain B8 residue 16 VAL Chi-restraints excluded: chain B8 residue 24 MET Chi-restraints excluded: chain BD residue 9 THR Chi-restraints excluded: chain BD residue 10 SER Chi-restraints excluded: chain BD residue 26 THR Chi-restraints excluded: chain BD residue 37 LEU Chi-restraints excluded: chain BD residue 49 LEU Chi-restraints excluded: chain BD residue 64 VAL Chi-restraints excluded: chain BD residue 78 VAL Chi-restraints excluded: chain BD residue 80 THR Chi-restraints excluded: chain BD residue 104 ILE Chi-restraints excluded: chain BD residue 229 ASP Chi-restraints excluded: chain BD residue 255 LEU Chi-restraints excluded: chain BD residue 265 LYS Chi-restraints excluded: chain BE residue 5 ILE Chi-restraints excluded: chain BE residue 16 PHE Chi-restraints excluded: chain BE residue 26 THR Chi-restraints excluded: chain BE residue 40 THR Chi-restraints excluded: chain BE residue 91 TYR Chi-restraints excluded: chain BE residue 98 LYS Chi-restraints excluded: chain BE residue 106 GLU Chi-restraints excluded: chain BE residue 111 THR Chi-restraints excluded: chain BE residue 124 LYS Chi-restraints excluded: chain BE residue 134 SER Chi-restraints excluded: chain BE residue 140 HIS Chi-restraints excluded: chain BE residue 187 LEU Chi-restraints excluded: chain BE residue 188 ILE Chi-restraints excluded: chain BF residue 17 ILE Chi-restraints excluded: chain BF residue 39 MET Chi-restraints excluded: chain BF residue 63 LYS Chi-restraints excluded: chain BF residue 75 GLN Chi-restraints excluded: chain BF residue 77 SER Chi-restraints excluded: chain BF residue 78 ILE Chi-restraints excluded: chain BF residue 110 ILE Chi-restraints excluded: chain BF residue 123 ILE Chi-restraints excluded: chain BF residue 124 ILE Chi-restraints excluded: chain BF residue 154 ILE Chi-restraints excluded: chain BF residue 156 THR Chi-restraints excluded: chain BF residue 174 THR Chi-restraints excluded: chain BG residue 17 MET Chi-restraints excluded: chain BG residue 46 ASN Chi-restraints excluded: chain BG residue 58 THR Chi-restraints excluded: chain BG residue 71 LYS Chi-restraints excluded: chain BG residue 77 PHE Chi-restraints excluded: chain BG residue 100 LEU Chi-restraints excluded: chain BG residue 108 LEU Chi-restraints excluded: chain BG residue 125 ARG Chi-restraints excluded: chain BG residue 132 ILE Chi-restraints excluded: chain BG residue 148 LYS Chi-restraints excluded: chain BH residue 24 THR Chi-restraints excluded: chain BH residue 35 THR Chi-restraints excluded: chain BH residue 51 LEU Chi-restraints excluded: chain BH residue 69 THR Chi-restraints excluded: chain BH residue 90 LEU Chi-restraints excluded: chain BH residue 93 VAL Chi-restraints excluded: chain BH residue 103 LYS Chi-restraints excluded: chain BH residue 112 HIS Chi-restraints excluded: chain BJ residue 13 GLU Chi-restraints excluded: chain BJ residue 28 VAL Chi-restraints excluded: chain BJ residue 43 LYS Chi-restraints excluded: chain BJ residue 89 VAL Chi-restraints excluded: chain BK residue 56 VAL Chi-restraints excluded: chain BM residue 12 ILE Chi-restraints excluded: chain BM residue 19 VAL Chi-restraints excluded: chain BM residue 44 THR Chi-restraints excluded: chain BM residue 46 THR Chi-restraints excluded: chain BM residue 51 THR Chi-restraints excluded: chain BM residue 55 VAL Chi-restraints excluded: chain BM residue 59 ASN Chi-restraints excluded: chain BM residue 65 LEU Chi-restraints excluded: chain BM residue 89 THR Chi-restraints excluded: chain BM residue 91 LEU Chi-restraints excluded: chain BM residue 97 TYR Chi-restraints excluded: chain BM residue 110 LEU Chi-restraints excluded: chain BN residue 8 LEU Chi-restraints excluded: chain BN residue 34 ASN Chi-restraints excluded: chain BN residue 51 VAL Chi-restraints excluded: chain BN residue 57 VAL Chi-restraints excluded: chain BN residue 65 THR Chi-restraints excluded: chain BN residue 96 THR Chi-restraints excluded: chain BN residue 114 ILE Chi-restraints excluded: chain BN residue 116 SER Chi-restraints excluded: chain BO residue 12 SER Chi-restraints excluded: chain BO residue 25 SER Chi-restraints excluded: chain BO residue 27 ASN Chi-restraints excluded: chain BO residue 67 THR Chi-restraints excluded: chain BO residue 69 ILE Chi-restraints excluded: chain BO residue 79 LEU Chi-restraints excluded: chain BO residue 94 GLU Chi-restraints excluded: chain BO residue 95 LEU Chi-restraints excluded: chain BO residue 102 ILE Chi-restraints excluded: chain BO residue 117 LEU Chi-restraints excluded: chain BP residue 2 LEU Chi-restraints excluded: chain BP residue 29 PHE Chi-restraints excluded: chain BP residue 32 PHE Chi-restraints excluded: chain BP residue 43 THR Chi-restraints excluded: chain BP residue 45 ARG Chi-restraints excluded: chain BP residue 47 ILE Chi-restraints excluded: chain BP residue 54 MET Chi-restraints excluded: chain BP residue 55 THR Chi-restraints excluded: chain BP residue 56 ARG Chi-restraints excluded: chain BP residue 71 SER Chi-restraints excluded: chain BP residue 75 THR Chi-restraints excluded: chain BP residue 79 LEU Chi-restraints excluded: chain BP residue 102 VAL Chi-restraints excluded: chain BP residue 125 LEU Chi-restraints excluded: chain BQ residue 10 SER Chi-restraints excluded: chain BQ residue 17 LEU Chi-restraints excluded: chain BQ residue 21 THR Chi-restraints excluded: chain BQ residue 23 ASP Chi-restraints excluded: chain BQ residue 32 THR Chi-restraints excluded: chain BQ residue 33 THR Chi-restraints excluded: chain BQ residue 48 ILE Chi-restraints excluded: chain BQ residue 49 THR Chi-restraints excluded: chain BQ residue 56 LEU Chi-restraints excluded: chain BQ residue 74 GLU Chi-restraints excluded: chain BQ residue 76 ASN Chi-restraints excluded: chain BQ residue 89 THR Chi-restraints excluded: chain BQ residue 101 ILE Chi-restraints excluded: chain BQ residue 117 ILE Chi-restraints excluded: chain BR residue 6 SER Chi-restraints excluded: chain BR residue 17 ARG Chi-restraints excluded: chain BR residue 40 ILE Chi-restraints excluded: chain BR residue 47 ASP Chi-restraints excluded: chain BR residue 48 VAL Chi-restraints excluded: chain BR residue 52 THR Chi-restraints excluded: chain BR residue 63 LEU Chi-restraints excluded: chain BR residue 101 LEU Chi-restraints excluded: chain BR residue 103 HIS Chi-restraints excluded: chain BR residue 105 ARG Chi-restraints excluded: chain BR residue 115 GLU Chi-restraints excluded: chain BS residue 20 LEU Chi-restraints excluded: chain BS residue 31 VAL Chi-restraints excluded: chain BS residue 33 VAL Chi-restraints excluded: chain BS residue 49 VAL Chi-restraints excluded: chain BS residue 50 VAL Chi-restraints excluded: chain BS residue 88 GLU Chi-restraints excluded: chain BS residue 116 ILE Chi-restraints excluded: chain BT residue 11 ARG Chi-restraints excluded: chain BT residue 31 LEU Chi-restraints excluded: chain BT residue 42 SER Chi-restraints excluded: chain BT residue 49 ASP Chi-restraints excluded: chain BT residue 57 PHE Chi-restraints excluded: chain BT residue 63 THR Chi-restraints excluded: chain BT residue 77 SER Chi-restraints excluded: chain BT residue 83 LEU Chi-restraints excluded: chain BT residue 94 MET Chi-restraints excluded: chain BT residue 104 THR Chi-restraints excluded: chain BU residue 48 VAL Chi-restraints excluded: chain BV residue 4 LYS Chi-restraints excluded: chain BV residue 24 ILE Chi-restraints excluded: chain BV residue 33 VAL Chi-restraints excluded: chain BV residue 35 ILE Chi-restraints excluded: chain BV residue 50 VAL Chi-restraints excluded: chain BV residue 64 MET Chi-restraints excluded: chain BV residue 67 ASN Chi-restraints excluded: chain BV residue 70 VAL Chi-restraints excluded: chain BV residue 104 THR Chi-restraints excluded: chain BV residue 106 VAL Chi-restraints excluded: chain BV residue 107 VAL Chi-restraints excluded: chain BW residue 12 VAL Chi-restraints excluded: chain BW residue 56 ILE Chi-restraints excluded: chain BW residue 58 ASN Chi-restraints excluded: chain BW residue 81 VAL Chi-restraints excluded: chain BX residue 33 VAL Chi-restraints excluded: chain BX residue 56 ILE Chi-restraints excluded: chain BX residue 77 GLU Chi-restraints excluded: chain BX residue 81 VAL Chi-restraints excluded: chain BX residue 93 VAL Chi-restraints excluded: chain BZ residue 40 THR Chi-restraints excluded: chain BZ residue 88 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 883 optimal weight: 6.9990 chunk 930 optimal weight: 10.0000 chunk 849 optimal weight: 0.0040 chunk 905 optimal weight: 0.7980 chunk 544 optimal weight: 50.0000 chunk 394 optimal weight: 9.9990 chunk 710 optimal weight: 10.0000 chunk 277 optimal weight: 20.0000 chunk 818 optimal weight: 7.9990 chunk 856 optimal weight: 0.0980 chunk 902 optimal weight: 6.9990 overall best weight: 2.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 37 HIS ** B2 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B7 38 GLN ** B8 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 153 GLN ** BD 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BE 135 HIS BE 140 HIS BF 67 GLN ** BF 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BM 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BP 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 27 ASN BQ 68 ASN BR 103 HIS BS 39 ASN BT 52 GLN ** BT 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BU 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BU 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BU 88 HIS ** BX 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 67 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.5792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 147759 Z= 0.173 Angle : 0.652 14.384 221796 Z= 0.331 Chirality : 0.034 0.356 27275 Planarity : 0.004 0.053 11493 Dihedral : 24.933 179.636 78905 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.68 % Allowed : 6.00 % Favored : 93.31 % Rotamer: Outliers : 6.36 % Allowed : 30.93 % Favored : 62.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 1.79 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.12), residues: 5563 helix: 1.71 (0.13), residues: 1755 sheet: -1.20 (0.17), residues: 891 loop : -1.09 (0.12), residues: 2917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPB0 29 HIS 0.020 0.002 HISBR 103 PHE 0.034 0.002 PHEBG 99 TYR 0.022 0.002 TYRBD 62 ARG 0.013 0.001 ARGBN 97 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1130 residues out of total 4740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 956 time to evaluate : 5.504 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: B1 9 LEU cc_start: 0.6411 (pp) cc_final: 0.6169 (pp) REVERT: B1 47 ARG cc_start: 0.8355 (ttp80) cc_final: 0.8105 (ttm170) REVERT: B2 9 LYS cc_start: 0.7992 (ptmt) cc_final: 0.7423 (pttp) REVERT: B4 10 LYS cc_start: 0.8701 (mtmm) cc_final: 0.8490 (mttm) REVERT: B4 20 PHE cc_start: 0.8837 (t80) cc_final: 0.8565 (t80) REVERT: B6 2 LYS cc_start: 0.8885 (ttmm) cc_final: 0.8647 (ttpp) REVERT: B6 18 PHE cc_start: 0.9096 (t80) cc_final: 0.8640 (t80) REVERT: B8 35 LYS cc_start: 0.8449 (ttpt) cc_final: 0.8183 (ttpt) REVERT: BD 24 ILE cc_start: 0.8982 (mm) cc_final: 0.8572 (tp) REVERT: BD 100 GLU cc_start: 0.7780 (tp30) cc_final: 0.7511 (tp30) REVERT: BD 101 LYS cc_start: 0.8890 (mttt) cc_final: 0.8483 (mtmm) REVERT: BD 236 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6705 (mm-30) REVERT: BE 138 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7895 (mtt180) REVERT: BE 172 GLN cc_start: 0.8221 (mt0) cc_final: 0.7893 (mt0) REVERT: BG 140 GLU cc_start: 0.6512 (pm20) cc_final: 0.6123 (pm20) REVERT: BH 58 ASP cc_start: 0.6676 (p0) cc_final: 0.6462 (p0) REVERT: BM 6 MET cc_start: 0.7236 (pmm) cc_final: 0.6671 (pmm) REVERT: BN 76 TYR cc_start: 0.7703 (m-80) cc_final: 0.7382 (m-80) REVERT: BP 45 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.7339 (mpp80) REVERT: BP 56 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7544 (tmm160) REVERT: BQ 14 LYS cc_start: 0.8347 (tttp) cc_final: 0.8103 (tttm) REVERT: BQ 34 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7974 (tt0) REVERT: BR 111 ASP cc_start: 0.7783 (t70) cc_final: 0.7571 (t0) REVERT: BT 8 THR cc_start: 0.8068 (m) cc_final: 0.7746 (t) REVERT: BX 40 MET cc_start: 0.7321 (tpt) cc_final: 0.6903 (tpt) REVERT: BX 83 TYR cc_start: 0.7308 (m-80) cc_final: 0.7014 (m-80) outliers start: 174 outliers final: 135 residues processed: 1040 average time/residue: 1.1266 time to fit residues: 2056.3378 Evaluate side-chains 1044 residues out of total 4740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 905 time to evaluate : 5.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AZ residue 86 ASP Chi-restraints excluded: chain B0 residue 7 ILE Chi-restraints excluded: chain B0 residue 13 THR Chi-restraints excluded: chain B0 residue 40 VAL Chi-restraints excluded: chain B0 residue 50 SER Chi-restraints excluded: chain B1 residue 10 THR Chi-restraints excluded: chain B1 residue 21 LEU Chi-restraints excluded: chain B2 residue 5 GLU Chi-restraints excluded: chain B2 residue 28 LEU Chi-restraints excluded: chain B2 residue 35 VAL Chi-restraints excluded: chain B3 residue 33 VAL Chi-restraints excluded: chain B4 residue 24 VAL Chi-restraints excluded: chain B4 residue 46 CYS Chi-restraints excluded: chain B5 residue 1 MET Chi-restraints excluded: chain B6 residue 41 VAL Chi-restraints excluded: chain B7 residue 17 THR Chi-restraints excluded: chain B7 residue 30 SER Chi-restraints excluded: chain B8 residue 7 VAL Chi-restraints excluded: chain B8 residue 16 VAL Chi-restraints excluded: chain B8 residue 17 ILE Chi-restraints excluded: chain BD residue 49 LEU Chi-restraints excluded: chain BD residue 64 VAL Chi-restraints excluded: chain BD residue 78 VAL Chi-restraints excluded: chain BD residue 82 GLU Chi-restraints excluded: chain BD residue 98 ASP Chi-restraints excluded: chain BD residue 104 ILE Chi-restraints excluded: chain BD residue 124 ILE Chi-restraints excluded: chain BD residue 153 GLN Chi-restraints excluded: chain BD residue 229 ASP Chi-restraints excluded: chain BD residue 255 LEU Chi-restraints excluded: chain BD residue 265 LYS Chi-restraints excluded: chain BE residue 5 ILE Chi-restraints excluded: chain BE residue 15 VAL Chi-restraints excluded: chain BE residue 16 PHE Chi-restraints excluded: chain BE residue 26 THR Chi-restraints excluded: chain BE residue 40 THR Chi-restraints excluded: chain BE residue 98 LYS Chi-restraints excluded: chain BE residue 106 GLU Chi-restraints excluded: chain BE residue 111 THR Chi-restraints excluded: chain BE residue 138 ARG Chi-restraints excluded: chain BE residue 177 VAL Chi-restraints excluded: chain BE residue 187 LEU Chi-restraints excluded: chain BE residue 188 ILE Chi-restraints excluded: chain BE residue 192 VAL Chi-restraints excluded: chain BF residue 17 ILE Chi-restraints excluded: chain BF residue 63 LYS Chi-restraints excluded: chain BF residue 78 ILE Chi-restraints excluded: chain BF residue 110 ILE Chi-restraints excluded: chain BF residue 119 ILE Chi-restraints excluded: chain BF residue 123 ILE Chi-restraints excluded: chain BF residue 154 ILE Chi-restraints excluded: chain BF residue 174 THR Chi-restraints excluded: chain BG residue 17 MET Chi-restraints excluded: chain BG residue 46 ASN Chi-restraints excluded: chain BG residue 71 LYS Chi-restraints excluded: chain BG residue 77 PHE Chi-restraints excluded: chain BG residue 81 GLU Chi-restraints excluded: chain BG residue 90 THR Chi-restraints excluded: chain BG residue 148 LYS Chi-restraints excluded: chain BH residue 24 THR Chi-restraints excluded: chain BH residue 51 LEU Chi-restraints excluded: chain BH residue 93 VAL Chi-restraints excluded: chain BH residue 103 LYS Chi-restraints excluded: chain BJ residue 13 GLU Chi-restraints excluded: chain BJ residue 89 VAL Chi-restraints excluded: chain BK residue 56 VAL Chi-restraints excluded: chain BM residue 12 ILE Chi-restraints excluded: chain BM residue 44 THR Chi-restraints excluded: chain BM residue 46 THR Chi-restraints excluded: chain BM residue 65 LEU Chi-restraints excluded: chain BM residue 89 THR Chi-restraints excluded: chain BM residue 110 LEU Chi-restraints excluded: chain BN residue 8 LEU Chi-restraints excluded: chain BN residue 51 VAL Chi-restraints excluded: chain BN residue 57 VAL Chi-restraints excluded: chain BN residue 65 THR Chi-restraints excluded: chain BN residue 96 THR Chi-restraints excluded: chain BN residue 114 ILE Chi-restraints excluded: chain BN residue 116 SER Chi-restraints excluded: chain BO residue 12 SER Chi-restraints excluded: chain BO residue 25 SER Chi-restraints excluded: chain BO residue 27 ASN Chi-restraints excluded: chain BO residue 61 LEU Chi-restraints excluded: chain BO residue 67 THR Chi-restraints excluded: chain BO residue 69 ILE Chi-restraints excluded: chain BO residue 117 LEU Chi-restraints excluded: chain BP residue 29 PHE Chi-restraints excluded: chain BP residue 43 THR Chi-restraints excluded: chain BP residue 45 ARG Chi-restraints excluded: chain BP residue 56 ARG Chi-restraints excluded: chain BP residue 71 SER Chi-restraints excluded: chain BP residue 75 THR Chi-restraints excluded: chain BP residue 102 VAL Chi-restraints excluded: chain BP residue 125 LEU Chi-restraints excluded: chain BQ residue 9 THR Chi-restraints excluded: chain BQ residue 10 SER Chi-restraints excluded: chain BQ residue 23 ASP Chi-restraints excluded: chain BQ residue 33 THR Chi-restraints excluded: chain BQ residue 34 GLU Chi-restraints excluded: chain BQ residue 49 THR Chi-restraints excluded: chain BQ residue 56 LEU Chi-restraints excluded: chain BQ residue 68 ASN Chi-restraints excluded: chain BQ residue 74 GLU Chi-restraints excluded: chain BQ residue 76 ASN Chi-restraints excluded: chain BQ residue 89 THR Chi-restraints excluded: chain BQ residue 101 ILE Chi-restraints excluded: chain BQ residue 117 ILE Chi-restraints excluded: chain BR residue 17 ARG Chi-restraints excluded: chain BR residue 40 ILE Chi-restraints excluded: chain BR residue 48 VAL Chi-restraints excluded: chain BR residue 63 LEU Chi-restraints excluded: chain BR residue 101 LEU Chi-restraints excluded: chain BR residue 103 HIS Chi-restraints excluded: chain BR residue 105 ARG Chi-restraints excluded: chain BR residue 115 GLU Chi-restraints excluded: chain BS residue 20 LEU Chi-restraints excluded: chain BS residue 33 VAL Chi-restraints excluded: chain BS residue 50 VAL Chi-restraints excluded: chain BS residue 116 ILE Chi-restraints excluded: chain BT residue 31 LEU Chi-restraints excluded: chain BT residue 42 SER Chi-restraints excluded: chain BT residue 49 ASP Chi-restraints excluded: chain BT residue 63 THR Chi-restraints excluded: chain BT residue 83 LEU Chi-restraints excluded: chain BT residue 94 MET Chi-restraints excluded: chain BV residue 24 ILE Chi-restraints excluded: chain BV residue 35 ILE Chi-restraints excluded: chain BV residue 70 VAL Chi-restraints excluded: chain BV residue 104 THR Chi-restraints excluded: chain BV residue 107 VAL Chi-restraints excluded: chain BW residue 14 THR Chi-restraints excluded: chain BW residue 56 ILE Chi-restraints excluded: chain BW residue 81 VAL Chi-restraints excluded: chain BX residue 33 VAL Chi-restraints excluded: chain BX residue 56 ILE Chi-restraints excluded: chain BX residue 77 GLU Chi-restraints excluded: chain BX residue 93 VAL Chi-restraints excluded: chain BZ residue 40 THR Chi-restraints excluded: chain BZ residue 88 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 594 optimal weight: 10.0000 chunk 957 optimal weight: 1.9990 chunk 584 optimal weight: 20.0000 chunk 454 optimal weight: 10.0000 chunk 665 optimal weight: 20.0000 chunk 1004 optimal weight: 4.9990 chunk 924 optimal weight: 8.9990 chunk 799 optimal weight: 10.0000 chunk 83 optimal weight: 30.0000 chunk 617 optimal weight: 10.0000 chunk 490 optimal weight: 10.0000 overall best weight: 7.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 33 GLN ** B2 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B8 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 153 GLN ** BD 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BG 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BH 107 ASN ** BP 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 27 ASN BQ 68 ASN BS 15 GLN BS 39 ASN BS 44 GLN ** BU 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BU 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BU 81 ASN ** BX 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 67 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.5955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 147759 Z= 0.304 Angle : 0.730 16.889 221796 Z= 0.368 Chirality : 0.038 0.376 27275 Planarity : 0.005 0.079 11493 Dihedral : 24.911 179.598 78905 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 20.09 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.59 % Favored : 91.73 % Rotamer: Outliers : 6.43 % Allowed : 31.52 % Favored : 62.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 1.79 % 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: -0.49 (0.12), residues: 5563 helix: 1.59 (0.13), residues: 1765 sheet: -1.29 (0.17), residues: 890 loop : -1.24 (0.12), residues: 2908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPB0 29 HIS 0.010 0.002 HISBR 103 PHE 0.021 0.003 PHEBG 20 TYR 0.031 0.002 TYRBM 97 ARG 0.015 0.001 ARGBQ 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11126 Ramachandran restraints generated. 5563 Oldfield, 0 Emsley, 5563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1069 residues out of total 4740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 893 time to evaluate : 5.502 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: B1 9 LEU cc_start: 0.6590 (pp) cc_final: 0.6263 (pp) REVERT: B1 47 ARG cc_start: 0.8447 (ttp80) cc_final: 0.8207 (ttm170) REVERT: B2 3 LYS cc_start: 0.7992 (mmmt) cc_final: 0.7482 (mmmt) REVERT: B2 9 LYS cc_start: 0.8018 (ptmt) cc_final: 0.7518 (pttp) REVERT: B4 20 PHE cc_start: 0.8925 (t80) cc_final: 0.8687 (t80) REVERT: B8 35 LYS cc_start: 0.8452 (ttpt) cc_final: 0.8222 (ttpt) REVERT: BD 24 ILE cc_start: 0.9020 (mm) cc_final: 0.8641 (tp) REVERT: BD 100 GLU cc_start: 0.7756 (tp30) cc_final: 0.7464 (tp30) REVERT: BD 101 LYS cc_start: 0.8900 (mttt) cc_final: 0.8512 (mtmm) REVERT: BD 128 ASN cc_start: 0.7820 (m-40) cc_final: 0.7213 (t0) REVERT: BD 153 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7470 (mp10) REVERT: BD 180 GLU cc_start: 0.4876 (mp0) cc_final: 0.4662 (tp30) REVERT: BD 236 GLU cc_start: 0.7338 (mm-30) cc_final: 0.6868 (mm-30) REVERT: BD 243 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7456 (ptm-80) REVERT: BE 133 MET cc_start: 0.8172 (mmm) cc_final: 0.7945 (tpt) REVERT: BE 138 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7918 (mtt180) REVERT: BE 159 LEU cc_start: 0.8956 (mt) cc_final: 0.8361 (mp) REVERT: BF 34 PHE cc_start: 0.9098 (t80) cc_final: 0.8801 (t80) REVERT: BG 140 GLU cc_start: 0.6984 (pm20) cc_final: 0.6466 (pm20) REVERT: BH 58 ASP cc_start: 0.6796 (p0) cc_final: 0.6401 (p0) REVERT: BM 6 MET cc_start: 0.7306 (pmm) cc_final: 0.6729 (pmm) REVERT: BM 136 GLN cc_start: 0.8596 (mp10) cc_final: 0.8236 (mp10) REVERT: BN 76 TYR cc_start: 0.7768 (m-80) cc_final: 0.7486 (m-80) REVERT: BP 45 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7498 (mpp80) REVERT: BP 56 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7445 (tpt90) REVERT: BP 79 LEU cc_start: 0.8916 (pp) cc_final: 0.8575 (mp) REVERT: BQ 14 LYS cc_start: 0.8389 (tttp) cc_final: 0.8181 (tttm) REVERT: BQ 34 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7975 (tt0) REVERT: BR 111 ASP cc_start: 0.7834 (t70) cc_final: 0.7583 (t0) REVERT: BT 8 THR cc_start: 0.8185 (m) cc_final: 0.7905 (t) REVERT: BT 19 LYS cc_start: 0.9035 (mmtt) cc_final: 0.8696 (mmmm) REVERT: BU 25 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8445 (pp) REVERT: BV 52 LYS cc_start: 0.8930 (mmtp) cc_final: 0.8690 (mmtp) REVERT: BW 26 TYR cc_start: 0.7547 (m-10) cc_final: 0.6324 (m-10) REVERT: BW 57 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7815 (ptm) REVERT: BX 83 TYR cc_start: 0.7437 (m-80) cc_final: 0.7054 (m-80) outliers start: 176 outliers final: 146 residues processed: 985 average time/residue: 1.1545 time to fit residues: 2001.1641 Evaluate side-chains 1036 residues out of total 4740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 882 time to evaluate : 4.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AZ residue 81 ASN Chi-restraints excluded: chain AZ residue 86 ASP Chi-restraints excluded: chain B0 residue 7 ILE Chi-restraints excluded: chain B0 residue 13 THR Chi-restraints excluded: chain B0 residue 40 VAL Chi-restraints excluded: chain B0 residue 50 SER Chi-restraints excluded: chain B1 residue 10 THR Chi-restraints excluded: chain B1 residue 21 LEU Chi-restraints excluded: chain B2 residue 5 GLU Chi-restraints excluded: chain B2 residue 35 VAL Chi-restraints excluded: chain B3 residue 33 VAL Chi-restraints excluded: chain B4 residue 24 VAL Chi-restraints excluded: chain B4 residue 46 CYS Chi-restraints excluded: chain B5 residue 28 ASP Chi-restraints excluded: chain B6 residue 41 VAL Chi-restraints excluded: chain B7 residue 17 THR Chi-restraints excluded: chain B7 residue 30 SER Chi-restraints excluded: chain B8 residue 7 VAL Chi-restraints excluded: chain B8 residue 16 VAL Chi-restraints excluded: chain B8 residue 17 ILE Chi-restraints excluded: chain BD residue 10 SER Chi-restraints excluded: chain BD residue 49 LEU Chi-restraints excluded: chain BD residue 64 VAL Chi-restraints excluded: chain BD residue 78 VAL Chi-restraints excluded: chain BD residue 82 GLU Chi-restraints excluded: chain BD residue 98 ASP Chi-restraints excluded: chain BD residue 104 ILE Chi-restraints excluded: chain BD residue 153 GLN Chi-restraints excluded: chain BD residue 154 LEU Chi-restraints excluded: chain BD residue 223 SER Chi-restraints excluded: chain BD residue 229 ASP Chi-restraints excluded: chain BD residue 243 ARG Chi-restraints excluded: chain BD residue 255 LEU Chi-restraints excluded: chain BD residue 265 LYS Chi-restraints excluded: chain BE residue 5 ILE Chi-restraints excluded: chain BE residue 16 PHE Chi-restraints excluded: chain BE residue 23 ILE Chi-restraints excluded: chain BE residue 26 THR Chi-restraints excluded: chain BE residue 40 THR Chi-restraints excluded: chain BE residue 98 LYS Chi-restraints excluded: chain BE residue 106 GLU Chi-restraints excluded: chain BE residue 111 THR Chi-restraints excluded: chain BE residue 124 LYS Chi-restraints excluded: chain BE residue 138 ARG Chi-restraints excluded: chain BE residue 177 VAL Chi-restraints excluded: chain BE residue 187 LEU Chi-restraints excluded: chain BE residue 188 ILE Chi-restraints excluded: chain BE residue 192 VAL Chi-restraints excluded: chain BE residue 199 LEU Chi-restraints excluded: chain BF residue 17 ILE Chi-restraints excluded: chain BF residue 63 LYS Chi-restraints excluded: chain BF residue 78 ILE Chi-restraints excluded: chain BF residue 110 ILE Chi-restraints excluded: chain BF residue 123 ILE Chi-restraints excluded: chain BF residue 154 ILE Chi-restraints excluded: chain BF residue 156 THR Chi-restraints excluded: chain BF residue 174 THR Chi-restraints excluded: chain BG residue 17 MET Chi-restraints excluded: chain BG residue 46 ASN Chi-restraints excluded: chain BG residue 71 LYS Chi-restraints excluded: chain BG residue 77 PHE Chi-restraints excluded: chain BG residue 90 THR Chi-restraints excluded: chain BG residue 148 LYS Chi-restraints excluded: chain BG residue 162 THR Chi-restraints excluded: chain BH residue 24 THR Chi-restraints excluded: chain BH residue 51 LEU Chi-restraints excluded: chain BH residue 73 LEU Chi-restraints excluded: chain BH residue 93 VAL Chi-restraints excluded: chain BH residue 103 LYS Chi-restraints excluded: chain BH residue 107 ASN Chi-restraints excluded: chain BH residue 112 HIS Chi-restraints excluded: chain BJ residue 13 GLU Chi-restraints excluded: chain BJ residue 28 VAL Chi-restraints excluded: chain BJ residue 89 VAL Chi-restraints excluded: chain BK residue 56 VAL Chi-restraints excluded: chain BM residue 44 THR Chi-restraints excluded: chain BM residue 46 THR Chi-restraints excluded: chain BM residue 51 THR Chi-restraints excluded: chain BM residue 65 LEU Chi-restraints excluded: chain BM residue 89 THR Chi-restraints excluded: chain BM residue 110 LEU Chi-restraints excluded: chain BN residue 8 LEU Chi-restraints excluded: chain BN residue 51 VAL Chi-restraints excluded: chain BN residue 57 VAL Chi-restraints excluded: chain BN residue 65 THR Chi-restraints excluded: chain BN residue 96 THR Chi-restraints excluded: chain BN residue 114 ILE Chi-restraints excluded: chain BN residue 116 SER Chi-restraints excluded: chain BO residue 12 SER Chi-restraints excluded: chain BO residue 25 SER Chi-restraints excluded: chain BO residue 27 ASN Chi-restraints excluded: chain BO residue 67 THR Chi-restraints excluded: chain BO residue 69 ILE Chi-restraints excluded: chain BO residue 82 LEU Chi-restraints excluded: chain BO residue 94 GLU Chi-restraints excluded: chain BO residue 117 LEU Chi-restraints excluded: chain BP residue 29 PHE Chi-restraints excluded: chain BP residue 34 ILE Chi-restraints excluded: chain BP residue 43 THR Chi-restraints excluded: chain BP residue 45 ARG Chi-restraints excluded: chain BP residue 56 ARG Chi-restraints excluded: chain BP residue 71 SER Chi-restraints excluded: chain BP residue 75 THR Chi-restraints excluded: chain BP residue 102 VAL Chi-restraints excluded: chain BQ residue 10 SER Chi-restraints excluded: chain BQ residue 17 LEU Chi-restraints excluded: chain BQ residue 23 ASP Chi-restraints excluded: chain BQ residue 33 THR Chi-restraints excluded: chain BQ residue 34 GLU Chi-restraints excluded: chain BQ residue 49 THR Chi-restraints excluded: chain BQ residue 56 LEU Chi-restraints excluded: chain BQ residue 74 GLU Chi-restraints excluded: chain BQ residue 76 ASN Chi-restraints excluded: chain BQ residue 89 THR Chi-restraints excluded: chain BQ residue 101 ILE Chi-restraints excluded: chain BQ residue 117 ILE Chi-restraints excluded: chain BR residue 17 ARG Chi-restraints excluded: chain BR residue 48 VAL Chi-restraints excluded: chain BR residue 63 LEU Chi-restraints excluded: chain BR residue 101 LEU Chi-restraints excluded: chain BR residue 105 ARG Chi-restraints excluded: chain BR residue 115 GLU Chi-restraints excluded: chain BS residue 16 LEU Chi-restraints excluded: chain BS residue 20 LEU Chi-restraints excluded: chain BS residue 33 VAL Chi-restraints excluded: chain BS residue 49 VAL Chi-restraints excluded: chain BS residue 50 VAL Chi-restraints excluded: chain BS residue 88 GLU Chi-restraints excluded: chain BS residue 116 ILE Chi-restraints excluded: chain BT residue 11 ARG Chi-restraints excluded: chain BT residue 31 LEU Chi-restraints excluded: chain BT residue 42 SER Chi-restraints excluded: chain BT residue 49 ASP Chi-restraints excluded: chain BT residue 63 THR Chi-restraints excluded: chain BT residue 77 SER Chi-restraints excluded: chain BT residue 83 LEU Chi-restraints excluded: chain BT residue 94 MET Chi-restraints excluded: chain BU residue 25 LEU Chi-restraints excluded: chain BV residue 4 LYS Chi-restraints excluded: chain BV residue 24 ILE Chi-restraints excluded: chain BV residue 35 ILE Chi-restraints excluded: chain BV residue 64 MET Chi-restraints excluded: chain BV residue 70 VAL Chi-restraints excluded: chain BV residue 104 THR Chi-restraints excluded: chain BV residue 107 VAL Chi-restraints excluded: chain BW residue 14 THR Chi-restraints excluded: chain BW residue 56 ILE Chi-restraints excluded: chain BW residue 57 MET Chi-restraints excluded: chain BW residue 81 VAL Chi-restraints excluded: chain BX residue 33 VAL Chi-restraints excluded: chain BX residue 93 VAL Chi-restraints excluded: chain BZ residue 40 THR Chi-restraints excluded: chain BZ residue 80 PHE Chi-restraints excluded: chain BZ residue 88 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1008 random chunks: chunk 635 optimal weight: 10.0000 chunk 851 optimal weight: 8.9990 chunk 244 optimal weight: 50.0000 chunk 737 optimal weight: 6.9990 chunk 118 optimal weight: 40.0000 chunk 222 optimal weight: 8.9990 chunk 800 optimal weight: 0.0370 chunk 335 optimal weight: 8.9990 chunk 822 optimal weight: 6.9990 chunk 101 optimal weight: 30.0000 chunk 147 optimal weight: 10.0000 overall best weight: 6.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 60 ASN ** B8 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BD 111 GLN ** BD 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BD 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BE 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BH 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BH 107 ASN ** BN 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BP 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 68 ASN ** BR 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BS 39 ASN BS 44 GLN BT 52 GLN ** BU 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BU 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 67 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.086045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.063769 restraints weight = 489852.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.065216 restraints weight = 146943.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.066059 restraints weight = 73434.150| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.5958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.292 147759 Z= 0.307 Angle : 0.761 60.976 221796 Z= 0.392 Chirality : 0.040 1.976 27275 Planarity : 0.005 0.196 11493 Dihedral : 24.911 179.625 78905 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.66 % Favored : 91.68 % Rotamer: Outliers : 6.79 % Allowed : 30.97 % Favored : 62.24 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 1.79 % 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: -0.50 (0.12), residues: 5563 helix: 1.59 (0.13), residues: 1765 sheet: -1.29 (0.17), residues: 890 loop : -1.25 (0.12), residues: 2908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRPB0 29 HIS 0.008 0.002 HISBR 103 PHE 0.021 0.002 PHEBZ 80 TYR 0.027 0.002 TYRBM 97 ARG 0.009 0.001 ARGBN 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31614.09 seconds wall clock time: 554 minutes 7.07 seconds (33247.07 seconds total)