Starting phenix.real_space_refine on Sun Mar 17 09:13:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qgu_13959/03_2024/7qgu_13959.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qgu_13959/03_2024/7qgu_13959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qgu_13959/03_2024/7qgu_13959.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qgu_13959/03_2024/7qgu_13959.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qgu_13959/03_2024/7qgu_13959.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qgu_13959/03_2024/7qgu_13959.pdb" } resolution = 4.75 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= -0.001 sd= 0.090 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 4656 5.49 5 S 91 5.16 5 C 65679 2.51 5 N 25732 2.21 5 O 39448 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "G ARG 172": "NH1" <-> "NH2" Residue "O ARG 11": "NH1" <-> "NH2" Residue "P ARG 42": "NH1" <-> "NH2" Residue "R ARG 89": "NH1" <-> "NH2" Residue "S ARG 86": "NH1" <-> "NH2" Residue "V ARG 28": "NH1" <-> "NH2" 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: 135606 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 62767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2923, 62767 Classifications: {'RNA': 2923} Modifications used: {'rna2p_pur': 271, 'rna2p_pyr': 148, 'rna3p_pur': 1424, 'rna3p_pyr': 1080} Link IDs: {'rna2p': 419, 'rna3p': 2503} Chain: "B" 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: "C" 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: "D" 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: "E" 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: "F" 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: "G" 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: "H" 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: "I" 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: "J" 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: "K" 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: "L" 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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: "V" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 630 Classifications: {'peptide': 82} Link IDs: {'CIS': 2, 'PTRANS': 2, 'TRANS': 77} Chain: "X" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 733 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 3, 'TRANS': 145} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 429 Unresolved non-hydrogen angles: 532 Unresolved non-hydrogen dihedrals: 349 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 15, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 195 Chain: "Y" 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: "Z" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 530 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "a" 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: "b" 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: "c" 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: "d" 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: "e" 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: "f" 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: "W" 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: "g" 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: "h" 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: "i" 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: "j" 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: "k" 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: "l" 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: "m" 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: "n" 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: "o" 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: "p" 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: "q" 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: "r" 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: "s" 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: "t" 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: "u" 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: "v" 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: "w" 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: "x" 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: "y" 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: "z" 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: "2" 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: "3" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 366 Classifications: {'peptide': 45} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 40} Time building chain proxies: 51.33, per 1000 atoms: 0.38 Number of scatterers: 135606 At special positions: 0 Unit cell: (233.06, 276.42, 260.16, 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 91 16.00 P 4656 15.00 O 39448 8.00 N 25732 7.00 C 65679 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: 56.98 Conformation dependent library (CDL) restraints added in 6.9 seconds 11382 Ramachandran restraints generated. 5691 Oldfield, 0 Emsley, 5691 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6240 Finding SS restraints... Secondary structure from input PDB file: 175 helices and 70 sheets defined 34.4% alpha, 13.5% beta 1639 base pairs and 2630 stacking pairs defined. Time for finding SS restraints: 50.29 Creating SS restraints... Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 197 through 203 removed outlier: 3.861A pdb=" N GLU C 201 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 214 removed outlier: 4.008A pdb=" N SER C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TRP C 213 " --> pdb=" O GLY C 209 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 268 removed outlier: 4.019A pdb=" N LYS C 268 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 61 Processing helix chain 'D' and resid 62 through 69 Processing helix chain 'D' and resid 121 through 127 Processing helix chain 'E' and resid 29 through 42 removed outlier: 3.933A pdb=" N PHE E 34 " --> pdb=" O GLU E 30 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASP E 35 " --> pdb=" O SER E 31 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA E 36 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET E 39 " --> pdb=" O ASP E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 120 removed outlier: 3.641A pdb=" N ILE E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL E 118 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE E 119 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP E 120 " --> pdb=" O SER E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 146 removed outlier: 3.524A pdb=" N LYS E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 166 Processing helix chain 'E' and resid 177 through 181 removed outlier: 3.874A pdb=" N ILE E 181 " --> pdb=" O ALA E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 removed outlier: 3.790A pdb=" N HIS E 189 " --> pdb=" O ASP E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 removed outlier: 3.741A pdb=" N GLU E 200 " --> pdb=" O LYS E 196 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS E 201 " --> pdb=" O ALA E 197 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU E 203 " --> pdb=" O VAL E 199 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU E 204 " --> pdb=" O GLU E 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 8 removed outlier: 3.743A pdb=" N TYR F 8 " --> pdb=" O LEU F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 20 removed outlier: 3.598A pdb=" N ALA F 15 " --> pdb=" O GLU F 11 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR F 18 " --> pdb=" O PRO F 14 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE F 20 " --> pdb=" O LEU F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 61 removed outlier: 4.121A pdb=" N ALA F 53 " --> pdb=" O ALA F 49 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU F 56 " --> pdb=" O SER F 52 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR F 58 " --> pdb=" O VAL F 54 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N PHE F 59 " --> pdb=" O GLU F 55 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 106 removed outlier: 4.172A pdb=" N TYR F 97 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS F 102 " --> pdb=" O ASP F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 111 removed outlier: 3.876A pdb=" N VAL F 111 " --> pdb=" O SER F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 174 removed outlier: 3.699A pdb=" N GLU F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU F 170 " --> pdb=" O ALA F 166 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN F 172 " --> pdb=" O GLU F 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 81 removed outlier: 3.922A pdb=" N GLY G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG G 70 " --> pdb=" O HIS G 66 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER G 71 " --> pdb=" O GLY G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 152 removed outlier: 3.741A pdb=" N VAL G 152 " --> pdb=" O ASN G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 20 removed outlier: 3.555A pdb=" N LYS H 9 " --> pdb=" O ILE H 5 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU H 13 " --> pdb=" O LYS H 9 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU H 14 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER H 17 " --> pdb=" O GLU H 13 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS H 20 " --> pdb=" O ALA H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 48 removed outlier: 3.610A pdb=" N GLU H 40 " --> pdb=" O SER H 36 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS H 43 " --> pdb=" O THR H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 67 removed outlier: 3.645A pdb=" N GLN H 66 " --> pdb=" O ARG H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 78 removed outlier: 4.353A pdb=" N THR H 77 " --> pdb=" O ASN H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 105 removed outlier: 3.869A pdb=" N ASN H 97 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE H 99 " --> pdb=" O VAL H 95 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU H 104 " --> pdb=" O ALA H 100 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA H 105 " --> pdb=" O LYS H 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 25 through 30 Processing helix chain 'I' and resid 34 through 46 removed outlier: 3.643A pdb=" N PHE I 38 " --> pdb=" O ASN I 34 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LYS I 40 " --> pdb=" O MET I 36 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLU I 41 " --> pdb=" O GLY I 37 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG I 45 " --> pdb=" O GLU I 41 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR I 46 " --> pdb=" O PHE I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 50 removed outlier: 3.557A pdb=" N ALA I 50 " --> pdb=" O ALA I 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 47 through 50' Processing helix chain 'I' and resid 76 through 84 removed outlier: 3.670A pdb=" N LYS I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 112 removed outlier: 3.586A pdb=" N GLU I 107 " --> pdb=" O ASP I 103 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 133 removed outlier: 3.576A pdb=" N ARG I 126 " --> pdb=" O GLU I 122 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR I 131 " --> pdb=" O MET I 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 39 removed outlier: 3.535A pdb=" N ALA J 34 " --> pdb=" O SER J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 63 removed outlier: 3.670A pdb=" N ILE J 63 " --> pdb=" O ALA J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 73 Processing helix chain 'J' and resid 90 through 96 Processing helix chain 'J' and resid 98 through 110 removed outlier: 3.756A pdb=" N LEU J 102 " --> pdb=" O PRO J 98 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA J 105 " --> pdb=" O MET J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 123 removed outlier: 3.934A pdb=" N PHE J 120 " --> pdb=" O GLY J 116 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 137 Processing helix chain 'K' and resid 104 through 109 removed outlier: 3.978A pdb=" N GLU K 108 " --> pdb=" O ARG K 104 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN K 109 " --> pdb=" O GLU K 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 104 through 109' Processing helix chain 'K' and resid 111 through 117 removed outlier: 3.744A pdb=" N VAL K 115 " --> pdb=" O PHE K 111 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU K 117 " --> pdb=" O LYS K 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 6 removed outlier: 3.837A pdb=" N LEU L 6 " --> pdb=" O LEU L 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 61 Processing helix chain 'L' and resid 78 through 85 removed outlier: 3.807A pdb=" N GLY L 84 " --> pdb=" O LYS L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 97 Processing helix chain 'L' and resid 129 through 138 removed outlier: 3.597A pdb=" N LYS L 133 " --> pdb=" O SER L 129 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU L 134 " --> pdb=" O ALA L 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 59 removed outlier: 3.635A pdb=" N ALA M 53 " --> pdb=" O ALA M 49 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG M 56 " --> pdb=" O ILE M 52 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR M 57 " --> pdb=" O ALA M 53 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS M 59 " --> pdb=" O THR M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 125 removed outlier: 3.501A pdb=" N ARG M 115 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU M 116 " --> pdb=" O GLU M 112 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG M 119 " --> pdb=" O ARG M 115 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA M 121 " --> pdb=" O ALA M 117 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS M 123 " --> pdb=" O ARG M 119 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS M 124 " --> pdb=" O LEU M 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 28 removed outlier: 3.625A pdb=" N LYS N 14 " --> pdb=" O SER N 10 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA N 15 " --> pdb=" O ALA N 11 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU N 20 " --> pdb=" O MET N 16 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE N 25 " --> pdb=" O THR N 21 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE N 26 " --> pdb=" O THR N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 54 removed outlier: 4.370A pdb=" N SER N 42 " --> pdb=" O LYS N 38 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL N 43 " --> pdb=" O GLU N 39 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS N 46 " --> pdb=" O SER N 42 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS N 52 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG N 53 " --> pdb=" O THR N 49 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLY N 54 " --> pdb=" O LEU N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 66 removed outlier: 3.501A pdb=" N ARG N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA N 64 " --> pdb=" O ARG N 60 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR N 65 " --> pdb=" O GLN N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 86 removed outlier: 4.225A pdb=" N LEU N 83 " --> pdb=" O ALA N 79 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE N 84 " --> pdb=" O LEU N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 91 Processing helix chain 'O' and resid 8 through 22 removed outlier: 3.505A pdb=" N LYS O 13 " --> pdb=" O ALA O 9 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL O 18 " --> pdb=" O ARG O 14 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA O 20 " --> pdb=" O ALA O 16 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS O 21 " --> pdb=" O ARG O 17 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU O 22 " --> pdb=" O VAL O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 72 through 89 removed outlier: 3.530A pdb=" N LYS O 76 " --> pdb=" O SER O 72 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL O 77 " --> pdb=" O ALA O 73 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA O 82 " --> pdb=" O GLY O 78 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU O 87 " --> pdb=" O LYS O 83 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS O 88 " --> pdb=" O ARG O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 105 through 116 removed outlier: 3.552A pdb=" N LEU O 109 " --> pdb=" O ARG O 105 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA O 113 " --> pdb=" O LEU O 109 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG O 114 " --> pdb=" O ALA O 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 13 Processing helix chain 'P' and resid 14 through 16 No H-bonds generated for 'chain 'P' and resid 14 through 16' Processing helix chain 'P' and resid 56 through 59 Processing helix chain 'P' and resid 100 through 106 removed outlier: 3.727A pdb=" N LEU P 103 " --> pdb=" O LEU P 100 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG P 104 " --> pdb=" O TYR P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 114 removed outlier: 3.645A pdb=" N ARG P 112 " --> pdb=" O GLY P 108 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS P 114 " --> pdb=" O ALA P 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 6 through 22 removed outlier: 3.585A pdb=" N THR Q 10 " --> pdb=" O GLY Q 6 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG Q 13 " --> pdb=" O VAL Q 9 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS Q 15 " --> pdb=" O ARG Q 11 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL Q 17 " --> pdb=" O ARG Q 13 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU Q 18 " --> pdb=" O ARG Q 14 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 4.215A pdb=" N THR Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 31 through 72 removed outlier: 3.962A pdb=" N GLN Q 37 " --> pdb=" O LYS Q 33 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG Q 50 " --> pdb=" O ALA Q 46 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS Q 59 " --> pdb=" O ARG Q 55 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE Q 62 " --> pdb=" O ARG Q 58 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG Q 64 " --> pdb=" O LEU Q 60 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA Q 67 " --> pdb=" O THR Q 63 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG Q 70 " --> pdb=" O ASN Q 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 86 removed outlier: 3.612A pdb=" N LEU Q 85 " --> pdb=" O HIS Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 92 through 102 removed outlier: 3.615A pdb=" N ASN Q 101 " --> pdb=" O ASP Q 97 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP Q 102 " --> pdb=" O LEU Q 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 117 removed outlier: 3.537A pdb=" N ALA Q 110 " --> pdb=" O PHE Q 106 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA Q 113 " --> pdb=" O LEU Q 109 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS Q 114 " --> pdb=" O ALA Q 110 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA Q 115 " --> pdb=" O ASP Q 111 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU Q 117 " --> pdb=" O ALA Q 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.960A pdb=" N LEU S 19 " --> pdb=" O ARG S 15 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG S 25 " --> pdb=" O MET S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 31 Processing helix chain 'S' and resid 32 through 39 removed outlier: 3.782A pdb=" N LEU S 36 " --> pdb=" O ALA S 32 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN S 37 " --> pdb=" O VAL S 33 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU S 38 " --> pdb=" O SER S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 60 removed outlier: 4.518A pdb=" N ILE S 46 " --> pdb=" O ALA S 42 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA S 58 " --> pdb=" O ALA S 54 " (cutoff:3.500A) Processing helix chain 'S' and resid 88 through 92 removed outlier: 3.659A pdb=" N ARG S 92 " --> pdb=" O ALA S 89 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 6 removed outlier: 3.626A pdb=" N ASP T 6 " --> pdb=" O ASP T 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 3 through 6' Processing helix chain 'T' and resid 14 through 21 removed outlier: 3.632A pdb=" N LEU T 20 " --> pdb=" O ARG T 16 " (cutoff:3.500A) Processing helix chain 'T' and resid 35 through 47 removed outlier: 3.572A pdb=" N ASP T 41 " --> pdb=" O THR T 37 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU T 44 " --> pdb=" O LYS T 40 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 68 No H-bonds generated for 'chain 'U' and resid 66 through 68' Processing helix chain 'X' and resid 40 through 66 removed outlier: 3.522A pdb=" N ILE X 44 " --> pdb=" O ASN X 40 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLN X 50 " --> pdb=" O ALA X 46 " (cutoff:3.500A) Processing helix chain 'X' and resid 96 through 101 Processing helix chain 'X' and resid 102 through 104 No H-bonds generated for 'chain 'X' and resid 102 through 104' Processing helix chain 'X' and resid 111 through 115 removed outlier: 3.931A pdb=" N LEU X 115 " --> pdb=" O LYS X 112 " (cutoff:3.500A) Processing helix chain 'Y' and resid 50 through 55 removed outlier: 3.614A pdb=" N LYS Y 55 " --> pdb=" O ALA Y 51 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2 through 8 removed outlier: 3.586A pdb=" N ASP Z 8 " --> pdb=" O ASN Z 4 " (cutoff:3.500A) Processing helix chain 'Z' and resid 10 through 35 removed outlier: 3.514A pdb=" N PHE Z 26 " --> pdb=" O LYS Z 22 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN Z 27 " --> pdb=" O GLU Z 23 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE Z 30 " --> pdb=" O PHE Z 26 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN Z 31 " --> pdb=" O ASN Z 27 " (cutoff:3.500A) Processing helix chain 'Z' and resid 39 through 65 removed outlier: 3.686A pdb=" N ARG Z 47 " --> pdb=" O ILE Z 43 " (cutoff:3.500A) Processing helix chain 'a' and resid 16 through 27 Processing helix chain 'a' and resid 40 through 50 removed outlier: 3.758A pdb=" N MET a 46 " --> pdb=" O ALA a 42 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 18 Processing helix chain 'd' and resid 8 through 17 Processing helix chain 'd' and resid 17 through 23 Processing helix chain 'd' and resid 24 through 37 removed outlier: 3.582A pdb=" N LYS d 37 " --> pdb=" O ARG d 33 " (cutoff:3.500A) Processing helix chain 'e' and resid 7 through 14 Processing helix chain 'e' and resid 37 through 46 removed outlier: 4.007A pdb=" N LYS e 46 " --> pdb=" O ARG e 42 " (cutoff:3.500A) Processing helix chain 'e' and resid 51 through 59 removed outlier: 4.072A pdb=" N ARG e 57 " --> pdb=" O GLY e 53 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE e 58 " --> pdb=" O ASP e 54 " (cutoff:3.500A) Processing helix chain 'f' and resid 29 through 33 Processing helix chain 'g' and resid 8 through 13 Processing helix chain 'g' and resid 24 through 28 Processing helix chain 'g' and resid 42 through 64 removed outlier: 3.969A pdb=" N ALA g 62 " --> pdb=" O LYS g 58 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU g 63 " --> pdb=" O ASN g 59 " (cutoff:3.500A) Processing helix chain 'g' and resid 76 through 88 removed outlier: 3.835A pdb=" N VAL g 80 " --> pdb=" O ALA g 76 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS g 81 " --> pdb=" O GLN g 77 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU g 82 " --> pdb=" O ASP g 78 " (cutoff:3.500A) Processing helix chain 'g' and resid 104 through 121 Processing helix chain 'g' and resid 130 through 149 removed outlier: 4.104A pdb=" N LYS g 146 " --> pdb=" O GLU g 142 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE g 147 " --> pdb=" O ARG g 143 " (cutoff:3.500A) Processing helix chain 'g' and resid 150 through 154 removed outlier: 3.538A pdb=" N ASP g 153 " --> pdb=" O GLY g 150 " (cutoff:3.500A) Processing helix chain 'g' and resid 169 through 179 Processing helix chain 'g' and resid 192 through 196 removed outlier: 3.556A pdb=" N GLU g 195 " --> pdb=" O ASP g 192 " (cutoff:3.500A) Processing helix chain 'g' and resid 206 through 225 removed outlier: 3.755A pdb=" N LEU g 213 " --> pdb=" O ALA g 209 " (cutoff:3.500A) Processing helix chain 'h' and resid 7 through 12 removed outlier: 3.967A pdb=" N ILE h 12 " --> pdb=" O VAL h 8 " (cutoff:3.500A) Processing helix chain 'h' and resid 27 through 46 removed outlier: 3.611A pdb=" N PHE h 31 " --> pdb=" O ASP h 27 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU h 32 " --> pdb=" O TYR h 28 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS h 44 " --> pdb=" O GLU h 40 " (cutoff:3.500A) Processing helix chain 'h' and resid 72 through 77 Processing helix chain 'h' and resid 80 through 95 removed outlier: 3.512A pdb=" N GLU h 84 " --> pdb=" O GLY h 80 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU h 93 " --> pdb=" O ALA h 89 " (cutoff:3.500A) Processing helix chain 'h' and resid 107 through 110 Processing helix chain 'h' and resid 111 through 125 Processing helix chain 'h' and resid 128 through 144 Processing helix chain 'i' and resid 8 through 16 Processing helix chain 'i' and resid 45 through 62 removed outlier: 4.452A pdb=" N MET i 60 " --> pdb=" O LYS i 56 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N TYR i 61 " --> pdb=" O LEU i 57 " (cutoff:3.500A) Processing helix chain 'i' and resid 64 through 78 Processing helix chain 'i' and resid 81 through 91 Processing helix chain 'i' and resid 93 through 101 Processing helix chain 'i' and resid 106 through 117 Processing helix chain 'i' and resid 142 through 146 removed outlier: 3.577A pdb=" N ARG i 146 " --> pdb=" O GLU i 143 " (cutoff:3.500A) Processing helix chain 'i' and resid 148 through 157 removed outlier: 4.029A pdb=" N VAL i 157 " --> pdb=" O GLU i 153 " (cutoff:3.500A) Processing helix chain 'i' and resid 190 through 198 removed outlier: 3.772A pdb=" N ILE i 194 " --> pdb=" O ASN i 190 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR i 198 " --> pdb=" O ILE i 194 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 70 removed outlier: 3.836A pdb=" N ASN j 70 " --> pdb=" O ASP j 66 " (cutoff:3.500A) Processing helix chain 'j' and resid 108 through 119 Processing helix chain 'j' and resid 132 through 147 Processing helix chain 'j' and resid 149 through 157 Processing helix chain 'k' and resid 15 through 33 Processing helix chain 'k' and resid 70 through 82 removed outlier: 3.968A pdb=" N GLU k 74 " --> pdb=" O ALA k 70 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ARG k 77 " --> pdb=" O GLN k 73 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER k 82 " --> pdb=" O LEU k 78 " (cutoff:3.500A) Processing helix chain 'l' and resid 20 through 31 removed outlier: 3.910A pdb=" N SER l 24 " --> pdb=" O SER l 20 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET l 31 " --> pdb=" O ILE l 27 " (cutoff:3.500A) Processing helix chain 'l' and resid 35 through 53 Processing helix chain 'l' and resid 57 through 69 Processing helix chain 'l' and resid 92 through 110 removed outlier: 3.551A pdb=" N LEU l 110 " --> pdb=" O ASN l 106 " (cutoff:3.500A) Processing helix chain 'l' and resid 115 through 129 Processing helix chain 'l' and resid 131 through 145 removed outlier: 4.016A pdb=" N VAL l 135 " --> pdb=" O THR l 131 " (cutoff:3.500A) Processing helix chain 'l' and resid 149 through 153 Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 30 through 44 removed outlier: 3.611A pdb=" N ILE m 36 " --> pdb=" O LEU m 32 " (cutoff:3.500A) Processing helix chain 'm' and resid 115 through 122 Processing helix chain 'n' and resid 35 through 39 removed outlier: 3.702A pdb=" N ILE n 39 " --> pdb=" O ILE n 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 35 through 39' Processing helix chain 'n' and resid 43 through 55 removed outlier: 3.560A pdb=" N ASP n 47 " --> pdb=" O ALA n 43 " (cutoff:3.500A) Proline residue: n 51 - end of helix Processing helix chain 'n' and resid 71 through 91 removed outlier: 3.973A pdb=" N ASP n 91 " --> pdb=" O LEU n 87 " (cutoff:3.500A) Processing helix chain 'n' and resid 94 through 102 removed outlier: 3.810A pdb=" N ARG n 100 " --> pdb=" O THR n 96 " (cutoff:3.500A) Processing helix chain 'o' and resid 14 through 31 removed outlier: 3.576A pdb=" N LEU o 18 " --> pdb=" O ASP o 14 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR o 28 " --> pdb=" O LYS o 24 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA o 29 " --> pdb=" O ILE o 25 " (cutoff:3.500A) Processing helix chain 'o' and resid 80 through 88 removed outlier: 3.516A pdb=" N MET o 88 " --> pdb=" O VAL o 84 " (cutoff:3.500A) Processing helix chain 'p' and resid 48 through 52 Processing helix chain 'p' and resid 55 through 59 removed outlier: 4.040A pdb=" N ARG p 58 " --> pdb=" O ARG p 55 " (cutoff:3.500A) Processing helix chain 'p' and resid 61 through 80 removed outlier: 3.590A pdb=" N ALA p 65 " --> pdb=" O THR p 61 " (cutoff:3.500A) Processing helix chain 'p' and resid 93 through 105 removed outlier: 3.890A pdb=" N ARG p 100 " --> pdb=" O GLU p 96 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 11 removed outlier: 3.761A pdb=" N LEU q 7 " --> pdb=" O THR q 3 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE q 8 " --> pdb=" O ILE q 4 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG q 9 " --> pdb=" O ASN q 5 " (cutoff:3.500A) Processing helix chain 'r' and resid 14 through 21 Processing helix chain 'r' and resid 26 through 38 Processing helix chain 'r' and resid 51 through 63 removed outlier: 3.539A pdb=" N LEU r 63 " --> pdb=" O ILE r 59 " (cutoff:3.500A) Processing helix chain 'r' and resid 65 through 83 Processing helix chain 'r' and resid 86 through 94 removed outlier: 3.899A pdb=" N GLY r 94 " --> pdb=" O ARG r 90 " (cutoff:3.500A) Processing helix chain 'r' and resid 106 through 111 removed outlier: 4.024A pdb=" N LYS r 110 " --> pdb=" O ALA r 106 " (cutoff:3.500A) Processing helix chain 's' and resid 3 through 12 Processing helix chain 's' and resid 16 through 20 removed outlier: 3.648A pdb=" N GLU s 20 " --> pdb=" O LYS s 17 " (cutoff:3.500A) Processing helix chain 's' and resid 40 through 51 Processing helix chain 't' and resid 4 through 16 removed outlier: 3.549A pdb=" N ASN t 13 " --> pdb=" O ASN t 9 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU t 14 " --> pdb=" O GLN t 10 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE t 15 " --> pdb=" O LEU t 11 " (cutoff:3.500A) Processing helix chain 't' and resid 23 through 46 removed outlier: 4.024A pdb=" N VAL t 27 " --> pdb=" O GLY t 23 " (cutoff:3.500A) Processing helix chain 't' and resid 49 through 74 Processing helix chain 't' and resid 74 through 86 Processing helix chain 'u' and resid 54 through 63 Processing helix chain 'u' and resid 67 through 77 Processing helix chain 'u' and resid 79 through 88 removed outlier: 3.811A pdb=" N PHE u 83 " --> pdb=" O ILE u 79 " (cutoff:3.500A) Processing helix chain 'w' and resid 18 through 22 Processing helix chain 'w' and resid 31 through 38 Processing helix chain 'w' and resid 46 through 51 Processing helix chain 'w' and resid 53 through 70 Processing helix chain 'x' and resid 13 through 25 Processing helix chain 'x' and resid 41 through 45 Processing helix chain 'y' and resid 7 through 41 Processing helix chain 'y' and resid 45 through 63 removed outlier: 3.840A pdb=" N LYS y 63 " --> pdb=" O ASP y 59 " (cutoff:3.500A) Processing helix chain 'y' and resid 69 through 88 removed outlier: 4.365A pdb=" N ALA y 73 " --> pdb=" O LYS y 69 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER y 87 " --> pdb=" O VAL y 83 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5 removed outlier: 4.054A pdb=" N THR C 18 " --> pdb=" O LYS C 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 35 Processing sheet with id=AA3, first strand: chain 'C' and resid 101 through 105 removed outlier: 3.627A pdb=" N ARG C 102 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE C 94 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASN C 95 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N VAL C 78 " --> pdb=" O ASN C 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 129 through 131 removed outlier: 3.606A pdb=" N ALA C 190 " --> pdb=" O LEU C 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 172 through 175 removed outlier: 3.817A pdb=" N VAL C 181 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG C 272 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N MET C 183 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ILE C 270 " --> pdb=" O MET C 183 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 12 through 14 removed outlier: 7.094A pdb=" N LEU D 185 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N VAL D 179 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU D 187 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU D 175 " --> pdb=" O LYS D 189 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N THR D 170 " --> pdb=" O GLY D 112 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLY D 112 " --> pdb=" O THR D 170 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLN D 172 " --> pdb=" O VAL D 110 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N VAL D 110 " --> pdb=" O GLN D 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 80 through 81 removed outlier: 4.214A pdb=" N GLN D 37 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N GLY D 52 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL D 35 " --> pdb=" O GLY D 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 118 through 120 removed outlier: 3.579A pdb=" N GLY D 118 " --> pdb=" O MET D 164 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 6 through 7 removed outlier: 3.620A pdb=" N ILE E 124 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE E 194 " --> pdb=" O ILE E 124 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR E 174 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE E 154 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL E 176 " --> pdb=" O ILE E 154 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 36 through 37 removed outlier: 3.651A pdb=" N VAL F 89 " --> pdb=" O ILE F 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 130 through 132 Processing sheet with id=AB3, first strand: chain 'G' and resid 9 through 10 removed outlier: 4.079A pdb=" N GLU G 43 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 16 through 17 removed outlier: 3.782A pdb=" N THR G 16 " --> pdb=" O LYS G 28 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL G 25 " --> pdb=" O ARG G 36 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG G 36 " --> pdb=" O VAL G 25 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 96 through 100 removed outlier: 3.870A pdb=" N ARG G 96 " --> pdb=" O ASN G 107 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS G 103 " --> pdb=" O SER G 100 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 122 through 125 removed outlier: 3.646A pdb=" N GLU G 125 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL G 133 " --> pdb=" O GLU G 125 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 56 through 58 removed outlier: 3.676A pdb=" N ILE I 69 " --> pdb=" O GLU I 57 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 99 through 100 Processing sheet with id=AB9, first strand: chain 'J' and resid 124 through 125 removed outlier: 6.109A pdb=" N LEU J 17 " --> pdb=" O ILE J 56 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 74 through 75 removed outlier: 3.731A pdb=" N ARG J 88 " --> pdb=" O TYR J 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 7 through 9 removed outlier: 6.334A pdb=" N ALA K 16 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ALA K 46 " --> pdb=" O ALA K 16 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLU K 18 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL K 24 " --> pdb=" O VAL K 38 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N VAL K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 69 through 70 removed outlier: 3.843A pdb=" N TYR K 76 " --> pdb=" O THR P 76 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL P 64 " --> pdb=" O ARG P 75 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR P 61 " --> pdb=" O ARG P 54 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 102 through 103 removed outlier: 5.929A pdb=" N VAL K 102 " --> pdb=" O ILE K 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'L' and resid 122 through 125 removed outlier: 3.976A pdb=" N VAL L 123 " --> pdb=" O THR L 142 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU L 144 " --> pdb=" O VAL L 123 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA L 125 " --> pdb=" O GLU L 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'M' and resid 35 through 36 removed outlier: 3.717A pdb=" N GLN M 35 " --> pdb=" O LYS M 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 42 through 43 removed outlier: 4.056A pdb=" N ILE M 42 " --> pdb=" O ALA M 95 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA M 76 " --> pdb=" O PRO M 90 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLY M 92 " --> pdb=" O TYR M 74 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR M 74 " --> pdb=" O GLY M 92 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 29 through 33 Processing sheet with id=AC9, first strand: chain 'N' and resid 29 through 33 Processing sheet with id=AD1, first strand: chain 'O' and resid 51 through 57 removed outlier: 6.354A pdb=" N THR O 52 " --> pdb=" O ASP O 46 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ASP O 46 " --> pdb=" O THR O 52 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA O 54 " --> pdb=" O ILE O 44 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE O 34 " --> pdb=" O TYR O 41 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN O 43 " --> pdb=" O ASN O 32 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE O 45 " --> pdb=" O ARG O 30 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG O 30 " --> pdb=" O ILE O 45 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'P' and resid 41 through 47 removed outlier: 3.921A pdb=" N VAL P 33 " --> pdb=" O GLN P 44 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE P 46 " --> pdb=" O VAL P 31 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL P 31 " --> pdb=" O PHE P 46 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR P 28 " --> pdb=" O VAL P 90 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU P 88 " --> pdb=" O ARG P 30 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LYS P 86 " --> pdb=" O HIS P 32 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LYS P 34 " --> pdb=" O ILE P 84 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ILE P 84 " --> pdb=" O LYS P 34 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'R' and resid 3 through 6 Processing sheet with id=AD4, first strand: chain 'R' and resid 60 through 67 removed outlier: 7.226A pdb=" N LYS R 94 " --> pdb=" O GLU R 63 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N GLN R 65 " --> pdb=" O TYR R 92 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TYR R 92 " --> pdb=" O GLN R 65 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 71 through 74 Processing sheet with id=AD6, first strand: chain 'S' and resid 3 through 6 Processing sheet with id=AD7, first strand: chain 'S' and resid 3 through 6 Processing sheet with id=AD8, first strand: chain 'S' and resid 82 through 86 Processing sheet with id=AD9, first strand: chain 'T' and resid 8 through 11 removed outlier: 4.498A pdb=" N ARG T 10 " --> pdb=" O GLU T 29 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL T 81 " --> pdb=" O TYR T 26 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS T 53 " --> pdb=" O LYS T 82 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'U' and resid 8 through 10 removed outlier: 4.082A pdb=" N ALA U 25 " --> pdb=" O LEU U 34 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'U' and resid 81 through 82 Processing sheet with id=AE3, first strand: chain 'V' and resid 30 through 31 removed outlier: 4.208A pdb=" N GLY V 30 " --> pdb=" O ARG V 47 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG V 47 " --> pdb=" O GLY V 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'V' and resid 38 through 39 removed outlier: 3.653A pdb=" N VAL V 39 " --> pdb=" O GLY V 73 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY V 73 " --> pdb=" O VAL V 39 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'V' and resid 59 through 61 removed outlier: 4.023A pdb=" N PHE V 68 " --> pdb=" O GLY V 60 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'X' and resid 84 through 85 Processing sheet with id=AE7, first strand: chain 'Y' and resid 13 through 17 removed outlier: 3.736A pdb=" N SER Y 25 " --> pdb=" O ASN Y 17 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'a' and resid 34 through 38 Processing sheet with id=AE9, first strand: chain 'b' and resid 48 through 49 Processing sheet with id=AF1, first strand: chain 'c' and resid 17 through 20 removed outlier: 3.631A pdb=" N LYS c 41 " --> pdb=" O CYS c 36 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'e' and resid 15 through 16 removed outlier: 4.243A pdb=" N LYS e 15 " --> pdb=" O LYS e 23 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS e 23 " --> pdb=" O LYS e 15 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'f' and resid 15 through 19 Processing sheet with id=AF4, first strand: chain 'g' and resid 31 through 34 removed outlier: 6.889A pdb=" N ILE g 40 " --> pdb=" O PHE g 32 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'g' and resid 67 through 69 removed outlier: 6.071A pdb=" N LEU g 68 " --> pdb=" O PHE g 162 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'g' and resid 184 through 187 removed outlier: 3.608A pdb=" N GLY g 185 " --> pdb=" O VAL g 198 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'h' and resid 20 through 21 removed outlier: 3.659A pdb=" N LYS h 53 " --> pdb=" O HIS h 68 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'h' and resid 164 through 170 removed outlier: 3.684A pdb=" N GLY h 147 " --> pdb=" O TYR h 202 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'i' and resid 124 through 125 removed outlier: 3.764A pdb=" N GLY i 140 " --> pdb=" O LEU i 120 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'j' and resid 15 through 25 removed outlier: 5.419A pdb=" N LEU j 15 " --> pdb=" O VAL j 38 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL j 38 " --> pdb=" O LEU j 15 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'j' and resid 85 through 86 Processing sheet with id=AG3, first strand: chain 'k' and resid 36 through 47 removed outlier: 6.767A pdb=" N THR k 38 " --> pdb=" O GLN k 66 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N GLN k 66 " --> pdb=" O THR k 38 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N THR k 40 " --> pdb=" O ASN k 64 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASN k 64 " --> pdb=" O THR k 40 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ASP k 42 " --> pdb=" O ILE k 62 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE k 62 " --> pdb=" O ASP k 42 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG k 87 " --> pdb=" O ILE k 9 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'l' and resid 73 through 74 Processing sheet with id=AG5, first strand: chain 'l' and resid 77 through 78 Processing sheet with id=AG6, first strand: chain 'm' and resid 24 through 27 removed outlier: 3.540A pdb=" N ASP m 48 " --> pdb=" O PHE m 63 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'm' and resid 76 through 78 removed outlier: 5.132A pdb=" N VAL m 127 " --> pdb=" O SER m 107 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N SER m 107 " --> pdb=" O VAL m 127 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL m 131 " --> pdb=" O ILE m 103 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE m 103 " --> pdb=" O VAL m 131 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'n' and resid 6 through 11 removed outlier: 4.044A pdb=" N TYR n 6 " --> pdb=" O LEU n 21 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY n 8 " --> pdb=" O VAL n 19 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL n 19 " --> pdb=" O GLY n 8 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL n 29 " --> pdb=" O VAL n 65 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL n 67 " --> pdb=" O VAL n 29 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'o' and resid 7 through 12 Processing sheet with id=AH1, first strand: chain 'o' and resid 47 through 52 Processing sheet with id=AH2, first strand: chain 'p' and resid 41 through 47 removed outlier: 3.944A pdb=" N ASN p 42 " --> pdb=" O ASP p 38 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ILE p 36 " --> pdb=" O ILE p 44 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N TRP p 46 " --> pdb=" O VAL p 34 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL p 34 " --> pdb=" O TRP p 46 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR p 87 " --> pdb=" O ALA p 23 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'q' and resid 43 through 53 removed outlier: 6.447A pdb=" N ARG q 67 " --> pdb=" O THR q 48 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL q 50 " --> pdb=" O TYR q 65 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N TYR q 65 " --> pdb=" O VAL q 50 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR q 52 " --> pdb=" O ARG q 63 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ARG q 63 " --> pdb=" O THR q 52 " (cutoff:3.500A) removed outlier: 10.140A pdb=" N TYR q 108 " --> pdb=" O GLU q 75 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N THR q 77 " --> pdb=" O TYR q 108 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ILE q 110 " --> pdb=" O THR q 77 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N TYR q 79 " --> pdb=" O ILE q 110 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'u' and resid 3 through 6 Processing sheet with id=AH5, first strand: chain 'u' and resid 39 through 41 removed outlier: 3.624A pdb=" N LYS u 50 " --> pdb=" O THR u 39 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'v' and resid 37 through 49 removed outlier: 4.456A pdb=" N LYS v 38 " --> pdb=" O HIS v 33 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N HIS v 33 " --> pdb=" O LYS v 38 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR v 29 " --> pdb=" O TYR v 42 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR v 24 " --> pdb=" O VAL v 15 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLU v 28 " --> pdb=" O GLN v 11 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N GLN v 11 " --> pdb=" O GLU v 28 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N LYS v 62 " --> pdb=" O VAL v 78 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL v 78 " --> pdb=" O LYS v 62 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ARG v 74 " --> pdb=" O THR v 66 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'x' and resid 31 through 33 1494 hydrogen bonds defined for protein. 4176 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4120 hydrogen bonds 6430 hydrogen bond angles 0 basepair planarities 1639 basepair parallelities 2630 stacking parallelities Total time for adding SS restraints: 232.24 Time building geometry restraints manager: 61.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.23: 6614 1.23 - 1.38: 37782 1.38 - 1.52: 73331 1.52 - 1.67: 29993 1.67 - 1.81: 165 Bond restraints: 147885 Sorted by residual: bond pdb=" C LYS X 69 " pdb=" O LYS X 69 " ideal model delta sigma weight residual 1.235 1.088 0.147 1.26e-02 6.30e+03 1.36e+02 bond pdb=" C GLU X 63 " pdb=" O GLU X 63 " ideal model delta sigma weight residual 1.236 1.144 0.092 1.29e-02 6.01e+03 5.06e+01 bond pdb=" CA GLN S 95 " pdb=" C GLN S 95 " ideal model delta sigma weight residual 1.523 1.447 0.077 1.24e-02 6.50e+03 3.82e+01 bond pdb=" C GLU X 54 " pdb=" O GLU X 54 " ideal model delta sigma weight residual 1.235 1.153 0.081 1.38e-02 5.25e+03 3.48e+01 bond pdb=" CA ASN X 48 " pdb=" C ASN X 48 " ideal model delta sigma weight residual 1.524 1.454 0.071 1.28e-02 6.10e+03 3.05e+01 ... (remaining 147880 not shown) Histogram of bond angle deviations from ideal: 82.81 - 97.07: 7 97.07 - 111.33: 90449 111.33 - 125.59: 116724 125.59 - 139.85: 14718 139.85 - 154.11: 2 Bond angle restraints: 221900 Sorted by residual: angle pdb=" C4' G A 589 " pdb=" C3' G A 589 " pdb=" O3' G A 589 " ideal model delta sigma weight residual 109.40 140.78 -31.38 1.50e+00 4.44e-01 4.38e+02 angle pdb=" C4' G A 83 " pdb=" C3' G A 83 " pdb=" O3' G A 83 " ideal model delta sigma weight residual 109.40 82.81 26.59 1.50e+00 4.44e-01 3.14e+02 angle pdb=" C LYS X 69 " pdb=" N GLU X 70 " pdb=" CA GLU X 70 " ideal model delta sigma weight residual 121.54 154.11 -32.57 1.91e+00 2.74e-01 2.91e+02 angle pdb=" N LYS X 51 " pdb=" CA LYS X 51 " pdb=" C LYS X 51 " ideal model delta sigma weight residual 111.07 93.10 17.97 1.07e+00 8.73e-01 2.82e+02 angle pdb=" C4' G A 82 " pdb=" C3' G A 82 " pdb=" O3' G A 82 " ideal model delta sigma weight residual 113.00 89.99 23.01 1.50e+00 4.44e-01 2.35e+02 ... (remaining 221895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 79029 35.99 - 71.98: 11028 71.98 - 107.97: 1358 107.97 - 143.96: 53 143.96 - 179.95: 90 Dihedral angle restraints: 91558 sinusoidal: 79508 harmonic: 12050 Sorted by residual: dihedral pdb=" CA LYS X 69 " pdb=" C LYS X 69 " pdb=" N GLU X 70 " pdb=" CA GLU X 70 " ideal model delta harmonic sigma weight residual 180.00 104.69 75.31 0 5.00e+00 4.00e-02 2.27e+02 dihedral pdb=" C5' A A1092 " pdb=" C4' A A1092 " pdb=" C3' A A1092 " pdb=" O3' A A1092 " ideal model delta sinusoidal sigma weight residual 147.00 76.02 70.98 1 8.00e+00 1.56e-02 1.01e+02 dihedral pdb=" C4' A A2295 " pdb=" C3' A A2295 " pdb=" C2' A A2295 " pdb=" C1' A A2295 " ideal model delta sinusoidal sigma weight residual -35.00 35.43 -70.43 1 8.00e+00 1.56e-02 9.98e+01 ... (remaining 91555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.179: 27139 0.179 - 0.359: 147 0.359 - 0.538: 7 0.538 - 0.717: 3 0.717 - 0.897: 1 Chirality restraints: 27297 Sorted by residual: chirality pdb=" C3' G A 589 " pdb=" C4' G A 589 " pdb=" O3' G A 589 " pdb=" C2' G A 589 " both_signs ideal model delta sigma weight residual False -2.74 -1.85 -0.90 2.00e-01 2.50e+01 2.01e+01 chirality pdb=" C4' A A1173 " pdb=" C5' A A1173 " pdb=" O4' A A1173 " pdb=" C3' A A1173 " 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' A A1173 " pdb=" O4' A A1173 " pdb=" C2' A A1173 " pdb=" N9 A A1173 " both_signs ideal model delta sigma weight residual False 2.44 1.80 0.63 2.00e-01 2.50e+01 1.01e+01 ... (remaining 27294 not shown) Planarity restraints: 11599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A A 366 " -0.138 2.00e-02 2.50e+03 9.83e-02 2.66e+02 pdb=" N9 A A 366 " 0.038 2.00e-02 2.50e+03 pdb=" C8 A A 366 " 0.029 2.00e-02 2.50e+03 pdb=" N7 A A 366 " 0.081 2.00e-02 2.50e+03 pdb=" C5 A A 366 " 0.066 2.00e-02 2.50e+03 pdb=" C6 A A 366 " 0.100 2.00e-02 2.50e+03 pdb=" N6 A A 366 " -0.241 2.00e-02 2.50e+03 pdb=" N1 A A 366 " 0.071 2.00e-02 2.50e+03 pdb=" C2 A A 366 " 0.011 2.00e-02 2.50e+03 pdb=" N3 A A 366 " -0.026 2.00e-02 2.50e+03 pdb=" C4 A A 366 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 841 " 0.093 2.00e-02 2.50e+03 9.37e-02 2.41e+02 pdb=" N9 A A 841 " 0.020 2.00e-02 2.50e+03 pdb=" C8 A A 841 " -0.030 2.00e-02 2.50e+03 pdb=" N7 A A 841 " -0.087 2.00e-02 2.50e+03 pdb=" C5 A A 841 " -0.069 2.00e-02 2.50e+03 pdb=" C6 A A 841 " -0.108 2.00e-02 2.50e+03 pdb=" N6 A A 841 " 0.236 2.00e-02 2.50e+03 pdb=" N1 A A 841 " -0.075 2.00e-02 2.50e+03 pdb=" C2 A A 841 " -0.008 2.00e-02 2.50e+03 pdb=" N3 A A 841 " 0.032 2.00e-02 2.50e+03 pdb=" C4 A A 841 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A1661 " 0.090 2.00e-02 2.50e+03 9.30e-02 2.38e+02 pdb=" N9 A A1661 " 0.025 2.00e-02 2.50e+03 pdb=" C8 A A1661 " -0.030 2.00e-02 2.50e+03 pdb=" N7 A A1661 " -0.086 2.00e-02 2.50e+03 pdb=" C5 A A1661 " -0.070 2.00e-02 2.50e+03 pdb=" C6 A A1661 " -0.107 2.00e-02 2.50e+03 pdb=" N6 A A1661 " 0.235 2.00e-02 2.50e+03 pdb=" N1 A A1661 " -0.074 2.00e-02 2.50e+03 pdb=" C2 A A1661 " -0.008 2.00e-02 2.50e+03 pdb=" N3 A A1661 " 0.031 2.00e-02 2.50e+03 pdb=" C4 A A1661 " -0.005 2.00e-02 2.50e+03 ... (remaining 11596 not shown) Histogram of nonbonded interaction distances: 1.07 - 1.84: 28 1.84 - 2.60: 2923 2.60 - 3.37: 162396 3.37 - 4.13: 440946 4.13 - 4.90: 600629 Nonbonded interactions: 1206922 Sorted by model distance: nonbonded pdb=" N2 G A2198 " pdb=" OP2 G A2199 " model vdw 1.073 2.520 nonbonded pdb=" N3 U A2147 " pdb=" O2' A A2176 " model vdw 1.078 2.520 nonbonded pdb=" O2 U A2147 " pdb=" C2' A A2176 " model vdw 1.375 3.470 nonbonded pdb=" C2 U A2147 " pdb=" C2' A A2176 " model vdw 1.380 3.690 nonbonded pdb=" O3' G A2185 " pdb=" O4' G A2186 " model vdw 1.423 3.040 ... (remaining 1206917 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: 10.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 44.200 Check model and map are aligned: 1.450 Set scattering table: 0.920 Process input model: 483.540 Find NCS groups from input model: 2.730 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 546.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5537 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 0.147 147885 Z= 0.560 Angle : 1.504 32.567 221900 Z= 0.640 Chirality : 0.037 0.897 27297 Planarity : 0.016 0.392 11599 Dihedral : 24.125 179.951 85318 Min Nonbonded Distance : 1.073 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 2.34 % Allowed : 6.64 % Favored : 91.02 % Rotamer: Outliers : 0.26 % Allowed : 1.28 % Favored : 98.46 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.87 % Cis-general : 1.75 % 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: -1.82 (0.11), residues: 5691 helix: -2.96 (0.07), residues: 1636 sheet: -2.72 (0.15), residues: 817 loop : 0.43 (0.12), residues: 3238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP Q 61 HIS 0.006 0.001 HIS S 60 PHE 0.013 0.001 PHE S 85 TYR 0.015 0.001 TYR N 91 ARG 0.005 0.000 ARG S 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11382 Ramachandran restraints generated. 5691 Oldfield, 0 Emsley, 5691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11382 Ramachandran restraints generated. 5691 Oldfield, 0 Emsley, 5691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1355 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1348 time to evaluate : 4.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 93 LEU cc_start: 0.6513 (tp) cc_final: 0.5848 (tp) REVERT: C 185 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7253 (tp) REVERT: D 40 THR cc_start: 0.7812 (p) cc_final: 0.6618 (p) REVERT: D 125 ARG cc_start: 0.6455 (ttt90) cc_final: 0.6114 (ttm-80) REVERT: E 99 TYR cc_start: 0.6536 (p90) cc_final: 0.6330 (p90) REVERT: E 142 ILE cc_start: 0.8004 (mt) cc_final: 0.7770 (tp) REVERT: J 32 GLU cc_start: 0.8145 (tt0) cc_final: 0.7857 (tt0) REVERT: K 10 VAL cc_start: 0.7477 (t) cc_final: 0.7038 (m) REVERT: K 20 LEU cc_start: 0.8888 (tp) cc_final: 0.8679 (tp) REVERT: K 96 THR cc_start: 0.7858 (p) cc_final: 0.7486 (p) REVERT: L 58 PHE cc_start: 0.7192 (p90) cc_final: 0.6311 (p90) REVERT: N 80 LEU cc_start: 0.7234 (mp) cc_final: 0.6765 (tt) REVERT: N 87 ILE cc_start: 0.8475 (mp) cc_final: 0.8230 (mp) REVERT: N 99 THR cc_start: 0.7328 (p) cc_final: 0.6727 (p) REVERT: O 1 MET cc_start: 0.0778 (ttt) cc_final: 0.0414 (ttt) REVERT: O 47 ASP cc_start: 0.6323 (m-30) cc_final: 0.6048 (m-30) REVERT: O 51 VAL cc_start: 0.6675 (t) cc_final: 0.6337 (p) REVERT: P 29 LEU cc_start: 0.7495 (pp) cc_final: 0.6892 (pp) REVERT: P 62 PHE cc_start: 0.6991 (p90) cc_final: 0.6683 (p90) REVERT: P 63 THR cc_start: 0.7937 (p) cc_final: 0.7112 (p) REVERT: P 102 TYR cc_start: 0.7008 (p90) cc_final: 0.6693 (p90) REVERT: Q 19 LYS cc_start: 0.8479 (mptt) cc_final: 0.8161 (mmtt) REVERT: S 70 VAL cc_start: 0.8212 (t) cc_final: 0.7367 (m) REVERT: S 100 THR cc_start: 0.5515 (m) cc_final: 0.4957 (p) REVERT: T 1 MET cc_start: 0.5796 (mmm) cc_final: 0.2631 (mtt) REVERT: Y 39 LEU cc_start: 0.7727 (mp) cc_final: 0.7412 (tp) REVERT: b 39 SER cc_start: 0.7036 (m) cc_final: 0.6737 (t) outliers start: 7 outliers final: 3 residues processed: 1351 average time/residue: 1.3602 time to fit residues: 3000.2490 Evaluate side-chains 832 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 828 time to evaluate : 5.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1019 random chunks: chunk 860 optimal weight: 0.9990 chunk 772 optimal weight: 10.0000 chunk 428 optimal weight: 7.9990 chunk 263 optimal weight: 10.0000 chunk 520 optimal weight: 6.9990 chunk 412 optimal weight: 8.9990 chunk 798 optimal weight: 50.0000 chunk 309 optimal weight: 8.9990 chunk 485 optimal weight: 5.9990 chunk 594 optimal weight: 3.9990 chunk 925 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 ASN C 197 ASN C 199 GLN ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 ASN D 172 GLN ** E 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN F 37 ASN ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 HIS K 4 GLN ** L 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 ASN ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 80 HIS Q 37 GLN ** Q 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 102 HIS U 2 HIS V 37 GLN Y 34 GLN Z 16 GLN ** a 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 37 HIS b 40 HIS ** c 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 8 ASN e 60 GLN f 36 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5837 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.173 147885 Z= 0.254 Angle : 0.704 15.508 221900 Z= 0.360 Chirality : 0.036 0.342 27297 Planarity : 0.006 0.129 11599 Dihedral : 24.830 179.721 78745 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 23.80 Ramachandran Plot: Outliers : 0.88 % Allowed : 5.64 % Favored : 93.48 % Rotamer: Outliers : 0.07 % Allowed : 4.30 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.87 % Cis-general : 1.75 % 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: -1.05 (0.11), residues: 5691 helix: -0.38 (0.11), residues: 1722 sheet: -2.21 (0.15), residues: 940 loop : -0.19 (0.12), residues: 3029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 250 HIS 0.024 0.002 HIS E 49 PHE 0.040 0.003 PHE V 80 TYR 0.020 0.003 TYR C 103 ARG 0.025 0.001 ARG D 125 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11382 Ramachandran restraints generated. 5691 Oldfield, 0 Emsley, 5691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11382 Ramachandran restraints generated. 5691 Oldfield, 0 Emsley, 5691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1008 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1006 time to evaluate : 5.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 TYR cc_start: 0.7933 (t80) cc_final: 0.7654 (t80) REVERT: C 93 LEU cc_start: 0.6591 (tp) cc_final: 0.6133 (tp) REVERT: C 204 ASN cc_start: 0.6730 (t0) cc_final: 0.6294 (t0) REVERT: C 265 LYS cc_start: 0.7515 (mmpt) cc_final: 0.7210 (mmtt) REVERT: D 51 LEU cc_start: 0.7798 (tp) cc_final: 0.7516 (tp) REVERT: D 185 LEU cc_start: 0.8550 (tp) cc_final: 0.8254 (tp) REVERT: E 142 ILE cc_start: 0.8677 (mt) cc_final: 0.8247 (tp) REVERT: F 21 ASN cc_start: 0.7852 (t0) cc_final: 0.7443 (t0) REVERT: F 60 ILE cc_start: 0.8365 (mp) cc_final: 0.7761 (mm) REVERT: F 79 LEU cc_start: 0.6077 (pt) cc_final: 0.5805 (pt) REVERT: F 91 LEU cc_start: 0.7725 (pp) cc_final: 0.7414 (pp) REVERT: F 96 MET cc_start: 0.8293 (mmm) cc_final: 0.7183 (mmm) REVERT: I 127 MET cc_start: -0.2706 (mmt) cc_final: -0.3108 (mmt) REVERT: J 68 LYS cc_start: 0.8849 (tmtt) cc_final: 0.8197 (tmtt) REVERT: J 103 GLU cc_start: 0.8108 (pm20) cc_final: 0.7826 (pm20) REVERT: K 19 VAL cc_start: 0.7895 (t) cc_final: 0.7673 (t) REVERT: K 79 PHE cc_start: 0.5959 (m-80) cc_final: 0.5214 (m-80) REVERT: K 82 ASN cc_start: 0.7277 (m-40) cc_final: 0.6722 (m-40) REVERT: L 6 LEU cc_start: 0.6738 (mt) cc_final: 0.6318 (mt) REVERT: L 57 LEU cc_start: 0.7674 (tt) cc_final: 0.7336 (tt) REVERT: L 58 PHE cc_start: 0.8061 (p90) cc_final: 0.6379 (p90) REVERT: N 40 LEU cc_start: 0.9135 (tp) cc_final: 0.8847 (tp) REVERT: N 73 GLU cc_start: 0.7802 (mp0) cc_final: 0.7188 (mp0) REVERT: N 80 LEU cc_start: 0.7339 (mp) cc_final: 0.6999 (mp) REVERT: N 99 THR cc_start: 0.7591 (p) cc_final: 0.6938 (p) REVERT: N 119 LEU cc_start: 0.8290 (pp) cc_final: 0.8010 (pp) REVERT: P 16 LEU cc_start: 0.7697 (mt) cc_final: 0.7222 (mt) REVERT: P 62 PHE cc_start: 0.7175 (p90) cc_final: 0.6751 (p90) REVERT: Q 32 TYR cc_start: 0.8565 (t80) cc_final: 0.7842 (t80) REVERT: Q 52 GLN cc_start: 0.8220 (tp-100) cc_final: 0.7949 (tp-100) REVERT: R 7 THR cc_start: 0.5977 (p) cc_final: 0.5701 (p) REVERT: R 80 LYS cc_start: 0.6846 (mtpt) cc_final: 0.6561 (mtpt) REVERT: S 14 PRO cc_start: 0.8913 (Cg_exo) cc_final: 0.8678 (Cg_endo) REVERT: S 36 LEU cc_start: 0.8497 (pp) cc_final: 0.8168 (pp) REVERT: S 67 ASN cc_start: 0.7552 (p0) cc_final: 0.7311 (p0) REVERT: S 69 LEU cc_start: 0.8328 (mt) cc_final: 0.7533 (mt) REVERT: S 108 SER cc_start: 0.5799 (m) cc_final: 0.3843 (p) REVERT: T 1 MET cc_start: 0.5864 (mmm) cc_final: 0.2413 (mtt) REVERT: T 39 VAL cc_start: 0.8854 (t) cc_final: 0.8611 (t) REVERT: U 80 ARG cc_start: 0.5656 (mtm180) cc_final: 0.4970 (mtm180) REVERT: V 65 ASP cc_start: 0.8690 (m-30) cc_final: 0.8146 (t0) REVERT: Z 30 PHE cc_start: 0.7070 (m-10) cc_final: 0.6824 (m-10) REVERT: b 39 SER cc_start: 0.8642 (m) cc_final: 0.8033 (t) REVERT: b 44 LYS cc_start: 0.8512 (mmpt) cc_final: 0.8137 (mmmt) REVERT: c 5 ILE cc_start: 0.5493 (pt) cc_final: 0.5249 (pt) REVERT: f 23 VAL cc_start: 0.8555 (t) cc_final: 0.8252 (t) outliers start: 2 outliers final: 0 residues processed: 1006 average time/residue: 1.3464 time to fit residues: 2245.2167 Evaluate side-chains 759 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 759 time to evaluate : 5.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1019 random chunks: chunk 514 optimal weight: 20.0000 chunk 287 optimal weight: 20.0000 chunk 770 optimal weight: 20.0000 chunk 630 optimal weight: 20.0000 chunk 255 optimal weight: 20.0000 chunk 927 optimal weight: 40.0000 chunk 1001 optimal weight: 2.9990 chunk 825 optimal weight: 50.0000 chunk 919 optimal weight: 50.0000 chunk 316 optimal weight: 8.9990 chunk 743 optimal weight: 20.0000 overall best weight: 14.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN ** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN C 199 GLN ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN ** M 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 44 GLN Q 37 GLN ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 HIS ** Z 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 32 ASN ** c 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 36 GLN ** 3 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.6395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.159 147885 Z= 0.601 Angle : 1.248 25.138 221900 Z= 0.611 Chirality : 0.056 0.497 27297 Planarity : 0.010 0.202 11599 Dihedral : 26.188 179.767 78745 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 70.03 Ramachandran Plot: Outliers : 0.88 % Allowed : 8.12 % Favored : 91.00 % Rotamer: Outliers : 1.21 % Allowed : 6.57 % Favored : 92.22 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.87 % Cis-general : 1.75 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.55 (0.11), residues: 5691 helix: -0.02 (0.12), residues: 1733 sheet: -2.36 (0.15), residues: 937 loop : -1.12 (0.11), residues: 3021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.007 TRP C 250 HIS 0.024 0.005 HIS J 81 PHE 0.037 0.005 PHE V 38 TYR 0.084 0.005 TYR c 17 ARG 0.058 0.003 ARG D 142 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11382 Ramachandran restraints generated. 5691 Oldfield, 0 Emsley, 5691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11382 Ramachandran restraints generated. 5691 Oldfield, 0 Emsley, 5691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 924 time to evaluate : 5.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 GLN cc_start: 0.8184 (tt0) cc_final: 0.7570 (mt0) REVERT: C 62 TYR cc_start: 0.8345 (t80) cc_final: 0.7321 (t80) REVERT: C 74 ILE cc_start: 0.7164 (tp) cc_final: 0.6432 (tp) REVERT: C 93 LEU cc_start: 0.8330 (tp) cc_final: 0.7673 (tp) REVERT: D 21 ASP cc_start: 0.6357 (p0) cc_final: 0.6126 (p0) REVERT: D 184 ASN cc_start: 0.8084 (m-40) cc_final: 0.7382 (m110) REVERT: E 120 ASP cc_start: 0.7654 (p0) cc_final: 0.6976 (p0) REVERT: E 185 ASP cc_start: 0.8048 (m-30) cc_final: 0.7358 (m-30) REVERT: E 189 HIS cc_start: 0.6862 (m90) cc_final: 0.6371 (m-70) REVERT: E 206 LEU cc_start: 0.8677 (pp) cc_final: 0.8385 (mt) REVERT: F 21 ASN cc_start: 0.8338 (t0) cc_final: 0.7980 (t0) REVERT: F 26 MET cc_start: 0.6402 (ppp) cc_final: 0.5901 (ppp) REVERT: F 96 MET cc_start: 0.8743 (mmm) cc_final: 0.7921 (mmm) REVERT: F 173 VAL cc_start: 0.7894 (t) cc_final: 0.7165 (t) REVERT: I 127 MET cc_start: -0.3343 (mmt) cc_final: -0.3694 (mmt) REVERT: J 68 LYS cc_start: 0.9176 (tmtt) cc_final: 0.8342 (tmtt) REVERT: J 71 THR cc_start: 0.9153 (p) cc_final: 0.8813 (p) REVERT: J 74 ILE cc_start: 0.7968 (tp) cc_final: 0.7755 (tp) REVERT: J 103 GLU cc_start: 0.8198 (pm20) cc_final: 0.7966 (pm20) REVERT: J 142 GLU cc_start: 0.7933 (pp20) cc_final: 0.7713 (pp20) REVERT: K 1 MET cc_start: 0.4749 (ptm) cc_final: 0.4252 (ppp) REVERT: K 19 VAL cc_start: 0.8218 (t) cc_final: 0.7883 (p) REVERT: K 20 LEU cc_start: 0.8139 (tp) cc_final: 0.7869 (tp) REVERT: K 79 PHE cc_start: 0.6850 (m-80) cc_final: 0.6271 (m-80) REVERT: K 102 VAL cc_start: 0.8633 (p) cc_final: 0.8326 (p) REVERT: L 1 MET cc_start: 0.5601 (OUTLIER) cc_final: 0.4449 (ptp) REVERT: M 66 ILE cc_start: 0.8159 (mp) cc_final: 0.7955 (mp) REVERT: M 127 ILE cc_start: 0.8079 (mt) cc_final: 0.7818 (mt) REVERT: N 12 GLN cc_start: 0.8043 (tm-30) cc_final: 0.6562 (tm-30) REVERT: N 16 MET cc_start: 0.8616 (ptm) cc_final: 0.8022 (ptm) REVERT: N 40 LEU cc_start: 0.9250 (tp) cc_final: 0.8922 (tp) REVERT: P 11 ILE cc_start: 0.9131 (pt) cc_final: 0.8846 (pt) REVERT: P 16 LEU cc_start: 0.7930 (mt) cc_final: 0.7592 (mt) REVERT: P 39 ASN cc_start: 0.7676 (p0) cc_final: 0.7440 (p0) REVERT: P 68 SER cc_start: 0.8411 (p) cc_final: 0.7779 (p) REVERT: S 55 ILE cc_start: 0.9445 (mt) cc_final: 0.9194 (mt) REVERT: S 57 ASN cc_start: 0.8247 (m-40) cc_final: 0.7859 (m-40) REVERT: S 69 LEU cc_start: 0.9051 (mt) cc_final: 0.8567 (mt) REVERT: S 76 VAL cc_start: 0.6804 (t) cc_final: 0.6410 (t) REVERT: T 1 MET cc_start: 0.4403 (mmm) cc_final: 0.2065 (mtt) REVERT: U 75 THR cc_start: 0.7838 (p) cc_final: 0.7613 (p) REVERT: V 65 ASP cc_start: 0.8999 (m-30) cc_final: 0.8177 (m-30) REVERT: V 85 LYS cc_start: 0.6257 (tptm) cc_final: 0.5741 (tptm) REVERT: Z 29 ARG cc_start: 0.7800 (ptp-110) cc_final: 0.7322 (ptp-110) REVERT: Z 42 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.5149 (mpt180) REVERT: Z 65 ASN cc_start: 0.7643 (p0) cc_final: 0.7384 (p0) REVERT: b 13 LYS cc_start: 0.8954 (tttp) cc_final: 0.8427 (tptt) REVERT: b 15 LEU cc_start: 0.9336 (mt) cc_final: 0.8715 (mt) REVERT: c 5 ILE cc_start: 0.7334 (pt) cc_final: 0.7045 (pt) REVERT: c 44 LEU cc_start: 0.9063 (tp) cc_final: 0.6656 (tp) REVERT: d 34 ARG cc_start: 0.8475 (ttp80) cc_final: 0.8112 (ptm-80) REVERT: e 61 MET cc_start: 0.6565 (ppp) cc_final: 0.6123 (ppp) REVERT: f 10 ILE cc_start: 0.9247 (mt) cc_final: 0.8970 (mm) outliers start: 33 outliers final: 9 residues processed: 946 average time/residue: 1.3653 time to fit residues: 2143.1781 Evaluate side-chains 710 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 699 time to evaluate : 5.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1019 random chunks: chunk 915 optimal weight: 6.9990 chunk 696 optimal weight: 10.0000 chunk 481 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 442 optimal weight: 9.9990 chunk 622 optimal weight: 7.9990 chunk 930 optimal weight: 50.0000 chunk 984 optimal weight: 10.0000 chunk 486 optimal weight: 6.9990 chunk 881 optimal weight: 0.0070 chunk 265 optimal weight: 8.9990 overall best weight: 5.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 ASN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 GLN ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 GLN ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN ** I 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 124 ASN ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 5 GLN P 80 HIS Q 37 GLN ** Q 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 116 GLN ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN ** S 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 39 ASN U 67 ASN Z 4 ASN ** a 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 48 ASN c 16 ASN ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 32 HIS f 36 GLN ** 3 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.6089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 147885 Z= 0.247 Angle : 0.732 14.580 221900 Z= 0.372 Chirality : 0.037 0.362 27297 Planarity : 0.005 0.118 11599 Dihedral : 26.136 179.523 78745 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 34.27 Ramachandran Plot: Outliers : 0.83 % Allowed : 6.17 % Favored : 93.01 % Rotamer: Outliers : 0.07 % Allowed : 3.67 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.87 % Cis-general : 1.75 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.11), residues: 5691 helix: 0.83 (0.13), residues: 1753 sheet: -1.99 (0.15), residues: 935 loop : -1.00 (0.11), residues: 3003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 250 HIS 0.013 0.002 HIS L 4 PHE 0.025 0.003 PHE D 119 TYR 0.024 0.002 TYR T 26 ARG 0.037 0.001 ARG H 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11382 Ramachandran restraints generated. 5691 Oldfield, 0 Emsley, 5691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11382 Ramachandran restraints generated. 5691 Oldfield, 0 Emsley, 5691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 921 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 919 time to evaluate : 5.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 GLN cc_start: 0.8031 (tt0) cc_final: 0.7480 (mt0) REVERT: C 74 ILE cc_start: 0.6500 (tp) cc_final: 0.5563 (tp) REVERT: C 93 LEU cc_start: 0.8166 (tp) cc_final: 0.7534 (tp) REVERT: C 115 GLU cc_start: 0.7733 (tp30) cc_final: 0.7161 (tp30) REVERT: C 220 VAL cc_start: 0.7696 (t) cc_final: 0.7218 (p) REVERT: C 225 MET cc_start: 0.6910 (mmp) cc_final: 0.6287 (tpp) REVERT: D 5 ILE cc_start: 0.6991 (mt) cc_final: 0.6770 (tp) REVERT: D 22 LEU cc_start: 0.7782 (tp) cc_final: 0.7421 (tt) REVERT: D 154 VAL cc_start: 0.7429 (t) cc_final: 0.5690 (t) REVERT: E 97 TYR cc_start: 0.7043 (m-10) cc_final: 0.6818 (m-10) REVERT: E 120 ASP cc_start: 0.7759 (p0) cc_final: 0.7166 (p0) REVERT: E 185 ASP cc_start: 0.7657 (m-30) cc_final: 0.6952 (m-30) REVERT: E 189 HIS cc_start: 0.6621 (m90) cc_final: 0.6390 (m170) REVERT: E 206 LEU cc_start: 0.8476 (pp) cc_final: 0.8239 (mt) REVERT: F 26 MET cc_start: 0.6148 (ppp) cc_final: 0.5823 (ppp) REVERT: F 97 TYR cc_start: 0.5845 (m-80) cc_final: 0.5104 (m-10) REVERT: F 173 VAL cc_start: 0.7755 (t) cc_final: 0.7273 (t) REVERT: H 99 PHE cc_start: 0.7255 (p90) cc_final: 0.7032 (p90) REVERT: J 68 LYS cc_start: 0.9337 (tmtt) cc_final: 0.9050 (tmtt) REVERT: J 117 ARG cc_start: 0.8072 (ptp-170) cc_final: 0.7229 (ptp-170) REVERT: J 124 ASN cc_start: 0.5987 (OUTLIER) cc_final: 0.5043 (p0) REVERT: K 1 MET cc_start: 0.5229 (ptm) cc_final: 0.4997 (ppp) REVERT: K 19 VAL cc_start: 0.8073 (t) cc_final: 0.7564 (p) REVERT: K 85 VAL cc_start: 0.8791 (m) cc_final: 0.8590 (p) REVERT: L 1 MET cc_start: 0.4355 (mtm) cc_final: 0.3174 (mpp) REVERT: L 5 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6530 (mm-30) REVERT: L 6 LEU cc_start: 0.7246 (mt) cc_final: 0.6815 (mt) REVERT: M 25 THR cc_start: 0.7377 (p) cc_final: 0.7107 (p) REVERT: M 48 GLU cc_start: 0.7572 (mp0) cc_final: 0.7262 (mp0) REVERT: M 116 GLU cc_start: 0.5968 (tm-30) cc_final: 0.4495 (tm-30) REVERT: M 120 LEU cc_start: 0.8449 (pp) cc_final: 0.7584 (pp) REVERT: N 40 LEU cc_start: 0.9204 (tp) cc_final: 0.8977 (tp) REVERT: N 44 VAL cc_start: 0.9258 (m) cc_final: 0.9045 (m) REVERT: N 87 ILE cc_start: 0.8745 (pt) cc_final: 0.8454 (pt) REVERT: N 99 THR cc_start: 0.7887 (p) cc_final: 0.7639 (p) REVERT: N 103 LYS cc_start: 0.6102 (pttm) cc_final: 0.4936 (pttt) REVERT: N 114 MET cc_start: 0.8414 (mmp) cc_final: 0.7286 (mmm) REVERT: N 119 LEU cc_start: 0.8688 (pp) cc_final: 0.8048 (pp) REVERT: O 111 ASP cc_start: 0.8538 (m-30) cc_final: 0.8250 (m-30) REVERT: P 11 ILE cc_start: 0.9198 (pt) cc_final: 0.8934 (pt) REVERT: P 16 LEU cc_start: 0.7811 (mt) cc_final: 0.7498 (mt) REVERT: S 15 ARG cc_start: 0.7652 (mtp180) cc_final: 0.7089 (mtp180) REVERT: S 55 ILE cc_start: 0.9693 (mt) cc_final: 0.9167 (mt) REVERT: S 57 ASN cc_start: 0.7287 (m-40) cc_final: 0.6683 (t0) REVERT: S 67 ASN cc_start: 0.8796 (p0) cc_final: 0.8559 (p0) REVERT: S 69 LEU cc_start: 0.8830 (mt) cc_final: 0.8146 (mt) REVERT: S 76 VAL cc_start: 0.6683 (t) cc_final: 0.6088 (t) REVERT: T 1 MET cc_start: 0.5147 (mmm) cc_final: 0.2760 (mtt) REVERT: T 31 ASP cc_start: 0.6632 (t0) cc_final: 0.5136 (t70) REVERT: U 16 ASP cc_start: 0.7004 (p0) cc_final: 0.6661 (p0) REVERT: U 75 THR cc_start: 0.7445 (p) cc_final: 0.7178 (p) REVERT: Z 21 LEU cc_start: 0.7785 (mt) cc_final: 0.7137 (mt) REVERT: Z 39 ASN cc_start: 0.2872 (t0) cc_final: 0.2538 (t0) REVERT: b 13 LYS cc_start: 0.8857 (tttp) cc_final: 0.8292 (tttp) REVERT: b 15 LEU cc_start: 0.9172 (mt) cc_final: 0.8571 (mt) REVERT: c 7 LEU cc_start: 0.6543 (tp) cc_final: 0.6297 (tp) REVERT: c 44 LEU cc_start: 0.9068 (tp) cc_final: 0.8703 (tp) REVERT: d 39 ARG cc_start: 0.7047 (mmt90) cc_final: 0.6768 (mmm-85) REVERT: f 10 ILE cc_start: 0.8618 (mt) cc_final: 0.8316 (mm) outliers start: 2 outliers final: 1 residues processed: 921 average time/residue: 1.3243 time to fit residues: 2025.1796 Evaluate side-chains 716 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 714 time to evaluate : 5.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1019 random chunks: chunk 820 optimal weight: 10.0000 chunk 559 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 733 optimal weight: 20.0000 chunk 406 optimal weight: 20.0000 chunk 840 optimal weight: 6.9990 chunk 680 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 502 optimal weight: 5.9990 chunk 884 optimal weight: 50.0000 chunk 248 optimal weight: 20.0000 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 GLN ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 ASN ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 ASN ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 16 ASN ** Z 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 48 ASN ** a 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 36 GLN ** 3 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.6887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.124 147885 Z= 0.344 Angle : 0.808 14.620 221900 Z= 0.407 Chirality : 0.041 0.433 27297 Planarity : 0.006 0.086 11599 Dihedral : 26.259 179.614 78745 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 46.81 Ramachandran Plot: Outliers : 0.83 % Allowed : 7.98 % Favored : 91.20 % Rotamer: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.87 % Cis-general : 1.75 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.94 (0.11), residues: 5691 helix: 1.00 (0.13), residues: 1738 sheet: -1.92 (0.16), residues: 927 loop : -1.15 (0.11), residues: 3026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP M 93 HIS 0.015 0.003 HIS L 4 PHE 0.027 0.003 PHE V 38 TYR 0.035 0.003 TYR C 96 ARG 0.028 0.001 ARG c 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11382 Ramachandran restraints generated. 5691 Oldfield, 0 Emsley, 5691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11382 Ramachandran restraints generated. 5691 Oldfield, 0 Emsley, 5691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 888 time to evaluate : 5.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 TYR cc_start: 0.8348 (t80) cc_final: 0.7469 (t80) REVERT: C 65 ILE cc_start: 0.7061 (mm) cc_final: 0.6631 (mm) REVERT: C 68 LYS cc_start: 0.7646 (mttt) cc_final: 0.7445 (mmmm) REVERT: C 93 LEU cc_start: 0.7668 (tp) cc_final: 0.7339 (tp) REVERT: C 117 MET cc_start: 0.5510 (tpp) cc_final: 0.5294 (tpp) REVERT: C 185 LEU cc_start: 0.8788 (tp) cc_final: 0.7965 (tp) REVERT: E 65 TRP cc_start: 0.7702 (p90) cc_final: 0.7114 (p90) REVERT: E 99 TYR cc_start: 0.6915 (p90) cc_final: 0.6446 (p90) REVERT: E 120 ASP cc_start: 0.8030 (p0) cc_final: 0.7229 (p0) REVERT: E 185 ASP cc_start: 0.7926 (m-30) cc_final: 0.7082 (m-30) REVERT: E 189 HIS cc_start: 0.7113 (m90) cc_final: 0.6810 (m170) REVERT: E 206 LEU cc_start: 0.8477 (pp) cc_final: 0.8194 (mt) REVERT: F 26 MET cc_start: 0.6267 (ppp) cc_final: 0.5982 (ppp) REVERT: F 144 ASP cc_start: 0.9006 (m-30) cc_final: 0.8766 (t0) REVERT: H 99 PHE cc_start: 0.7470 (p90) cc_final: 0.7234 (p90) REVERT: J 63 ILE cc_start: 0.6679 (tp) cc_final: 0.6285 (tp) REVERT: J 74 ILE cc_start: 0.8265 (tp) cc_final: 0.8041 (tp) REVERT: K 79 PHE cc_start: 0.6811 (m-80) cc_final: 0.6386 (m-10) REVERT: L 1 MET cc_start: 0.4233 (mtm) cc_final: 0.2506 (mpp) REVERT: L 6 LEU cc_start: 0.7308 (mt) cc_final: 0.6894 (mt) REVERT: L 27 ASN cc_start: 0.8023 (t0) cc_final: 0.7669 (m110) REVERT: L 121 LEU cc_start: 0.5892 (mt) cc_final: 0.5560 (mp) REVERT: M 48 GLU cc_start: 0.8044 (mp0) cc_final: 0.7610 (mp0) REVERT: N 40 LEU cc_start: 0.9287 (tp) cc_final: 0.9068 (tp) REVERT: N 49 THR cc_start: 0.7898 (m) cc_final: 0.7582 (p) REVERT: N 99 THR cc_start: 0.8101 (p) cc_final: 0.7630 (p) REVERT: N 103 LYS cc_start: 0.6407 (pttm) cc_final: 0.4444 (pttt) REVERT: N 119 LEU cc_start: 0.8709 (pp) cc_final: 0.8467 (pp) REVERT: O 1 MET cc_start: 0.0876 (mtt) cc_final: 0.0467 (mpp) REVERT: P 16 LEU cc_start: 0.8003 (mt) cc_final: 0.7671 (mt) REVERT: P 52 LYS cc_start: 0.8578 (tttm) cc_final: 0.8317 (ptmm) REVERT: P 63 THR cc_start: 0.8098 (p) cc_final: 0.7646 (p) REVERT: Q 52 GLN cc_start: 0.8614 (tp-100) cc_final: 0.7865 (tp-100) REVERT: S 47 ILE cc_start: 0.9433 (mt) cc_final: 0.9203 (mt) REVERT: S 55 ILE cc_start: 0.9698 (mt) cc_final: 0.9352 (mt) REVERT: S 57 ASN cc_start: 0.7942 (m-40) cc_final: 0.7133 (t0) REVERT: S 69 LEU cc_start: 0.8804 (mt) cc_final: 0.8380 (mt) REVERT: S 76 VAL cc_start: 0.6869 (t) cc_final: 0.6194 (t) REVERT: T 1 MET cc_start: 0.5632 (mmm) cc_final: 0.3309 (mtt) REVERT: T 4 PRO cc_start: 0.8803 (Cg_exo) cc_final: 0.8530 (Cg_endo) REVERT: T 57 MET cc_start: 0.6181 (mmp) cc_final: 0.5898 (mmp) REVERT: U 16 ASP cc_start: 0.7337 (p0) cc_final: 0.7132 (p0) REVERT: Z 60 ARG cc_start: 0.8556 (mtt180) cc_final: 0.8336 (mtt180) REVERT: b 13 LYS cc_start: 0.8953 (tttp) cc_final: 0.8522 (tttp) REVERT: b 15 LEU cc_start: 0.9222 (mt) cc_final: 0.8244 (mt) REVERT: b 37 LYS cc_start: 0.8601 (tmtt) cc_final: 0.8271 (tmtt) REVERT: b 38 LEU cc_start: 0.9045 (pp) cc_final: 0.8492 (pp) REVERT: d 33 ARG cc_start: 0.8505 (ptt90) cc_final: 0.8299 (ptt90) REVERT: f 10 ILE cc_start: 0.9006 (mt) cc_final: 0.8692 (mm) outliers start: 0 outliers final: 0 residues processed: 888 average time/residue: 1.3137 time to fit residues: 1941.5941 Evaluate side-chains 703 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 703 time to evaluate : 5.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1019 random chunks: chunk 331 optimal weight: 10.0000 chunk 887 optimal weight: 3.9990 chunk 194 optimal weight: 20.0000 chunk 578 optimal weight: 6.9990 chunk 243 optimal weight: 20.0000 chunk 985 optimal weight: 50.0000 chunk 818 optimal weight: 50.0000 chunk 456 optimal weight: 20.0000 chunk 81 optimal weight: 10.0000 chunk 326 optimal weight: 40.0000 chunk 517 optimal weight: 3.9990 overall best weight: 6.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 GLN ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 ASN ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 73 GLN ** S 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 48 ASN ** a 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 moved from start: 0.7186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 147885 Z= 0.281 Angle : 0.735 14.051 221900 Z= 0.374 Chirality : 0.038 0.371 27297 Planarity : 0.005 0.085 11599 Dihedral : 26.351 179.337 78745 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 40.46 Ramachandran Plot: Outliers : 0.83 % Allowed : 6.87 % Favored : 92.30 % Rotamer: Outliers : 0.04 % Allowed : 2.94 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.87 % Cis-general : 1.75 % 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: -0.92 (0.11), residues: 5691 helix: 1.07 (0.13), residues: 1780 sheet: -1.97 (0.15), residues: 948 loop : -1.18 (0.11), residues: 2963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP C 250 HIS 0.014 0.002 HIS c 45 PHE 0.020 0.003 PHE I 42 TYR 0.035 0.003 TYR Q 45 ARG 0.034 0.001 ARG 3 58 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11382 Ramachandran restraints generated. 5691 Oldfield, 0 Emsley, 5691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11382 Ramachandran restraints generated. 5691 Oldfield, 0 Emsley, 5691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 872 time to evaluate : 5.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 TYR cc_start: 0.8296 (t80) cc_final: 0.7540 (t80) REVERT: C 65 ILE cc_start: 0.7841 (mm) cc_final: 0.7378 (mm) REVERT: C 93 LEU cc_start: 0.8308 (tp) cc_final: 0.8066 (tp) REVERT: C 140 VAL cc_start: 0.7732 (p) cc_final: 0.7495 (p) REVERT: C 172 VAL cc_start: 0.6958 (m) cc_final: 0.6742 (m) REVERT: C 185 LEU cc_start: 0.8835 (tp) cc_final: 0.8084 (tt) REVERT: D 21 ASP cc_start: 0.5736 (p0) cc_final: 0.5507 (p0) REVERT: D 88 MET cc_start: 0.6019 (mmp) cc_final: 0.5771 (mmp) REVERT: D 124 LYS cc_start: 0.8298 (mmtt) cc_final: 0.8073 (mmtt) REVERT: E 185 ASP cc_start: 0.7830 (m-30) cc_final: 0.6999 (m-30) REVERT: E 189 HIS cc_start: 0.7066 (m90) cc_final: 0.6702 (m170) REVERT: F 26 MET cc_start: 0.5966 (ppp) cc_final: 0.5713 (ppp) REVERT: F 96 MET cc_start: 0.8639 (mmm) cc_final: 0.7965 (mmm) REVERT: F 97 TYR cc_start: 0.5806 (m-80) cc_final: 0.5491 (m-10) REVERT: F 144 ASP cc_start: 0.8982 (m-30) cc_final: 0.8733 (t0) REVERT: G 22 ASN cc_start: 0.7315 (t0) cc_final: 0.6785 (m-40) REVERT: H 80 ASN cc_start: 0.5046 (t0) cc_final: 0.4722 (t0) REVERT: H 99 PHE cc_start: 0.7401 (p90) cc_final: 0.7092 (p90) REVERT: K 79 PHE cc_start: 0.6775 (m-80) cc_final: 0.6304 (m-80) REVERT: K 91 LYS cc_start: 0.8731 (mmtm) cc_final: 0.8388 (tttt) REVERT: L 1 MET cc_start: 0.3605 (mtm) cc_final: 0.1684 (mpp) REVERT: L 6 LEU cc_start: 0.7820 (mt) cc_final: 0.7398 (mp) REVERT: L 27 ASN cc_start: 0.8012 (t0) cc_final: 0.7557 (m110) REVERT: L 121 LEU cc_start: 0.5948 (mt) cc_final: 0.5693 (mp) REVERT: M 113 VAL cc_start: 0.8946 (m) cc_final: 0.8138 (m) REVERT: M 127 ILE cc_start: 0.8603 (mt) cc_final: 0.8361 (mt) REVERT: N 20 LEU cc_start: 0.8184 (mm) cc_final: 0.7648 (mm) REVERT: N 40 LEU cc_start: 0.9282 (tp) cc_final: 0.8976 (tp) REVERT: N 49 THR cc_start: 0.8298 (m) cc_final: 0.7933 (p) REVERT: N 103 LYS cc_start: 0.5631 (pttm) cc_final: 0.5411 (pttt) REVERT: N 114 MET cc_start: 0.7898 (mmp) cc_final: 0.6577 (mmm) REVERT: N 116 ILE cc_start: 0.7861 (tp) cc_final: 0.6951 (tp) REVERT: N 119 LEU cc_start: 0.8662 (pp) cc_final: 0.8443 (pp) REVERT: O 22 LEU cc_start: 0.7030 (pt) cc_final: 0.6462 (mt) REVERT: P 16 LEU cc_start: 0.8121 (mt) cc_final: 0.7792 (mt) REVERT: P 63 THR cc_start: 0.7977 (p) cc_final: 0.7510 (p) REVERT: Q 52 GLN cc_start: 0.8683 (tp-100) cc_final: 0.7826 (tp-100) REVERT: R 36 GLU cc_start: 0.7267 (mp0) cc_final: 0.6957 (mp0) REVERT: S 69 LEU cc_start: 0.8760 (mt) cc_final: 0.8510 (mt) REVERT: S 76 VAL cc_start: 0.6729 (t) cc_final: 0.6141 (t) REVERT: T 1 MET cc_start: 0.5703 (mmm) cc_final: 0.3531 (mtt) REVERT: T 4 PRO cc_start: 0.8773 (Cg_exo) cc_final: 0.8490 (Cg_endo) REVERT: U 16 ASP cc_start: 0.7260 (p0) cc_final: 0.7037 (p0) REVERT: U 75 THR cc_start: 0.7757 (p) cc_final: 0.7497 (p) REVERT: Z 39 ASN cc_start: 0.3349 (t0) cc_final: 0.3116 (t0) REVERT: Z 60 ARG cc_start: 0.8497 (mtt180) cc_final: 0.8128 (mtt180) REVERT: e 61 MET cc_start: 0.6308 (ppp) cc_final: 0.5882 (ppp) REVERT: f 10 ILE cc_start: 0.9076 (mt) cc_final: 0.8790 (mm) REVERT: f 17 ILE cc_start: 0.7618 (pt) cc_final: 0.6979 (mp) outliers start: 1 outliers final: 0 residues processed: 873 average time/residue: 1.2751 time to fit residues: 1858.4370 Evaluate side-chains 686 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 686 time to evaluate : 5.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1019 random chunks: chunk 950 optimal weight: 40.0000 chunk 111 optimal weight: 40.0000 chunk 561 optimal weight: 10.0000 chunk 719 optimal weight: 20.0000 chunk 557 optimal weight: 5.9990 chunk 829 optimal weight: 20.0000 chunk 550 optimal weight: 0.8980 chunk 982 optimal weight: 0.7980 chunk 614 optimal weight: 0.8980 chunk 598 optimal weight: 1.9990 chunk 453 optimal weight: 6.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 ASN Q 44 ASN ** Q 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 28 GLN S 61 ASN ** S 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 67 ASN ** V 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6334 moved from start: 0.6970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 147885 Z= 0.169 Angle : 0.655 27.512 221900 Z= 0.331 Chirality : 0.034 0.337 27297 Planarity : 0.005 0.180 11599 Dihedral : 26.036 179.943 78745 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 27.25 Ramachandran Plot: Outliers : 0.76 % Allowed : 6.50 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.87 % Cis-general : 1.75 % 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: -0.69 (0.11), residues: 5691 helix: 1.34 (0.13), residues: 1793 sheet: -1.73 (0.16), residues: 900 loop : -1.16 (0.11), residues: 2998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP M 93 HIS 0.010 0.002 HIS c 45 PHE 0.020 0.002 PHE V 80 TYR 0.026 0.002 TYR J 75 ARG 0.015 0.001 ARG d 12 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11382 Ramachandran restraints generated. 5691 Oldfield, 0 Emsley, 5691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11382 Ramachandran restraints generated. 5691 Oldfield, 0 Emsley, 5691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 889 time to evaluate : 5.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 25 THR cc_start: 0.8397 (p) cc_final: 0.8086 (p) REVERT: C 48 LYS cc_start: 0.7621 (mmtt) cc_final: 0.7287 (mmtm) REVERT: C 62 TYR cc_start: 0.8038 (t80) cc_final: 0.7643 (t80) REVERT: C 68 LYS cc_start: 0.7881 (mttt) cc_final: 0.7173 (mmmm) REVERT: C 74 ILE cc_start: 0.5851 (tp) cc_final: 0.5465 (tp) REVERT: C 93 LEU cc_start: 0.8032 (tp) cc_final: 0.7799 (tp) REVERT: C 102 ARG cc_start: 0.5393 (mpp-170) cc_final: 0.5142 (mtm-85) REVERT: C 117 MET cc_start: 0.3961 (tpp) cc_final: 0.3244 (tpp) REVERT: C 185 LEU cc_start: 0.8793 (tp) cc_final: 0.7738 (tt) REVERT: C 244 LYS cc_start: 0.4861 (tppt) cc_final: 0.4376 (tppt) REVERT: E 120 ASP cc_start: 0.7914 (p0) cc_final: 0.7297 (p0) REVERT: E 185 ASP cc_start: 0.7659 (m-30) cc_final: 0.6924 (m-30) REVERT: E 189 HIS cc_start: 0.6833 (m90) cc_final: 0.6497 (m170) REVERT: F 26 MET cc_start: 0.5753 (ppp) cc_final: 0.5462 (ppp) REVERT: G 22 ASN cc_start: 0.7198 (t0) cc_final: 0.6786 (m-40) REVERT: H 99 PHE cc_start: 0.7280 (p90) cc_final: 0.7031 (p90) REVERT: I 127 MET cc_start: -0.3084 (mmt) cc_final: -0.3707 (mmt) REVERT: J 110 LEU cc_start: 0.9159 (pp) cc_final: 0.8820 (pp) REVERT: J 119 MET cc_start: 0.7700 (ptp) cc_final: 0.7394 (ptm) REVERT: J 129 SER cc_start: 0.8974 (m) cc_final: 0.8629 (m) REVERT: K 91 LYS cc_start: 0.8867 (mmtm) cc_final: 0.8422 (pttt) REVERT: L 1 MET cc_start: 0.2904 (mtm) cc_final: 0.1129 (mpp) REVERT: L 6 LEU cc_start: 0.7438 (mt) cc_final: 0.7109 (mp) REVERT: L 27 ASN cc_start: 0.7748 (t0) cc_final: 0.7506 (m110) REVERT: L 66 PHE cc_start: 0.4275 (p90) cc_final: 0.4054 (p90) REVERT: M 48 GLU cc_start: 0.7751 (mp0) cc_final: 0.7460 (mp0) REVERT: M 107 SER cc_start: 0.8174 (p) cc_final: 0.7232 (p) REVERT: M 113 VAL cc_start: 0.8957 (m) cc_final: 0.8303 (m) REVERT: N 32 THR cc_start: 0.8120 (t) cc_final: 0.7507 (t) REVERT: N 40 LEU cc_start: 0.8959 (tp) cc_final: 0.8683 (tp) REVERT: N 49 THR cc_start: 0.7839 (m) cc_final: 0.7413 (p) REVERT: N 80 LEU cc_start: 0.8518 (mp) cc_final: 0.8227 (mp) REVERT: N 103 LYS cc_start: 0.5517 (pttm) cc_final: 0.4038 (pttt) REVERT: O 22 LEU cc_start: 0.7051 (pt) cc_final: 0.6600 (mt) REVERT: P 16 LEU cc_start: 0.8141 (mt) cc_final: 0.7802 (mt) REVERT: P 52 LYS cc_start: 0.7867 (ptmm) cc_final: 0.7654 (tttm) REVERT: Q 25 PHE cc_start: 0.7960 (t80) cc_final: 0.7630 (t80) REVERT: Q 37 GLN cc_start: 0.8676 (mm110) cc_final: 0.8108 (mm-40) REVERT: Q 47 PHE cc_start: 0.8118 (t80) cc_final: 0.7885 (t80) REVERT: Q 52 GLN cc_start: 0.8516 (tp-100) cc_final: 0.7550 (tp-100) REVERT: Q 56 ASP cc_start: 0.8689 (p0) cc_final: 0.8454 (p0) REVERT: S 18 ARG cc_start: 0.8289 (mtt180) cc_final: 0.8017 (mtt180) REVERT: S 57 ASN cc_start: 0.7264 (m-40) cc_final: 0.7034 (t0) REVERT: S 69 LEU cc_start: 0.8961 (mt) cc_final: 0.8701 (mt) REVERT: S 76 VAL cc_start: 0.6638 (t) cc_final: 0.5912 (t) REVERT: T 1 MET cc_start: 0.5631 (mmm) cc_final: 0.3694 (mtt) REVERT: T 31 ASP cc_start: 0.8168 (t70) cc_final: 0.7868 (t70) REVERT: U 75 THR cc_start: 0.7366 (p) cc_final: 0.7085 (p) REVERT: Z 60 ARG cc_start: 0.8500 (mtt180) cc_final: 0.8000 (mtt180) REVERT: d 36 ARG cc_start: 0.8998 (ttt-90) cc_final: 0.8518 (mmm-85) REVERT: e 61 MET cc_start: 0.6094 (ppp) cc_final: 0.5852 (ppp) REVERT: f 17 ILE cc_start: 0.7259 (pt) cc_final: 0.6936 (mp) outliers start: 0 outliers final: 0 residues processed: 889 average time/residue: 1.3813 time to fit residues: 2076.1680 Evaluate side-chains 715 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 715 time to evaluate : 5.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1019 random chunks: chunk 607 optimal weight: 6.9990 chunk 392 optimal weight: 5.9990 chunk 586 optimal weight: 40.0000 chunk 295 optimal weight: 20.0000 chunk 192 optimal weight: 20.0000 chunk 190 optimal weight: 20.0000 chunk 624 optimal weight: 2.9990 chunk 669 optimal weight: 20.0000 chunk 485 optimal weight: 7.9990 chunk 91 optimal weight: 20.0000 chunk 771 optimal weight: 10.0000 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 ASN Q 44 ASN ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 0.7514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 147885 Z= 0.277 Angle : 0.708 13.466 221900 Z= 0.358 Chirality : 0.037 0.324 27297 Planarity : 0.005 0.093 11599 Dihedral : 26.155 179.880 78745 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 40.54 Ramachandran Plot: Outliers : 0.77 % Allowed : 7.85 % Favored : 91.37 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.87 % Cis-general : 1.75 % 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: -0.72 (0.11), residues: 5691 helix: 1.45 (0.13), residues: 1768 sheet: -1.75 (0.16), residues: 918 loop : -1.26 (0.11), residues: 3005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.005 TRP E 65 HIS 0.007 0.002 HIS 3 40 PHE 0.025 0.003 PHE P 46 TYR 0.028 0.003 TYR O 102 ARG 0.022 0.001 ARG E 107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11382 Ramachandran restraints generated. 5691 Oldfield, 0 Emsley, 5691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11382 Ramachandran restraints generated. 5691 Oldfield, 0 Emsley, 5691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 833 time to evaluate : 5.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 25 THR cc_start: 0.8690 (p) cc_final: 0.8335 (p) REVERT: C 30 GLU cc_start: 0.7585 (pp20) cc_final: 0.7111 (pp20) REVERT: C 61 GLN cc_start: 0.6957 (mp10) cc_final: 0.6414 (mp10) REVERT: C 62 TYR cc_start: 0.7997 (t80) cc_final: 0.7475 (t80) REVERT: C 65 ILE cc_start: 0.7750 (mm) cc_final: 0.7294 (mm) REVERT: C 172 VAL cc_start: 0.6889 (m) cc_final: 0.6674 (m) REVERT: C 205 ILE cc_start: 0.8370 (mt) cc_final: 0.8154 (mt) REVERT: C 257 PHE cc_start: 0.6784 (t80) cc_final: 0.6183 (t80) REVERT: D 88 MET cc_start: 0.5409 (mmp) cc_final: 0.4944 (mmp) REVERT: D 124 LYS cc_start: 0.8307 (mmtt) cc_final: 0.8032 (mmtt) REVERT: E 99 TYR cc_start: 0.7039 (p90) cc_final: 0.6837 (p90) REVERT: E 120 ASP cc_start: 0.8013 (p0) cc_final: 0.7399 (p0) REVERT: F 96 MET cc_start: 0.8613 (mmm) cc_final: 0.8245 (mmm) REVERT: G 22 ASN cc_start: 0.7427 (t0) cc_final: 0.7035 (m-40) REVERT: H 99 PHE cc_start: 0.7405 (p90) cc_final: 0.7202 (p90) REVERT: I 127 MET cc_start: -0.2702 (mmt) cc_final: -0.3218 (mmt) REVERT: J 63 ILE cc_start: 0.6581 (tp) cc_final: 0.6297 (tp) REVERT: J 68 LYS cc_start: 0.9142 (tmtt) cc_final: 0.8207 (tmtt) REVERT: J 129 SER cc_start: 0.9068 (m) cc_final: 0.8660 (m) REVERT: K 91 LYS cc_start: 0.8819 (mmtm) cc_final: 0.8306 (tttt) REVERT: L 1 MET cc_start: 0.3861 (mtm) cc_final: 0.1629 (mpp) REVERT: L 6 LEU cc_start: 0.7851 (mt) cc_final: 0.7523 (mt) REVERT: L 27 ASN cc_start: 0.7746 (t0) cc_final: 0.7508 (m110) REVERT: L 121 LEU cc_start: 0.5954 (mt) cc_final: 0.5556 (mp) REVERT: M 107 SER cc_start: 0.8443 (p) cc_final: 0.7348 (p) REVERT: N 24 LEU cc_start: 0.8754 (pp) cc_final: 0.8534 (pp) REVERT: N 40 LEU cc_start: 0.9025 (tp) cc_final: 0.8736 (tp) REVERT: N 49 THR cc_start: 0.7907 (m) cc_final: 0.7502 (p) REVERT: N 80 LEU cc_start: 0.8647 (mp) cc_final: 0.8445 (mp) REVERT: N 102 MET cc_start: 0.3516 (ttt) cc_final: 0.3145 (ttt) REVERT: N 103 LYS cc_start: 0.5572 (pttm) cc_final: 0.4720 (pttt) REVERT: N 114 MET cc_start: 0.8174 (mmp) cc_final: 0.7030 (mmm) REVERT: O 7 LYS cc_start: 0.7686 (mttp) cc_final: 0.6955 (tttt) REVERT: O 22 LEU cc_start: 0.7333 (pt) cc_final: 0.6732 (mt) REVERT: P 16 LEU cc_start: 0.8125 (mt) cc_final: 0.7833 (mt) REVERT: Q 37 GLN cc_start: 0.8789 (mm110) cc_final: 0.8228 (mm-40) REVERT: Q 52 GLN cc_start: 0.8609 (tp-100) cc_final: 0.7867 (tp-100) REVERT: Q 56 ASP cc_start: 0.8675 (p0) cc_final: 0.8383 (p0) REVERT: S 69 LEU cc_start: 0.9066 (mt) cc_final: 0.8658 (mt) REVERT: S 76 VAL cc_start: 0.6776 (t) cc_final: 0.6163 (t) REVERT: T 1 MET cc_start: 0.5442 (mmm) cc_final: 0.4055 (mtt) REVERT: T 30 VAL cc_start: 0.7855 (m) cc_final: 0.7616 (p) REVERT: U 16 ASP cc_start: 0.7036 (p0) cc_final: 0.6824 (p0) REVERT: Z 23 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8336 (mp0) REVERT: Z 60 ARG cc_start: 0.8362 (mtt180) cc_final: 0.8011 (mtt180) REVERT: b 13 LYS cc_start: 0.9028 (tttp) cc_final: 0.8434 (tppt) REVERT: c 44 LEU cc_start: 0.8748 (tp) cc_final: 0.8534 (tp) REVERT: d 9 ASN cc_start: 0.7723 (m-40) cc_final: 0.7370 (m-40) REVERT: e 4 MET cc_start: 0.6137 (mmt) cc_final: 0.5936 (mmt) REVERT: e 61 MET cc_start: 0.6453 (ppp) cc_final: 0.6219 (ppp) REVERT: f 17 ILE cc_start: 0.7556 (pt) cc_final: 0.7094 (mp) outliers start: 0 outliers final: 0 residues processed: 833 average time/residue: 1.2906 time to fit residues: 1797.6747 Evaluate side-chains 687 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 687 time to evaluate : 5.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1019 random chunks: chunk 893 optimal weight: 9.9990 chunk 940 optimal weight: 0.3980 chunk 858 optimal weight: 50.0000 chunk 915 optimal weight: 50.0000 chunk 550 optimal weight: 4.9990 chunk 398 optimal weight: 30.0000 chunk 718 optimal weight: 20.0000 chunk 280 optimal weight: 20.0000 chunk 827 optimal weight: 50.0000 chunk 865 optimal weight: 5.9990 chunk 912 optimal weight: 0.9980 overall best weight: 4.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 46 GLN ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN E 188 ASN ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 ASN Q 44 ASN ** Q 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 moved from start: 0.7607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 147885 Z= 0.202 Angle : 0.658 14.110 221900 Z= 0.333 Chirality : 0.035 0.304 27297 Planarity : 0.005 0.206 11599 Dihedral : 26.151 179.802 78745 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 33.79 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.36 % Favored : 91.95 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.87 % Cis-general : 1.75 % 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: -0.68 (0.11), residues: 5691 helix: 1.49 (0.13), residues: 1770 sheet: -1.61 (0.16), residues: 901 loop : -1.28 (0.11), residues: 3020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP J 16 HIS 0.013 0.002 HIS J 54 PHE 0.053 0.003 PHE Z 26 TYR 0.028 0.002 TYR M 57 ARG 0.027 0.001 ARG E 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11382 Ramachandran restraints generated. 5691 Oldfield, 0 Emsley, 5691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11382 Ramachandran restraints generated. 5691 Oldfield, 0 Emsley, 5691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 852 time to evaluate : 5.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 25 THR cc_start: 0.8614 (p) cc_final: 0.8362 (p) REVERT: C 33 LEU cc_start: 0.8378 (pp) cc_final: 0.8171 (pp) REVERT: C 50 THR cc_start: 0.6820 (p) cc_final: 0.6600 (p) REVERT: C 61 GLN cc_start: 0.6841 (mp10) cc_final: 0.6308 (mp10) REVERT: C 62 TYR cc_start: 0.8086 (t80) cc_final: 0.7581 (t80) REVERT: C 65 ILE cc_start: 0.8037 (mm) cc_final: 0.7603 (mm) REVERT: C 68 LYS cc_start: 0.8006 (mttt) cc_final: 0.7114 (mmmm) REVERT: C 93 LEU cc_start: 0.8438 (tp) cc_final: 0.8031 (tp) REVERT: C 117 MET cc_start: 0.4254 (tpp) cc_final: 0.3335 (tpp) REVERT: C 185 LEU cc_start: 0.8866 (tp) cc_final: 0.8651 (tp) REVERT: C 244 LYS cc_start: 0.5354 (tppt) cc_final: 0.5011 (tppt) REVERT: C 257 PHE cc_start: 0.6803 (t80) cc_final: 0.6210 (t80) REVERT: C 269 PHE cc_start: 0.6901 (m-80) cc_final: 0.6255 (m-80) REVERT: D 88 MET cc_start: 0.5385 (mmp) cc_final: 0.5060 (mmp) REVERT: D 98 LYS cc_start: 0.8360 (mmpt) cc_final: 0.8028 (mmmt) REVERT: D 164 MET cc_start: 0.7408 (mpp) cc_final: 0.7171 (mpp) REVERT: E 99 TYR cc_start: 0.6820 (p90) cc_final: 0.6508 (p90) REVERT: E 120 ASP cc_start: 0.7987 (p0) cc_final: 0.7407 (p0) REVERT: G 22 ASN cc_start: 0.7379 (t0) cc_final: 0.6899 (m-40) REVERT: H 80 ASN cc_start: 0.5886 (t0) cc_final: 0.4409 (t0) REVERT: H 99 PHE cc_start: 0.7393 (p90) cc_final: 0.7172 (p90) REVERT: I 127 MET cc_start: -0.2918 (mmt) cc_final: -0.3369 (mmt) REVERT: J 143 LEU cc_start: 0.7600 (pp) cc_final: 0.7262 (pp) REVERT: K 20 LEU cc_start: 0.9169 (pp) cc_final: 0.8839 (tt) REVERT: K 91 LYS cc_start: 0.8816 (mmtm) cc_final: 0.8376 (pttt) REVERT: L 1 MET cc_start: 0.4193 (mtm) cc_final: 0.1914 (mpp) REVERT: L 27 ASN cc_start: 0.7784 (t0) cc_final: 0.7537 (m110) REVERT: M 44 ASN cc_start: 0.7834 (m110) cc_final: 0.7579 (m110) REVERT: M 66 ILE cc_start: 0.7933 (tp) cc_final: 0.7680 (tp) REVERT: M 107 SER cc_start: 0.8254 (p) cc_final: 0.7216 (p) REVERT: M 113 VAL cc_start: 0.8982 (m) cc_final: 0.7795 (m) REVERT: N 40 LEU cc_start: 0.8915 (tp) cc_final: 0.8704 (tp) REVERT: N 49 THR cc_start: 0.7903 (m) cc_final: 0.7430 (p) REVERT: N 80 LEU cc_start: 0.8668 (mp) cc_final: 0.8466 (mp) REVERT: N 103 LYS cc_start: 0.5313 (pttm) cc_final: 0.4277 (pttt) REVERT: N 114 MET cc_start: 0.8174 (mmp) cc_final: 0.7199 (mmm) REVERT: O 7 LYS cc_start: 0.7580 (mttp) cc_final: 0.6959 (tttt) REVERT: O 22 LEU cc_start: 0.7255 (pt) cc_final: 0.6822 (mt) REVERT: O 64 ASN cc_start: 0.7234 (m-40) cc_final: 0.5919 (t0) REVERT: P 16 LEU cc_start: 0.8108 (mt) cc_final: 0.7836 (mt) REVERT: P 34 LYS cc_start: 0.7764 (pttt) cc_final: 0.7428 (pttm) REVERT: P 52 LYS cc_start: 0.8148 (ptmm) cc_final: 0.7776 (tmmt) REVERT: P 94 LYS cc_start: 0.7029 (tptt) cc_final: 0.6801 (tptt) REVERT: Q 52 GLN cc_start: 0.8692 (tp-100) cc_final: 0.7950 (tp-100) REVERT: Q 56 ASP cc_start: 0.8616 (p0) cc_final: 0.8325 (p0) REVERT: S 69 LEU cc_start: 0.9056 (mt) cc_final: 0.8643 (mt) REVERT: S 76 VAL cc_start: 0.6682 (t) cc_final: 0.6060 (t) REVERT: S 82 LEU cc_start: 0.6155 (tt) cc_final: 0.5557 (tp) REVERT: S 108 SER cc_start: 0.7406 (m) cc_final: 0.7081 (m) REVERT: T 1 MET cc_start: 0.5850 (mmm) cc_final: 0.4525 (mtt) REVERT: T 16 ARG cc_start: 0.7603 (mpt180) cc_final: 0.7281 (mmt-90) REVERT: T 30 VAL cc_start: 0.7783 (m) cc_final: 0.7414 (p) REVERT: b 5 PHE cc_start: 0.6563 (t80) cc_final: 0.6329 (t80) REVERT: b 13 LYS cc_start: 0.8904 (tttp) cc_final: 0.8268 (tppt) REVERT: d 36 ARG cc_start: 0.9015 (ttt-90) cc_final: 0.8556 (mmm160) REVERT: e 4 MET cc_start: 0.6022 (mmt) cc_final: 0.5798 (mmt) REVERT: e 61 MET cc_start: 0.6374 (ppp) cc_final: 0.6123 (ppp) REVERT: f 17 ILE cc_start: 0.7480 (pt) cc_final: 0.7072 (mp) outliers start: 0 outliers final: 0 residues processed: 852 average time/residue: 1.2654 time to fit residues: 1818.3455 Evaluate side-chains 694 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 694 time to evaluate : 5.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1019 random chunks: chunk 601 optimal weight: 4.9990 chunk 967 optimal weight: 50.0000 chunk 590 optimal weight: 9.9990 chunk 459 optimal weight: 20.0000 chunk 672 optimal weight: 20.0000 chunk 1015 optimal weight: 8.9990 chunk 934 optimal weight: 0.7980 chunk 808 optimal weight: 0.1980 chunk 83 optimal weight: 20.0000 chunk 624 optimal weight: 3.9990 chunk 495 optimal weight: 0.0870 overall best weight: 2.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN C 199 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 ASN Q 44 ASN ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6315 moved from start: 0.7493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 147885 Z= 0.153 Angle : 0.625 13.576 221900 Z= 0.315 Chirality : 0.033 0.387 27297 Planarity : 0.005 0.152 11599 Dihedral : 25.894 179.661 78745 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 26.42 Ramachandran Plot: Outliers : 0.69 % Allowed : 6.64 % Favored : 92.67 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.87 % Cis-general : 1.75 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.12), residues: 5691 helix: 1.65 (0.13), residues: 1778 sheet: -1.49 (0.16), residues: 893 loop : -1.24 (0.11), residues: 3020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.005 TRP E 83 HIS 0.008 0.002 HIS J 54 PHE 0.041 0.002 PHE C 269 TYR 0.048 0.002 TYR E 97 ARG 0.025 0.001 ARG S 84 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11382 Ramachandran restraints generated. 5691 Oldfield, 0 Emsley, 5691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11382 Ramachandran restraints generated. 5691 Oldfield, 0 Emsley, 5691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 855 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 855 time to evaluate : 5.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 GLN cc_start: 0.6774 (mp10) cc_final: 0.6503 (mp10) REVERT: C 62 TYR cc_start: 0.8006 (t80) cc_final: 0.7719 (t80) REVERT: C 68 LYS cc_start: 0.8067 (mttt) cc_final: 0.7172 (mmmm) REVERT: C 94 ILE cc_start: 0.7396 (tp) cc_final: 0.7000 (tp) REVERT: C 115 GLU cc_start: 0.6790 (tp30) cc_final: 0.6534 (mm-30) REVERT: C 117 MET cc_start: 0.4133 (tpp) cc_final: 0.3472 (tpp) REVERT: C 205 ILE cc_start: 0.8494 (mt) cc_final: 0.8289 (mt) REVERT: C 244 LYS cc_start: 0.5259 (tppt) cc_final: 0.4251 (tppt) REVERT: C 257 PHE cc_start: 0.6699 (t80) cc_final: 0.6159 (t80) REVERT: D 88 MET cc_start: 0.5127 (mmp) cc_final: 0.4919 (mmp) REVERT: D 98 LYS cc_start: 0.8119 (mmpt) cc_final: 0.7716 (mmmt) REVERT: E 99 TYR cc_start: 0.6830 (p90) cc_final: 0.6406 (p90) REVERT: E 120 ASP cc_start: 0.7846 (p0) cc_final: 0.7171 (p0) REVERT: E 185 ASP cc_start: 0.7587 (m-30) cc_final: 0.7055 (m-30) REVERT: G 22 ASN cc_start: 0.7264 (t0) cc_final: 0.6824 (m-40) REVERT: I 127 MET cc_start: -0.3115 (mmt) cc_final: -0.3508 (mmt) REVERT: J 32 GLU cc_start: 0.8025 (pt0) cc_final: 0.7659 (tt0) REVERT: J 57 ILE cc_start: 0.7988 (mp) cc_final: 0.7679 (mp) REVERT: J 110 LEU cc_start: 0.8931 (pp) cc_final: 0.8694 (pp) REVERT: K 1 MET cc_start: 0.4461 (ppp) cc_final: 0.4022 (ppp) REVERT: K 2 ILE cc_start: 0.8156 (tp) cc_final: 0.7462 (tp) REVERT: K 20 LEU cc_start: 0.9122 (pp) cc_final: 0.8784 (tt) REVERT: K 91 LYS cc_start: 0.8778 (mmtm) cc_final: 0.8319 (pttt) REVERT: L 1 MET cc_start: 0.3824 (mtm) cc_final: 0.1947 (mpp) REVERT: L 27 ASN cc_start: 0.7726 (t0) cc_final: 0.7427 (m110) REVERT: L 58 PHE cc_start: 0.8227 (p90) cc_final: 0.7918 (p90) REVERT: M 44 ASN cc_start: 0.7995 (m110) cc_final: 0.7793 (m110) REVERT: M 48 GLU cc_start: 0.8213 (mp0) cc_final: 0.7888 (mp0) REVERT: M 107 SER cc_start: 0.8148 (p) cc_final: 0.7065 (p) REVERT: N 32 THR cc_start: 0.7947 (t) cc_final: 0.7392 (t) REVERT: N 40 LEU cc_start: 0.9013 (tp) cc_final: 0.8652 (tp) REVERT: N 101 ILE cc_start: 0.7584 (mm) cc_final: 0.7296 (mm) REVERT: N 103 LYS cc_start: 0.5240 (pttm) cc_final: 0.4640 (pttt) REVERT: N 114 MET cc_start: 0.7957 (mmp) cc_final: 0.7328 (mmm) REVERT: N 116 ILE cc_start: 0.7781 (tp) cc_final: 0.7291 (tp) REVERT: N 117 ILE cc_start: 0.7665 (mp) cc_final: 0.7461 (mp) REVERT: O 1 MET cc_start: 0.1520 (mpp) cc_final: 0.1318 (mpp) REVERT: O 22 LEU cc_start: 0.7131 (pt) cc_final: 0.6927 (mt) REVERT: P 16 LEU cc_start: 0.8069 (mt) cc_final: 0.7765 (mt) REVERT: P 94 LYS cc_start: 0.6897 (tptt) cc_final: 0.6656 (tptt) REVERT: Q 37 GLN cc_start: 0.8595 (mm110) cc_final: 0.8248 (mm110) REVERT: Q 52 GLN cc_start: 0.8653 (tp-100) cc_final: 0.7837 (tp-100) REVERT: Q 56 ASP cc_start: 0.8450 (p0) cc_final: 0.8102 (p0) REVERT: S 15 ARG cc_start: 0.7665 (mtp180) cc_final: 0.7447 (mtp180) REVERT: S 25 ARG cc_start: 0.7944 (mtm180) cc_final: 0.7677 (mtm180) REVERT: S 69 LEU cc_start: 0.9000 (mt) cc_final: 0.8198 (mt) REVERT: S 76 VAL cc_start: 0.7000 (t) cc_final: 0.6451 (t) REVERT: S 108 SER cc_start: 0.7254 (m) cc_final: 0.6988 (p) REVERT: T 1 MET cc_start: 0.5775 (mmm) cc_final: 0.4917 (mtt) REVERT: T 16 ARG cc_start: 0.7449 (mpt180) cc_final: 0.7248 (mmt-90) REVERT: T 30 VAL cc_start: 0.7770 (m) cc_final: 0.7465 (p) REVERT: T 65 ARG cc_start: 0.7680 (ttp80) cc_final: 0.6652 (tmm-80) REVERT: Z 38 GLU cc_start: 0.5132 (tm-30) cc_final: 0.4765 (tm-30) REVERT: Z 60 ARG cc_start: 0.8445 (mtt180) cc_final: 0.8036 (mtt180) REVERT: a 24 ARG cc_start: 0.7659 (tpm170) cc_final: 0.7449 (tpm170) REVERT: d 9 ASN cc_start: 0.8102 (m-40) cc_final: 0.7858 (m-40) REVERT: d 35 ARG cc_start: 0.7578 (mtp180) cc_final: 0.7171 (tpp80) REVERT: d 36 ARG cc_start: 0.8815 (ttt-90) cc_final: 0.8305 (mmm160) REVERT: e 4 MET cc_start: 0.6118 (mmt) cc_final: 0.5895 (mmt) outliers start: 0 outliers final: 0 residues processed: 855 average time/residue: 1.2804 time to fit residues: 1842.1697 Evaluate side-chains 711 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 711 time to evaluate : 5.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1019 random chunks: chunk 642 optimal weight: 20.0000 chunk 861 optimal weight: 40.0000 chunk 247 optimal weight: 20.0000 chunk 745 optimal weight: 20.0000 chunk 119 optimal weight: 20.0000 chunk 224 optimal weight: 10.0000 chunk 809 optimal weight: 50.0000 chunk 338 optimal weight: 6.9990 chunk 831 optimal weight: 30.0000 chunk 102 optimal weight: 20.0000 chunk 149 optimal weight: 20.0000 overall best weight: 15.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 ASN ** O 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 23 ASN ** Z 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.057915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.051753 restraints weight = 2212500.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.052620 restraints weight = 1036766.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.053157 restraints weight = 631294.552| |-----------------------------------------------------------------------------| r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.9172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.187 147885 Z= 0.584 Angle : 1.146 14.318 221900 Z= 0.560 Chirality : 0.053 0.475 27297 Planarity : 0.009 0.142 11599 Dihedral : 26.840 179.990 78745 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 79.38 Ramachandran Plot: Outliers : 0.84 % Allowed : 10.21 % Favored : 88.95 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.87 % Cis-general : 1.74 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.59 (0.11), residues: 5691 helix: 0.65 (0.13), residues: 1751 sheet: -2.07 (0.16), residues: 910 loop : -1.79 (0.11), residues: 3030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.007 TRP E 83 HIS 0.024 0.005 HIS R 83 PHE 0.045 0.005 PHE Q 57 TYR 0.057 0.005 TYR e 28 ARG 0.108 0.002 ARG D 183 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29756.32 seconds wall clock time: 525 minutes 52.97 seconds (31552.97 seconds total)