Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 07:53:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qgu_13959/04_2023/7qgu_13959.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qgu_13959/04_2023/7qgu_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_13959/04_2023/7qgu_13959.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qgu_13959/04_2023/7qgu_13959.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qgu_13959/04_2023/7qgu_13959.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qgu_13959/04_2023/7qgu_13959.pdb" } resolution = 4.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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-1.21rc1-4938/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: 50.12, per 1000 atoms: 0.37 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: 53.10 Conformation dependent library (CDL) restraints added in 6.0 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: 48.89 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: 218.08 Time building geometry restraints manager: 57.27 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: 71502 35.99 - 71.98: 2845 71.98 - 107.97: 284 107.97 - 143.96: 53 143.96 - 179.95: 90 Dihedral angle restraints: 74774 sinusoidal: 62724 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 74771 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: 10.550 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: 0.070 Extract box with map and model: 48.250 Check model and map are aligned: 1.430 Set scattering table: 0.860 Process input model: 455.500 Find NCS groups from input model: 2.660 Set up NCS constraints: 0.300 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:1.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 521.630 ------------------------------------------------------------------------------- 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 : 15.779 179.951 68534 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 % 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 *********************** 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 : 5.457 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: 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clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 1351 average time/residue: 1.3765 time to fit residues: 3041.6587 Evaluate side-chains 825 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 822 time to evaluate : 4.951 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 1.7888 time to fit residues: 12.9178 ------------------------------------------------------------------------------- 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: 9.9990 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 86 ASN 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 ** E 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 a 48 ASN 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: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5852 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 147885 Z= 0.260 Angle : 0.741 15.531 221900 Z= 0.377 Chirality : 0.037 0.394 27297 Planarity : 0.006 0.109 11599 Dihedral : 16.460 179.555 61961 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 25.69 Ramachandran Plot: Outliers : 0.91 % Allowed : 5.13 % Favored : 93.96 % Rotamer Outliers : 0.07 % 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: -1.02 (0.11), residues: 5691 helix: -0.28 (0.11), residues: 1711 sheet: -2.22 (0.15), residues: 931 loop : -0.24 (0.12), residues: 3049 *********************** 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 1010 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1008 time to evaluate : 5.497 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 outliers start: 2 outliers final: 0 residues processed: 1008 average time/residue: 1.3593 time to fit residues: 2261.8522 Evaluate side-chains 744 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 744 time to evaluate : 5.440 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5019 ------------------------------------------------------------------------------- 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: 5.9990 chunk 287 optimal weight: 20.0000 chunk 770 optimal weight: 10.0000 chunk 630 optimal weight: 20.0000 chunk 255 optimal weight: 20.0000 chunk 927 optimal weight: 50.0000 chunk 1001 optimal weight: 5.9990 chunk 825 optimal weight: 50.0000 chunk 919 optimal weight: 50.0000 chunk 316 optimal weight: 7.9990 chunk 743 optimal weight: 20.0000 overall best weight: 9.9994 ------------------------------------------------------------------------------- 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 ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 ASN ** 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 37 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 I 117 ASN ** J 41 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** ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 GLN 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** ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 16 ASN ** 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 36 GLN ** 3 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.133 147885 Z= 0.435 Angle : 0.955 24.974 221900 Z= 0.477 Chirality : 0.045 0.537 27297 Planarity : 0.008 0.183 11599 Dihedral : 18.002 179.897 61961 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 48.64 Ramachandran Plot: Outliers : 0.86 % Allowed : 7.20 % Favored : 91.93 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.87 % Cis-general : 1.75 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.04 (0.11), residues: 5691 helix: 0.50 (0.12), residues: 1721 sheet: -2.12 (0.15), residues: 926 loop : -0.85 (0.11), residues: 3044 *********************** 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 950 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 934 time to evaluate : 5.657 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 outliers start: 16 outliers final: 3 residues processed: 943 average time/residue: 1.3983 time to fit residues: 2186.5299 Evaluate side-chains 716 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 713 time to evaluate : 5.471 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 1.1065 time to fit residues: 11.6632 ------------------------------------------------------------------------------- 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: 10.0000 chunk 696 optimal weight: 20.0000 chunk 481 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 442 optimal weight: 5.9990 chunk 622 optimal weight: 10.0000 chunk 930 optimal weight: 50.0000 chunk 984 optimal weight: 40.0000 chunk 486 optimal weight: 6.9990 chunk 881 optimal weight: 40.0000 chunk 265 optimal weight: 10.0000 overall best weight: 8.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 ASN ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN C 199 GLN ** C 228 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** D 172 GLN ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 54 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 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 GLN P 80 HIS ** Q 37 GLN ** 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 61 ASN ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 39 ASN U 67 ASN ** U 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 48 ASN ** c 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 40 GLN ** e 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 32 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6406 moved from start: 0.6059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.112 147885 Z= 0.327 Angle : 0.781 13.848 221900 Z= 0.399 Chirality : 0.040 0.395 27297 Planarity : 0.006 0.197 11599 Dihedral : 18.699 179.344 61961 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 39.34 Ramachandran Plot: Outliers : 0.81 % Allowed : 6.03 % Favored : 93.16 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.87 % Cis-general : 1.74 % 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: -0.76 (0.11), residues: 5691 helix: 1.00 (0.13), residues: 1746 sheet: -1.81 (0.16), residues: 916 loop : -0.95 (0.11), residues: 3029 *********************** 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 901 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 895 time to evaluate : 5.552 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 outliers start: 6 outliers final: 1 residues processed: 898 average time/residue: 1.3655 time to fit residues: 2032.5278 Evaluate side-chains 712 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 711 time to evaluate : 5.516 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.0713 time to fit residues: 7.4386 ------------------------------------------------------------------------------- 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: 30.0000 chunk 559 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 733 optimal weight: 20.0000 chunk 406 optimal weight: 4.9990 chunk 840 optimal weight: 5.9990 chunk 680 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 502 optimal weight: 1.9990 chunk 884 optimal weight: 40.0000 chunk 248 optimal weight: 20.0000 overall best weight: 4.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 ASN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN C 199 GLN ** C 228 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** ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN F 178 GLN ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 46 GLN ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 ASN ** Q 81 HIS ** 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 28 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** ** a 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 32 ASN ** c 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 40 GLN e 60 GLN f 32 HIS f 36 GLN ** 3 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6373 moved from start: 0.6266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 147885 Z= 0.227 Angle : 0.679 14.356 221900 Z= 0.345 Chirality : 0.036 0.358 27297 Planarity : 0.005 0.116 11599 Dihedral : 18.621 179.908 61961 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 33.56 Ramachandran Plot: Outliers : 0.81 % Allowed : 6.45 % Favored : 92.74 % Rotamer Outliers : 0.15 % 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: -0.57 (0.11), residues: 5691 helix: 1.36 (0.13), residues: 1780 sheet: -1.73 (0.16), residues: 907 loop : -0.99 (0.11), residues: 3004 *********************** 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 897 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 893 time to evaluate : 5.512 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 outliers start: 4 outliers final: 2 residues processed: 895 average time/residue: 1.3931 time to fit residues: 2074.1263 Evaluate side-chains 690 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 688 time to evaluate : 5.566 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 1.0223 time to fit residues: 9.3735 ------------------------------------------------------------------------------- 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: 50.0000 chunk 194 optimal weight: 20.0000 chunk 578 optimal weight: 7.9990 chunk 243 optimal weight: 20.0000 chunk 985 optimal weight: 50.0000 chunk 818 optimal weight: 50.0000 chunk 456 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 326 optimal weight: 10.0000 chunk 517 optimal weight: 5.9990 overall best weight: 8.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 ASN C 197 ASN C 199 GLN ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN ** D 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** J 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 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 46 GLN ** 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 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 16 ASN ** Z 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 31 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** ** c 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 60 GLN ** 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.7270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.130 147885 Z= 0.358 Angle : 0.819 14.089 221900 Z= 0.413 Chirality : 0.041 0.637 27297 Planarity : 0.006 0.168 11599 Dihedral : 19.336 179.398 61961 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 50.60 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.45 % Favored : 91.76 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.87 % Cis-general : 1.74 % 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: -0.88 (0.11), residues: 5691 helix: 1.06 (0.13), residues: 1784 sheet: -1.91 (0.16), residues: 900 loop : -1.16 (0.11), residues: 3007 *********************** 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 848 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 847 time to evaluate : 5.507 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 outliers start: 1 outliers final: 0 residues processed: 848 average time/residue: 1.3280 time to fit residues: 1890.6768 Evaluate side-chains 674 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 674 time to evaluate : 4.939 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.9940 ------------------------------------------------------------------------------- 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: 50.0000 chunk 111 optimal weight: 40.0000 chunk 561 optimal weight: 20.0000 chunk 719 optimal weight: 10.0000 chunk 557 optimal weight: 0.0980 chunk 829 optimal weight: 10.0000 chunk 550 optimal weight: 7.9990 chunk 982 optimal weight: 50.0000 chunk 614 optimal weight: 5.9990 chunk 598 optimal weight: 4.9990 chunk 453 optimal weight: 7.9990 overall best weight: 5.4188 ------------------------------------------------------------------------------- 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 134 ASN C 197 ASN ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 ASN ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 ASN ** 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 61 ASN S 73 GLN ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 99 GLN ** 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** ** c 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 40 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.7286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 147885 Z= 0.234 Angle : 0.694 13.850 221900 Z= 0.352 Chirality : 0.037 0.338 27297 Planarity : 0.005 0.112 11599 Dihedral : 19.261 179.545 61961 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 37.80 Ramachandran Plot: Outliers : 0.76 % Allowed : 6.94 % Favored : 92.30 % Rotamer Outliers : 0.04 % 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: -0.73 (0.11), residues: 5691 helix: 1.34 (0.13), residues: 1772 sheet: -1.81 (0.16), residues: 913 loop : -1.16 (0.11), residues: 3006 *********************** 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 863 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 862 time to evaluate : 5.601 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 outliers start: 1 outliers final: 0 residues processed: 863 average time/residue: 1.3414 time to fit residues: 1930.7570 Evaluate side-chains 703 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 703 time to evaluate : 5.481 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5713 ------------------------------------------------------------------------------- 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: 6.9990 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: 6.9990 chunk 669 optimal weight: 20.0000 chunk 485 optimal weight: 2.9990 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 134 ASN C 197 ASN ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 ASN ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 127 ASN ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 ASN ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 ASN ** 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 97 ASN ** 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 20 HIS ** 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** ** c 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 40 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.7728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.096 147885 Z= 0.283 Angle : 0.727 13.713 221900 Z= 0.368 Chirality : 0.038 0.330 27297 Planarity : 0.005 0.096 11599 Dihedral : 19.446 179.890 61961 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 43.37 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.57 % Favored : 91.67 % Rotamer Outliers : 0.04 % 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: -0.83 (0.11), residues: 5691 helix: 1.30 (0.13), residues: 1777 sheet: -1.81 (0.16), residues: 900 loop : -1.30 (0.11), residues: 3014 *********************** 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 849 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 848 time to evaluate : 5.627 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 outliers start: 1 outliers final: 0 residues processed: 849 average time/residue: 1.3213 time to fit residues: 1882.9672 Evaluate side-chains 680 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 680 time to evaluate : 5.454 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5515 ------------------------------------------------------------------------------- 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: 10.0000 chunk 940 optimal weight: 4.9990 chunk 858 optimal weight: 50.0000 chunk 915 optimal weight: 50.0000 chunk 550 optimal weight: 7.9990 chunk 398 optimal weight: 6.9990 chunk 718 optimal weight: 20.0000 chunk 280 optimal weight: 20.0000 chunk 827 optimal weight: 50.0000 chunk 865 optimal weight: 30.0000 chunk 912 optimal weight: 0.0020 overall best weight: 5.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 46 GLN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 GLN ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 ASN ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** 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 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 ASN ** 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 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 102 HIS ** 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** ** c 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 6 GLN ** e 40 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.7929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.094 147885 Z= 0.251 Angle : 0.698 13.633 221900 Z= 0.354 Chirality : 0.037 0.301 27297 Planarity : 0.005 0.210 11599 Dihedral : 19.480 179.398 61961 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 40.12 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.45 % Favored : 91.86 % Rotamer Outliers : 0.04 % 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: -0.83 (0.11), residues: 5691 helix: 1.38 (0.13), residues: 1783 sheet: -1.78 (0.16), residues: 909 loop : -1.36 (0.11), residues: 2999 *********************** 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 844 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 843 time to evaluate : 5.006 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 outliers start: 1 outliers final: 0 residues processed: 844 average time/residue: 1.2963 time to fit residues: 1835.0665 Evaluate side-chains 666 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 666 time to evaluate : 5.463 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5280 ------------------------------------------------------------------------------- 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: 10.0000 chunk 967 optimal weight: 50.0000 chunk 590 optimal weight: 10.0000 chunk 459 optimal weight: 9.9990 chunk 672 optimal weight: 20.0000 chunk 1015 optimal weight: 5.9990 chunk 934 optimal weight: 50.0000 chunk 808 optimal weight: 6.9990 chunk 83 optimal weight: 20.0000 chunk 624 optimal weight: 9.9990 chunk 495 optimal weight: 3.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 46 GLN ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 70 ASN ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 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** ** O 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 5 GLN Q 38 GLN Q 44 ASN ** Q 81 HIS ** 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 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 102 HIS ** 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 23 ASN ** 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** ** c 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 40 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.8385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 147885 Z= 0.301 Angle : 0.753 13.590 221900 Z= 0.380 Chirality : 0.039 0.338 27297 Planarity : 0.006 0.170 11599 Dihedral : 19.747 179.843 61961 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 47.39 Ramachandran Plot: Outliers : 0.65 % Allowed : 8.84 % Favored : 90.51 % Rotamer Outliers : 0.04 % 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: -0.98 (0.11), residues: 5691 helix: 1.28 (0.13), residues: 1782 sheet: -1.85 (0.16), residues: 889 loop : -1.48 (0.11), residues: 3020 ********************** 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 851 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 850 time to evaluate : 5.589 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 outliers start: 1 outliers final: 0 residues processed: 851 average time/residue: 1.3142 time to fit residues: 1888.1572 Evaluate side-chains 680 residues out of total 4850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 680 time to evaluate : 5.556 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5451 ------------------------------------------------------------------------------- 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: 10.0000 chunk 224 optimal weight: 10.0000 chunk 809 optimal weight: 20.0000 chunk 338 optimal weight: 9.9990 chunk 831 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 149 optimal weight: 20.0000 overall best weight: 13.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 GLN ** C 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN D 140 HIS ** D 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 136 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** ** L 4 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** ** O 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 ASN ** 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** ** 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** ** V 48 GLN ** 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** ** c 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 60 GLN ** e 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.056227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.050718 restraints weight = 2215941.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.051554 restraints weight = 1037665.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.052083 restraints weight = 639510.177| |-----------------------------------------------------------------------------| r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.9616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.119 147885 Z= 0.543 Angle : 1.063 13.787 221900 Z= 0.531 Chirality : 0.052 0.542 27297 Planarity : 0.008 0.182 11599 Dihedral : 20.978 179.913 61961 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 77.49 Ramachandran Plot: Outliers : 0.77 % Allowed : 10.91 % Favored : 88.31 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.87 % Cis-general : 1.74 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.78 (0.11), residues: 5691 helix: 0.60 (0.13), residues: 1734 sheet: -2.29 (0.16), residues: 898 loop : -1.93 (0.11), residues: 3059 =============================================================================== Job complete usr+sys time: 29179.38 seconds wall clock time: 517 minutes 23.30 seconds (31043.30 seconds total)