Starting phenix.real_space_refine on Wed Aug 27 01:41:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6em4_3889/08_2025/6em4_3889.cif Found real_map, /net/cci-nas-00/data/ceres_data/6em4_3889/08_2025/6em4_3889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6em4_3889/08_2025/6em4_3889.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6em4_3889/08_2025/6em4_3889.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6em4_3889/08_2025/6em4_3889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6em4_3889/08_2025/6em4_3889.map" } resolution = 4.1 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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: 4 Type Number sf(0) Gaussians P 1779 5.49 5 C 20921 2.51 5 N 6013 2.21 5 O 16687 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 45400 Number of models: 1 Model: "" Number of chains: 37 Chain: "x" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 1068 Classifications: {'peptide': 267} Incomplete info: {'backbone_only': 257} Link IDs: {'PTRANS': 12, 'TRANS': 254} Chain breaks: 3 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1248 Unresolved non-hydrogen angles: 1762 Unresolved non-hydrogen dihedrals: 829 Unresolved non-hydrogen chiralities: 329 Planarities with less than four sites: {'ASN:plan1': 19, 'ARG:plan': 23, 'GLN:plan1': 12, 'GLU:plan': 28, 'PHE:plan': 18, 'ASP:plan': 10, 'HIS:plan': 8, 'TYR:plan': 8, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 639 Chain: "F" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 964 Classifications: {'peptide': 241} Incomplete info: {'backbone_only': 226} Link IDs: {'PTRANS': 11, 'TRANS': 229} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1011 Unresolved non-hydrogen angles: 1441 Unresolved non-hydrogen dihedrals: 664 Unresolved non-hydrogen chiralities: 290 Planarities with less than four sites: {'GLU:plan': 16, 'GLN:plan1': 12, 'ARG:plan': 15, 'ASN:plan1': 14, 'TYR:plan': 10, 'ASP:plan': 4, 'HIS:plan': 4, 'PHE:plan': 10, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 453 Chain: "3" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 692 Classifications: {'peptide': 173} Incomplete info: {'backbone_only': 168} Link IDs: {'PTRANS': 5, 'TRANS': 167} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 770 Unresolved non-hydrogen angles: 1091 Unresolved non-hydrogen dihedrals: 515 Unresolved non-hydrogen chiralities: 209 Planarities with less than four sites: {'ASP:plan': 4, 'GLU:plan': 14, 'TRP:plan': 3, 'GLN:plan1': 9, 'ASN:plan1': 9, 'PHE:plan': 5, 'HIS:plan': 6, 'ARG:plan': 16, 'TYR:plan': 6} Unresolved non-hydrogen planarities: 373 Chain: "4" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 880 Classifications: {'peptide': 220} Incomplete info: {'backbone_only': 214} Link IDs: {'PTRANS': 7, 'TRANS': 212} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 1034 Unresolved non-hydrogen angles: 1475 Unresolved non-hydrogen dihedrals: 709 Unresolved non-hydrogen chiralities: 275 Planarities with less than four sites: {'ASN:plan1': 13, 'PHE:plan': 13, 'GLN:plan1': 8, 'ARG:plan': 15, 'GLU:plan': 12, 'TYR:plan': 10, 'TRP:plan': 7, 'ASP:plan': 16, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 524 Chain: "5" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 1540 Classifications: {'peptide': 385} Incomplete info: {'backbone_only': 361} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 372} Chain breaks: 3 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1573 Unresolved non-hydrogen angles: 2263 Unresolved non-hydrogen dihedrals: 1010 Unresolved non-hydrogen chiralities: 478 Planarities with less than four sites: {'ARG:plan': 15, 'ASP:plan': 26, 'GLU:plan': 24, 'ASN:plan1': 17, 'GLN:plan1': 11, 'PHE:plan': 19, 'HIS:plan': 8, 'TYR:plan': 11, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 696 Chain: "A" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 580 Classifications: {'peptide': 145} Incomplete info: {'backbone_only': 140} Link IDs: {'PTRANS': 10, 'TRANS': 134} Chain breaks: 2 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 666 Unresolved non-hydrogen angles: 953 Unresolved non-hydrogen dihedrals: 451 Unresolved non-hydrogen chiralities: 179 Planarities with less than four sites: {'ASN:plan1': 9, 'GLN:plan1': 8, 'ARG:plan': 10, 'TYR:plan': 6, 'HIS:plan': 7, 'ASP:plan': 7, 'GLU:plan': 6, 'PHE:plan': 8, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 336 Chain: "J" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 264 Classifications: {'peptide': 66} Incomplete info: {'backbone_only': 66} Link IDs: {'PTRANS': 1, 'TRANS': 64} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 296 Unresolved non-hydrogen angles: 426 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 83 Planarities with less than four sites: {'ASN:plan1': 3, 'HIS:plan': 4, 'GLU:plan': 7, 'ARG:plan': 3, 'GLN:plan1': 4, 'TRP:plan': 1, 'PHE:plan': 2, 'ASP:plan': 6, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 159 Chain: "u" Number of atoms: 464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 464 Classifications: {'peptide': 116} Incomplete info: {'backbone_only': 112} Link IDs: {'PTRANS': 4, 'TRANS': 111} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 533 Unresolved non-hydrogen angles: 743 Unresolved non-hydrogen dihedrals: 368 Unresolved non-hydrogen chiralities: 131 Planarities with less than four sites: {'ARG:plan': 18, 'TYR:plan': 4, 'GLN:plan1': 4, 'HIS:plan': 3, 'PHE:plan': 8, 'ASN:plan1': 6, 'ASP:plan': 2, 'GLU:plan': 6, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 278 Chain: "v" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 520 Classifications: {'peptide': 130} Incomplete info: {'backbone_only': 123} Link IDs: {'PTRANS': 2, 'TRANS': 127} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 583 Unresolved non-hydrogen angles: 813 Unresolved non-hydrogen dihedrals: 397 Unresolved non-hydrogen chiralities: 148 Planarities with less than four sites: {'ARG:plan': 13, 'ASN:plan1': 8, 'ASP:plan': 6, 'GLN:plan1': 7, 'TRP:plan': 3, 'TYR:plan': 5, 'GLU:plan': 10, 'HIS:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 279 Chain: "y" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 900 Classifications: {'peptide': 225} Incomplete info: {'backbone_only': 206} Link IDs: {'PTRANS': 7, 'TRANS': 217} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 823 Unresolved non-hydrogen angles: 1214 Unresolved non-hydrogen dihedrals: 474 Unresolved non-hydrogen chiralities: 287 Planarities with less than four sites: {'ARG:plan': 12, 'GLN:plan1': 12, 'PHE:plan': 6, 'GLU:plan': 16, 'ASN:plan1': 12, 'TYR:plan': 5, 'ASP:plan': 10, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 366 Chain: "B" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 1332 Classifications: {'peptide': 333} Incomplete info: {'backbone_only': 307} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 321} Chain breaks: 1 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1369 Unresolved non-hydrogen angles: 1956 Unresolved non-hydrogen dihedrals: 904 Unresolved non-hydrogen chiralities: 398 Planarities with less than four sites: {'HIS:plan': 11, 'PHE:plan': 14, 'ARG:plan': 26, 'ASP:plan': 16, 'TYR:plan': 11, 'GLU:plan': 18, 'TRP:plan': 4, 'ASN:plan1': 8, 'GLN:plan1': 7} Unresolved non-hydrogen planarities: 618 Chain: "C" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 1372 Classifications: {'peptide': 343} Incomplete info: {'backbone_only': 316} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 326} Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1289 Unresolved non-hydrogen angles: 1873 Unresolved non-hydrogen dihedrals: 813 Unresolved non-hydrogen chiralities: 415 Planarities with less than four sites: {'ARG:plan': 25, 'GLN:plan1': 12, 'HIS:plan': 9, 'GLU:plan': 14, 'ASN:plan1': 16, 'PHE:plan': 7, 'ASP:plan': 6, 'TYR:plan': 6, 'TRP:plan': 6} Unresolved non-hydrogen planarities: 528 Chain: "e" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 500 Classifications: {'peptide': 125} Incomplete info: {'backbone_only': 118} Link IDs: {'PTRANS': 5, 'TRANS': 119} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 531 Unresolved non-hydrogen angles: 752 Unresolved non-hydrogen dihedrals: 355 Unresolved non-hydrogen chiralities: 152 Planarities with less than four sites: {'HIS:plan': 8, 'PHE:plan': 4, 'ARG:plan': 11, 'ASP:plan': 3, 'TYR:plan': 3, 'GLU:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 225 Chain: "E" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 604 Classifications: {'peptide': 151} Incomplete info: {'backbone_only': 144} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 143} Chain breaks: 1 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 624 Unresolved non-hydrogen angles: 892 Unresolved non-hydrogen dihedrals: 402 Unresolved non-hydrogen chiralities: 190 Planarities with less than four sites: {'TRP:plan': 1, 'TYR:plan': 5, 'GLU:plan': 10, 'ASP:plan': 5, 'ARG:plan': 10, 'GLN:plan1': 3, 'PHE:plan': 6, 'HIS:plan': 2, 'ASN:plan1': 6} Unresolved non-hydrogen planarities: 250 Chain: "f" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 424 Classifications: {'peptide': 106} Incomplete info: {'backbone_only': 98} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 445 Unresolved non-hydrogen angles: 637 Unresolved non-hydrogen dihedrals: 296 Unresolved non-hydrogen chiralities: 126 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 3, 'ARG:plan': 11, 'TYR:plan': 6, 'GLN:plan1': 3, 'ASN:plan1': 7, 'ASP:plan': 1, 'PHE:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 215 Chain: "G" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 636 Classifications: {'peptide': 159} Incomplete info: {'backbone_only': 154} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 149} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 618 Unresolved non-hydrogen angles: 898 Unresolved non-hydrogen dihedrals: 385 Unresolved non-hydrogen chiralities: 201 Planarities with less than four sites: {'GLN:plan1': 3, 'PHE:plan': 5, 'TYR:plan': 6, 'ASP:plan': 7, 'ARG:plan': 5, 'ASN:plan1': 7, 'GLU:plan': 12, 'HIS:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 246 Chain: "h" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 476 Classifications: {'peptide': 119} Incomplete info: {'backbone_only': 117} Link IDs: {'PTRANS': 4, 'TRANS': 114} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 503 Unresolved non-hydrogen angles: 705 Unresolved non-hydrogen dihedrals: 321 Unresolved non-hydrogen chiralities: 149 Planarities with less than four sites: {'TYR:plan': 4, 'GLU:plan': 8, 'ARG:plan': 11, 'GLN:plan1': 11, 'ASP:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 189 Chain: "i" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 296 Classifications: {'peptide': 74} Incomplete info: {'backbone_only': 70} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 304 Unresolved non-hydrogen angles: 425 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 4, 'ARG:plan': 12, 'PHE:plan': 2, 'GLU:plan': 5, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 136 Chain: "j" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 284 Classifications: {'peptide': 71} Incomplete info: {'backbone_only': 64} Link IDs: {'PCIS': 1, 'TRANS': 69} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 295 Unresolved non-hydrogen angles: 414 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'HIS:plan': 4, 'ASN:plan1': 3, 'ARG:plan': 10, 'PHE:plan': 3, 'GLN:plan1': 2, 'TYR:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 149 Chain: "L" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 432 Classifications: {'peptide': 108} Incomplete info: {'backbone_only': 103} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 446 Unresolved non-hydrogen angles: 637 Unresolved non-hydrogen dihedrals: 281 Unresolved non-hydrogen chiralities: 131 Planarities with less than four sites: {'HIS:plan': 2, 'PHE:plan': 4, 'ASP:plan': 4, 'GLN:plan1': 5, 'ARG:plan': 16, 'ASN:plan1': 6, 'TYR:plan': 3, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 216 Chain: "M" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 536 Classifications: {'peptide': 134} Incomplete info: {'backbone_only': 127} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 128} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 521 Unresolved non-hydrogen angles: 750 Unresolved non-hydrogen dihedrals: 333 Unresolved non-hydrogen chiralities: 167 Planarities with less than four sites: {'ASP:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 4, 'ARG:plan': 11, 'GLU:plan': 5, 'GLN:plan1': 7, 'PHE:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 196 Chain: "N" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 708 Classifications: {'peptide': 177} Incomplete info: {'backbone_only': 167} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 838 Unresolved non-hydrogen angles: 1182 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 206 Planarities with less than four sites: {'TYR:plan': 10, 'GLU:plan': 7, 'GLN:plan1': 8, 'ARG:plan': 31, 'ASP:plan': 6, 'PHE:plan': 4, 'TRP:plan': 5, 'ASN:plan1': 9, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 463 Chain: "O" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 788 Classifications: {'peptide': 197} Incomplete info: {'backbone_only': 184} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 188} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 798 Unresolved non-hydrogen angles: 1138 Unresolved non-hydrogen dihedrals: 523 Unresolved non-hydrogen chiralities: 237 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 5, 'HIS:plan': 4, 'ARG:plan': 16, 'GLN:plan1': 4, 'ASN:plan1': 5, 'PHE:plan': 9, 'TYR:plan': 8, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 337 Chain: "P" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 548 Classifications: {'peptide': 137} Incomplete info: {'backbone_only': 130} Link IDs: {'PTRANS': 5, 'TRANS': 131} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 534 Unresolved non-hydrogen angles: 771 Unresolved non-hydrogen dihedrals: 341 Unresolved non-hydrogen chiralities: 161 Planarities with less than four sites: {'ASN:plan1': 7, 'ARG:plan': 8, 'TYR:plan': 3, 'PHE:plan': 5, 'GLU:plan': 10, 'GLN:plan1': 9, 'TRP:plan': 2, 'ASP:plan': 2, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 249 Chain: "Q" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 524 Classifications: {'peptide': 131} Incomplete info: {'backbone_only': 124} Link IDs: {'PTRANS': 7, 'TRANS': 123} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 501 Unresolved non-hydrogen angles: 726 Unresolved non-hydrogen dihedrals: 303 Unresolved non-hydrogen chiralities: 169 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 12, 'ASP:plan': 5, 'ASN:plan1': 6, 'TYR:plan': 2, 'PHE:plan': 6, 'GLN:plan1': 3, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 192 Chain: "S" Number of atoms: 680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 680 Classifications: {'peptide': 170} Incomplete info: {'backbone_only': 166} Link IDs: {'PTRANS': 7, 'TRANS': 162} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 789 Unresolved non-hydrogen angles: 1119 Unresolved non-hydrogen dihedrals: 541 Unresolved non-hydrogen chiralities: 209 Planarities with less than four sites: {'HIS:plan': 7, 'PHE:plan': 10, 'GLU:plan': 10, 'TYR:plan': 9, 'GLN:plan1': 7, 'ARG:plan': 16, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 392 Chain: "V" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 504 Classifications: {'peptide': 126} Incomplete info: {'backbone_only': 112} Link IDs: {'PTRANS': 7, 'TRANS': 118} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 447 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 280 Unresolved non-hydrogen chiralities: 144 Planarities with less than four sites: {'ARG:plan': 10, 'ASN:plan1': 7, 'ASP:plan': 5, 'TYR:plan': 2, 'GLU:plan': 4, 'GLN:plan1': 1, 'TRP:plan': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 168 Chain: "Y" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 500 Classifications: {'peptide': 125} Incomplete info: {'backbone_only': 118} Link IDs: {'PTRANS': 5, 'TRANS': 119} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 496 Unresolved non-hydrogen angles: 702 Unresolved non-hydrogen dihedrals: 312 Unresolved non-hydrogen chiralities: 153 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'ARG:plan': 12, 'TYR:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 186 Chain: "1" Number of atoms: 18672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1556, 18672 Classifications: {'RNA': 1556} Modifications used: {'rna3p_pur': 875, 'rna3p_pyr': 681} Link IDs: {'rna3p': 1555} Chain breaks: 12 Unresolved non-hydrogen bonds: 17089 Unresolved non-hydrogen angles: 27079 Unresolved non-hydrogen dihedrals: 16868 Unresolved non-hydrogen chiralities: 1556 Planarities with less than four sites: {' G%rna3p_pur:plan': 460, ' G%rna3p_pur:plan2': 460, ' U%rna3p_pyr:plan': 386, ' A%rna3p_pur:plan': 415, ' A%rna3p_pur:plan2': 415, ' C%rna3p_pyr:plan': 295, ' C%rna3p_pyr:plan2': 295} Unresolved non-hydrogen planarities: 16998 Chain: "2" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1896 Classifications: {'RNA': 158} Modifications used: {'rna3p_pur': 78, 'rna3p_pyr': 80} Link IDs: {'rna3p': 157} Chain breaks: 6 Unresolved non-hydrogen bonds: 1693 Unresolved non-hydrogen angles: 2676 Unresolved non-hydrogen dihedrals: 1650 Unresolved non-hydrogen chiralities: 158 Planarities with less than four sites: {' A%rna3p_pur:plan': 41, ' A%rna3p_pur:plan2': 41, ' C%rna3p_pyr:plan': 36, ' C%rna3p_pyr:plan2': 36, ' U%rna3p_pyr:plan': 44, ' G%rna3p_pur:plan': 37, ' G%rna3p_pur:plan2': 37} Unresolved non-hydrogen planarities: 1685 Chain: "D" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 776 Classifications: {'peptide': 194} Incomplete info: {'backbone_only': 186} Link IDs: {'PTRANS': 9, 'TRANS': 184} Chain breaks: 2 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 853 Unresolved non-hydrogen angles: 1224 Unresolved non-hydrogen dihedrals: 567 Unresolved non-hydrogen chiralities: 238 Planarities with less than four sites: {'TYR:plan': 13, 'ASP:plan': 13, 'ARG:plan': 9, 'PHE:plan': 11, 'ASN:plan1': 10, 'GLN:plan1': 10, 'GLU:plan': 8, 'HIS:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 424 Chain: "K" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 984 Classifications: {'peptide': 246} Incomplete info: {'backbone_only': 239} Link IDs: {'PTRANS': 10, 'TRANS': 235} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1036 Unresolved non-hydrogen angles: 1489 Unresolved non-hydrogen dihedrals: 659 Unresolved non-hydrogen chiralities: 321 Planarities with less than four sites: {'ARG:plan': 8, 'GLU:plan': 17, 'ASN:plan1': 15, 'PHE:plan': 11, 'ASP:plan': 13, 'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 8, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 427 Chain: "n" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 1248 Classifications: {'peptide': 312} Incomplete info: {'backbone_only': 302} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain breaks: 3 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1382 Unresolved non-hydrogen angles: 1984 Unresolved non-hydrogen dihedrals: 918 Unresolved non-hydrogen chiralities: 394 Planarities with less than four sites: {'PHE:plan': 21, 'ARG:plan': 21, 'GLN:plan1': 10, 'ASP:plan': 19, 'TYR:plan': 17, 'HIS:plan': 5, 'GLU:plan': 15, 'ASN:plan1': 11, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 668 Chain: "o" Number of atoms: 464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 464 Classifications: {'peptide': 116} Incomplete info: {'backbone_only': 109} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 525 Unresolved non-hydrogen angles: 732 Unresolved non-hydrogen dihedrals: 361 Unresolved non-hydrogen chiralities: 133 Planarities with less than four sites: {'GLU:plan': 10, 'TYR:plan': 7, 'ARG:plan': 7, 'HIS:plan': 5, 'PHE:plan': 5, 'GLN:plan1': 5, 'ASP:plan': 3, 'ASN:plan1': 6} Unresolved non-hydrogen planarities: 252 Chain: "t" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 992 Classifications: {'peptide': 248} Incomplete info: {'backbone_only': 235} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 238} Chain breaks: 1 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1001 Unresolved non-hydrogen angles: 1436 Unresolved non-hydrogen dihedrals: 617 Unresolved non-hydrogen chiralities: 318 Planarities with less than four sites: {'PHE:plan': 11, 'ARG:plan': 17, 'GLU:plan': 21, 'ASP:plan': 8, 'ASN:plan1': 14, 'GLN:plan1': 6, 'HIS:plan': 4, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 414 Chain: "6" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 780 Classifications: {'RNA': 65} Modifications used: {'rna3p_pur': 29, 'rna3p_pyr': 36} Link IDs: {'rna3p': 64} Chain breaks: 1 Unresolved non-hydrogen bonds: 684 Unresolved non-hydrogen angles: 1079 Unresolved non-hydrogen dihedrals: 660 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {' C%rna3p_pyr:plan': 11, ' C%rna3p_pyr:plan2': 11, ' U%rna3p_pyr:plan': 25, ' A%rna3p_pur:plan': 17, ' A%rna3p_pur:plan2': 17, ' G%rna3p_pur:plan': 12, ' G%rna3p_pur:plan2': 12} Unresolved non-hydrogen planarities: 670 Chain: "H" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 572 Classifications: {'peptide': 143} Incomplete info: {'backbone_only': 139} Link IDs: {'PTRANS': 15, 'TRANS': 127} Chain breaks: 1 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 675 Unresolved non-hydrogen angles: 955 Unresolved non-hydrogen dihedrals: 465 Unresolved non-hydrogen chiralities: 168 Planarities with less than four sites: {'ASP:plan': 3, 'TRP:plan': 3, 'PHE:plan': 4, 'ARG:plan': 14, 'HIS:plan': 1, 'GLU:plan': 23, 'ASN:plan1': 6, 'TYR:plan': 8, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 334 Residues with excluded nonbonded symmetry interactions: 204 residue: pdb=" N ASP 4 57 " occ=0.52 ... (2 atoms not shown) pdb=" O ASP 4 57 " occ=0.52 residue: pdb=" N VAL O 3 " occ=0.50 ... (2 atoms not shown) pdb=" O VAL O 3 " occ=0.50 residue: pdb=" N GLU O 4 " occ=0.50 ... (2 atoms not shown) pdb=" O GLU O 4 " occ=0.50 residue: pdb=" N PRO O 5 " occ=0.50 ... (2 atoms not shown) pdb=" O PRO O 5 " occ=0.50 residue: pdb=" N VAL O 6 " occ=0.50 ... (2 atoms not shown) pdb=" O VAL O 6 " occ=0.50 residue: pdb=" N VAL O 7 " occ=0.50 ... (2 atoms not shown) pdb=" O VAL O 7 " occ=0.50 residue: pdb=" N VAL O 8 " occ=0.50 ... (2 atoms not shown) pdb=" O VAL O 8 " occ=0.50 residue: pdb=" N ILE O 9 " occ=0.50 ... (2 atoms not shown) pdb=" O ILE O 9 " occ=0.50 residue: pdb=" N ASP O 10 " occ=0.50 ... (2 atoms not shown) pdb=" O ASP O 10 " occ=0.50 residue: pdb=" N GLY O 11 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY O 11 " occ=0.50 residue: pdb=" N LYS O 12 " occ=0.50 ... (2 atoms not shown) pdb=" O LYS O 12 " occ=0.50 residue: pdb=" N GLY O 13 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY O 13 " occ=0.50 ... (remaining 192 not shown) Time building chain proxies: 10.77, per 1000 atoms: 0.24 Number of scatterers: 45400 At special positions: 0 Unit cell: (214.632, 223.304, 311.108, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) P 1779 15.00 O 16687 8.00 N 6013 7.00 C 20921 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 - 3.00 Amino acid : True - 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: 3.57 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 476.8 nanoseconds 11790 Ramachandran restraints generated. 5895 Oldfield, 0 Emsley, 5895 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 0 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 63 sheets defined 39.7% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.08 Creating SS restraints... Processing helix chain 'x' and resid 11 through 44 removed outlier: 3.916A pdb=" N GLU x 17 " --> pdb=" O LEU x 13 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS x 28 " --> pdb=" O HIS x 24 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU x 43 " --> pdb=" O LYS x 39 " (cutoff:3.500A) Processing helix chain 'x' and resid 45 through 55 removed outlier: 3.725A pdb=" N GLU x 49 " --> pdb=" O PRO x 45 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN x 50 " --> pdb=" O GLU x 46 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG x 51 " --> pdb=" O LEU x 47 " (cutoff:3.500A) Processing helix chain 'x' and resid 79 through 85 removed outlier: 3.992A pdb=" N ARG x 83 " --> pdb=" O ASP x 79 " (cutoff:3.500A) Processing helix chain 'x' and resid 104 through 118 removed outlier: 3.747A pdb=" N TYR x 108 " --> pdb=" O LYS x 104 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE x 113 " --> pdb=" O GLU x 109 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU x 116 " --> pdb=" O ASN x 112 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE x 117 " --> pdb=" O ILE x 113 " (cutoff:3.500A) Processing helix chain 'x' and resid 132 through 142 removed outlier: 3.587A pdb=" N ILE x 138 " --> pdb=" O GLU x 134 " (cutoff:3.500A) Processing helix chain 'x' and resid 204 through 218 removed outlier: 3.530A pdb=" N VAL x 210 " --> pdb=" O LEU x 206 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU x 218 " --> pdb=" O PHE x 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 73 removed outlier: 3.840A pdb=" N ALA F 35 " --> pdb=" O ALA F 31 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA F 36 " --> pdb=" O ALA F 32 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS F 70 " --> pdb=" O LYS F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 removed outlier: 3.940A pdb=" N VAL F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 130 removed outlier: 3.627A pdb=" N LEU F 124 " --> pdb=" O THR F 120 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 151 removed outlier: 3.966A pdb=" N ILE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 174 removed outlier: 4.265A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 180 through 190 Processing helix chain 'F' and resid 194 through 202 Processing helix chain 'F' and resid 222 through 226 Processing helix chain 'F' and resid 235 through 244 removed outlier: 3.563A pdb=" N SER F 242 " --> pdb=" O LYS F 238 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 12 removed outlier: 3.530A pdb=" N VAL 3 9 " --> pdb=" O ILE 3 5 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN 3 12 " --> pdb=" O GLN 3 8 " (cutoff:3.500A) Processing helix chain '3' and resid 67 through 71 removed outlier: 3.512A pdb=" N ALA 3 70 " --> pdb=" O PRO 3 67 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N HIS 3 71 " --> pdb=" O GLU 3 68 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 67 through 71' Processing helix chain '3' and resid 85 through 97 removed outlier: 3.732A pdb=" N HIS 3 96 " --> pdb=" O GLN 3 92 " (cutoff:3.500A) Processing helix chain '3' and resid 101 through 117 removed outlier: 3.731A pdb=" N LYS 3 109 " --> pdb=" O ARG 3 105 " (cutoff:3.500A) Processing helix chain '3' and resid 120 through 127 Processing helix chain '3' and resid 140 through 145 Processing helix chain '3' and resid 148 through 157 removed outlier: 3.736A pdb=" N VAL 3 154 " --> pdb=" O ARG 3 150 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS 3 157 " --> pdb=" O LEU 3 153 " (cutoff:3.500A) Processing helix chain '3' and resid 157 through 171 removed outlier: 3.729A pdb=" N MET 3 167 " --> pdb=" O GLU 3 163 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARG 3 169 " --> pdb=" O GLU 3 165 " (cutoff:3.500A) Processing helix chain '4' and resid 14 through 31 Processing helix chain '4' and resid 38 through 55 removed outlier: 3.718A pdb=" N PHE 4 42 " --> pdb=" O LYS 4 38 " (cutoff:3.500A) Processing helix chain '4' and resid 58 through 76 removed outlier: 4.182A pdb=" N HIS 4 73 " --> pdb=" O LEU 4 69 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY 4 74 " --> pdb=" O GLY 4 70 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR 4 76 " --> pdb=" O LEU 4 72 " (cutoff:3.500A) Processing helix chain '4' and resid 78 through 82 removed outlier: 4.324A pdb=" N ASP 4 81 " --> pdb=" O ASP 4 78 " (cutoff:3.500A) Processing helix chain '4' and resid 94 through 110 removed outlier: 3.891A pdb=" N GLY 4 101 " --> pdb=" O LYS 4 97 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE 4 102 " --> pdb=" O PHE 4 98 " (cutoff:3.500A) Processing helix chain '4' and resid 117 through 135 removed outlier: 3.709A pdb=" N TYR 4 121 " --> pdb=" O ARG 4 117 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU 4 133 " --> pdb=" O LEU 4 129 " (cutoff:3.500A) Processing helix chain '4' and resid 142 through 155 Processing helix chain '4' and resid 167 through 177 removed outlier: 3.827A pdb=" N ILE 4 171 " --> pdb=" O THR 4 167 " (cutoff:3.500A) Processing helix chain '4' and resid 213 through 227 removed outlier: 3.691A pdb=" N VAL 4 217 " --> pdb=" O PRO 4 213 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE 4 221 " --> pdb=" O VAL 4 217 " (cutoff:3.500A) Processing helix chain '4' and resid 231 through 242 removed outlier: 3.524A pdb=" N ARG 4 235 " --> pdb=" O SER 4 231 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS 4 239 " --> pdb=" O ARG 4 235 " (cutoff:3.500A) Processing helix chain '5' and resid 42 through 45 Processing helix chain '5' and resid 119 through 127 removed outlier: 4.192A pdb=" N LEU 5 123 " --> pdb=" O ASP 5 119 " (cutoff:3.500A) Processing helix chain '5' and resid 297 through 301 removed outlier: 4.323A pdb=" N ARG 5 300 " --> pdb=" O LEU 5 297 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU 5 301 " --> pdb=" O PRO 5 298 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 297 through 301' Processing helix chain 'A' and resid 42 through 56 Processing helix chain 'A' and resid 73 through 82 removed outlier: 3.503A pdb=" N LEU A 80 " --> pdb=" O GLU A 76 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR A 81 " --> pdb=" O ILE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 159 removed outlier: 4.392A pdb=" N ILE A 152 " --> pdb=" O HIS A 148 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS A 158 " --> pdb=" O GLU A 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 208 Processing helix chain 'J' and resid 216 through 221 Processing helix chain 'J' and resid 240 through 261 removed outlier: 3.595A pdb=" N LEU J 244 " --> pdb=" O THR J 240 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE J 246 " --> pdb=" O ARG J 242 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA J 253 " --> pdb=" O GLN J 249 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL J 254 " --> pdb=" O SER J 250 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU J 255 " --> pdb=" O LEU J 251 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL J 256 " --> pdb=" O ASP J 252 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP J 259 " --> pdb=" O LEU J 255 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU J 260 " --> pdb=" O VAL J 256 " (cutoff:3.500A) Processing helix chain 'u' and resid 33 through 42 removed outlier: 3.517A pdb=" N HIS u 37 " --> pdb=" O ARG u 33 " (cutoff:3.500A) Processing helix chain 'u' and resid 52 through 59 removed outlier: 4.195A pdb=" N ARG u 56 " --> pdb=" O THR u 52 " (cutoff:3.500A) Processing helix chain 'u' and resid 82 through 113 removed outlier: 4.072A pdb=" N THR u 89 " --> pdb=" O LEU u 85 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS u 91 " --> pdb=" O ALA u 87 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU u 98 " --> pdb=" O ALA u 94 " (cutoff:3.500A) Processing helix chain 'v' and resid 4 through 12 removed outlier: 3.751A pdb=" N LYS v 8 " --> pdb=" O VAL v 4 " (cutoff:3.500A) Processing helix chain 'v' and resid 33 through 39 Processing helix chain 'v' and resid 45 through 54 Processing helix chain 'v' and resid 157 through 167 removed outlier: 3.650A pdb=" N GLU v 164 " --> pdb=" O LYS v 160 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER v 167 " --> pdb=" O GLU v 163 " (cutoff:3.500A) Processing helix chain 'v' and resid 178 through 192 Processing helix chain 'v' and resid 195 through 202 Processing helix chain 'v' and resid 211 through 226 Processing helix chain 'y' and resid 12 through 16 removed outlier: 4.020A pdb=" N PHE y 16 " --> pdb=" O GLU y 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 12 through 16' Processing helix chain 'y' and resid 32 through 42 removed outlier: 3.780A pdb=" N PHE y 38 " --> pdb=" O PHE y 34 " (cutoff:3.500A) Processing helix chain 'y' and resid 59 through 63 removed outlier: 3.538A pdb=" N MET y 62 " --> pdb=" O ILE y 59 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR y 63 " --> pdb=" O GLY y 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 59 through 63' Processing helix chain 'y' and resid 77 through 88 Processing helix chain 'y' and resid 122 through 133 removed outlier: 3.796A pdb=" N GLU y 126 " --> pdb=" O ASP y 122 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER y 130 " --> pdb=" O GLU y 126 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP y 131 " --> pdb=" O GLU y 127 " (cutoff:3.500A) Processing helix chain 'y' and resid 166 through 178 Processing helix chain 'y' and resid 192 through 196 Processing helix chain 'y' and resid 211 through 222 Processing helix chain 'B' and resid 111 through 118 removed outlier: 3.650A pdb=" N PHE B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 138 Processing helix chain 'B' and resid 143 through 154 Processing helix chain 'B' and resid 187 through 198 removed outlier: 3.505A pdb=" N LYS B 191 " --> pdb=" O SER B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 352 removed outlier: 3.915A pdb=" N GLU B 352 " --> pdb=" O ARG B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 381 removed outlier: 3.715A pdb=" N LYS B 376 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS B 377 " --> pdb=" O PRO B 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 43 removed outlier: 4.220A pdb=" N SER C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'C' and resid 132 through 139 Processing helix chain 'C' and resid 154 through 157 Processing helix chain 'C' and resid 161 through 173 Processing helix chain 'C' and resid 176 through 184 removed outlier: 4.745A pdb=" N LEU C 182 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS C 183 " --> pdb=" O LEU C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 196 removed outlier: 3.906A pdb=" N LYS C 193 " --> pdb=" O GLY C 190 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASN C 196 " --> pdb=" O LYS C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 219 Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'C' and resid 240 through 243 Processing helix chain 'C' and resid 252 through 263 removed outlier: 4.168A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 291 Processing helix chain 'C' and resid 294 through 298 Processing helix chain 'C' and resid 322 through 327 removed outlier: 3.635A pdb=" N ARG C 326 " --> pdb=" O GLN C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 337 Processing helix chain 'e' and resid 54 through 58 Processing helix chain 'e' and resid 60 through 64 removed outlier: 3.644A pdb=" N LYS e 64 " --> pdb=" O LYS e 61 " (cutoff:3.500A) Processing helix chain 'e' and resid 78 through 83 Processing helix chain 'e' and resid 101 through 116 removed outlier: 3.780A pdb=" N VAL e 106 " --> pdb=" O ALA e 102 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 103 through 107 removed outlier: 3.537A pdb=" N ALA E 107 " --> pdb=" O GLU E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 150 removed outlier: 3.563A pdb=" N VAL E 135 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA E 144 " --> pdb=" O VAL E 140 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA E 147 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N GLU E 148 " --> pdb=" O ALA E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 161 Processing helix chain 'f' and resid 37 through 42 Processing helix chain 'f' and resid 43 through 45 No H-bonds generated for 'chain 'f' and resid 43 through 45' Processing helix chain 'G' and resid 83 through 95 Processing helix chain 'G' and resid 101 through 117 Processing helix chain 'G' and resid 135 through 143 Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 165 through 174 Processing helix chain 'G' and resid 183 through 189 removed outlier: 4.284A pdb=" N LEU G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 206 No H-bonds generated for 'chain 'G' and resid 204 through 206' Processing helix chain 'G' and resid 207 through 222 Processing helix chain 'G' and resid 226 through 231 removed outlier: 3.568A pdb=" N VAL G 229 " --> pdb=" O TYR G 226 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS G 230 " --> pdb=" O ASP G 227 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 11 removed outlier: 3.623A pdb=" N LEU h 9 " --> pdb=" O LYS h 5 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N THR h 11 " --> pdb=" O TYR h 7 " (cutoff:3.500A) Processing helix chain 'h' and resid 13 through 34 removed outlier: 3.618A pdb=" N LEU h 17 " --> pdb=" O SER h 13 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL h 33 " --> pdb=" O ALA h 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 42 through 70 removed outlier: 3.994A pdb=" N THR h 46 " --> pdb=" O PRO h 42 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG h 48 " --> pdb=" O ILE h 44 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 99 Processing helix chain 'h' and resid 101 through 111 Processing helix chain 'i' and resid 34 through 48 removed outlier: 3.504A pdb=" N GLU i 46 " --> pdb=" O SER i 42 " (cutoff:3.500A) Processing helix chain 'i' and resid 51 through 77 removed outlier: 3.861A pdb=" N ASP i 59 " --> pdb=" O ARG i 55 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N GLU i 66 " --> pdb=" O ARG i 62 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N LYS i 67 " --> pdb=" O ASN i 63 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ARG i 68 " --> pdb=" O SER i 64 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA i 69 " --> pdb=" O GLY i 65 " (cutoff:3.500A) Processing helix chain 'i' and resid 79 through 100 removed outlier: 3.520A pdb=" N ALA i 83 " --> pdb=" O SER i 79 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA i 85 " --> pdb=" O THR i 81 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG i 99 " --> pdb=" O ALA i 95 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 57 removed outlier: 3.507A pdb=" N ARG j 55 " --> pdb=" O ALA j 51 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS j 57 " --> pdb=" O ALA j 53 " (cutoff:3.500A) Processing helix chain 'j' and resid 66 through 68 No H-bonds generated for 'chain 'j' and resid 66 through 68' Processing helix chain 'j' and resid 69 through 77 removed outlier: 3.507A pdb=" N ASN j 76 " --> pdb=" O ARG j 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 46 Processing helix chain 'L' and resid 76 through 84 Processing helix chain 'L' and resid 86 through 93 removed outlier: 3.761A pdb=" N THR L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 122 removed outlier: 3.716A pdb=" N PHE L 109 " --> pdb=" O ASN L 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 89 Processing helix chain 'M' and resid 89 through 96 Processing helix chain 'M' and resid 97 through 111 removed outlier: 3.622A pdb=" N LYS M 101 " --> pdb=" O SER M 97 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 135 Processing helix chain 'N' and resid 3 through 11 Processing helix chain 'N' and resid 16 through 33 removed outlier: 3.887A pdb=" N TRP N 28 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG N 31 " --> pdb=" O VAL N 27 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS N 33 " --> pdb=" O GLU N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 50 Processing helix chain 'N' and resid 97 through 110 Processing helix chain 'N' and resid 139 through 145 removed outlier: 4.299A pdb=" N ASP N 145 " --> pdb=" O ALA N 141 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 157 Proline residue: N 154 - end of helix removed outlier: 3.672A pdb=" N LYS N 157 " --> pdb=" O PRO N 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 159 through 163 removed outlier: 3.550A pdb=" N ARG N 162 " --> pdb=" O ARG N 159 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY N 163 " --> pdb=" O GLU N 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 159 through 163' Processing helix chain 'N' and resid 165 through 172 Processing helix chain 'N' and resid 186 through 195 removed outlier: 3.513A pdb=" N TRP N 191 " --> pdb=" O ARG N 187 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 29 Processing helix chain 'O' and resid 37 through 41 Processing helix chain 'O' and resid 46 through 60 removed outlier: 3.951A pdb=" N ASN O 50 " --> pdb=" O GLU O 46 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR O 54 " --> pdb=" O ASN O 50 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N PHE O 57 " --> pdb=" O LYS O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 65 through 69 removed outlier: 3.615A pdb=" N GLY O 69 " --> pdb=" O LYS O 66 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 86 removed outlier: 3.643A pdb=" N ALA O 83 " --> pdb=" O ILE O 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 97 removed outlier: 3.554A pdb=" N LYS O 96 " --> pdb=" O THR O 92 " (cutoff:3.500A) Processing helix chain 'O' and resid 98 through 102 Processing helix chain 'O' and resid 138 through 145 Processing helix chain 'O' and resid 149 through 186 removed outlier: 4.154A pdb=" N ARG O 160 " --> pdb=" O LEU O 156 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR O 167 " --> pdb=" O SER O 163 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR O 168 " --> pdb=" O SER O 164 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS O 177 " --> pdb=" O ALA O 173 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL O 178 " --> pdb=" O PHE O 174 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER O 180 " --> pdb=" O LYS O 176 " (cutoff:3.500A) Processing helix chain 'O' and resid 190 through 198 removed outlier: 3.530A pdb=" N LEU O 194 " --> pdb=" O VAL O 190 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA O 195 " --> pdb=" O ALA O 191 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 12 No H-bonds generated for 'chain 'P' and resid 10 through 12' Processing helix chain 'P' and resid 25 through 35 removed outlier: 3.826A pdb=" N GLU P 31 " --> pdb=" O LYS P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 53 Processing helix chain 'P' and resid 70 through 76 removed outlier: 3.627A pdb=" N GLY P 73 " --> pdb=" O THR P 70 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU P 75 " --> pdb=" O GLN P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 106 Processing helix chain 'Q' and resid 23 through 40 removed outlier: 4.038A pdb=" N PHE Q 35 " --> pdb=" O LYS Q 31 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG Q 38 " --> pdb=" O THR Q 34 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR Q 40 " --> pdb=" O LEU Q 36 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 53 removed outlier: 4.116A pdb=" N LYS Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL Q 47 " --> pdb=" O PRO Q 43 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 71 Processing helix chain 'Q' and resid 107 through 118 Processing helix chain 'Q' and resid 123 through 131 Processing helix chain 'S' and resid 33 through 49 removed outlier: 3.572A pdb=" N LYS S 47 " --> pdb=" O TYR S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 98 through 115 Processing helix chain 'S' and resid 137 through 142 removed outlier: 3.501A pdb=" N LYS S 141 " --> pdb=" O ARG S 137 " (cutoff:3.500A) Processing helix chain 'V' and resid 119 through 126 Processing helix chain 'V' and resid 126 through 132 Processing helix chain 'Y' and resid 11 through 21 Processing helix chain 'Y' and resid 23 through 31 removed outlier: 3.905A pdb=" N VAL Y 29 " --> pdb=" O SER Y 25 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 44 Processing helix chain 'Y' and resid 112 through 122 Processing helix chain 'D' and resid 275 through 287 removed outlier: 3.503A pdb=" N ASN D 287 " --> pdb=" O PHE D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 310 removed outlier: 3.855A pdb=" N TYR D 304 " --> pdb=" O ASN D 300 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU D 309 " --> pdb=" O TYR D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 337 removed outlier: 3.701A pdb=" N THR D 331 " --> pdb=" O LYS D 327 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE D 335 " --> pdb=" O THR D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 422 removed outlier: 4.138A pdb=" N ILE D 422 " --> pdb=" O GLU D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 433 removed outlier: 3.830A pdb=" N LYS D 431 " --> pdb=" O SER D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 456 removed outlier: 3.764A pdb=" N TYR D 450 " --> pdb=" O GLY D 446 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN D 452 " --> pdb=" O ARG D 448 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA D 453 " --> pdb=" O SER D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 475 removed outlier: 3.815A pdb=" N ALA D 471 " --> pdb=" O LYS D 467 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS D 472 " --> pdb=" O LEU D 468 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL D 473 " --> pdb=" O ASP D 469 " (cutoff:3.500A) Processing helix chain 'K' and resid 33 through 49 removed outlier: 3.918A pdb=" N VAL K 37 " --> pdb=" O PRO K 33 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU K 43 " --> pdb=" O LYS K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 76 removed outlier: 3.573A pdb=" N LYS K 76 " --> pdb=" O GLU K 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 72 through 76' Processing helix chain 'K' and resid 106 through 117 removed outlier: 3.769A pdb=" N GLU K 112 " --> pdb=" O LYS K 108 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA K 113 " --> pdb=" O PRO K 109 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER K 114 " --> pdb=" O TRP K 110 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA K 115 " --> pdb=" O LYS K 111 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR K 116 " --> pdb=" O GLU K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 133 removed outlier: 3.938A pdb=" N ILE K 132 " --> pdb=" O LYS K 128 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS K 133 " --> pdb=" O ASP K 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 128 through 133' Processing helix chain 'K' and resid 136 through 145 Processing helix chain 'K' and resid 158 through 163 removed outlier: 3.568A pdb=" N VAL K 163 " --> pdb=" O ASP K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 175 Processing helix chain 'K' and resid 184 through 188 removed outlier: 4.615A pdb=" N THR K 188 " --> pdb=" O ASP K 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 184 through 188' Processing helix chain 'K' and resid 189 through 194 removed outlier: 3.834A pdb=" N LEU K 193 " --> pdb=" O SER K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 200 Processing helix chain 'K' and resid 218 through 232 removed outlier: 3.572A pdb=" N LEU K 222 " --> pdb=" O SER K 218 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN K 224 " --> pdb=" O THR K 220 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS K 227 " --> pdb=" O THR K 223 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN K 232 " --> pdb=" O LYS K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 255 through 272 removed outlier: 3.631A pdb=" N VAL K 260 " --> pdb=" O PRO K 256 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP K 261 " --> pdb=" O GLU K 257 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU K 265 " --> pdb=" O ASP K 261 " (cutoff:3.500A) Processing helix chain 'n' and resid 17 through 26 removed outlier: 4.114A pdb=" N VAL n 22 " --> pdb=" O ARG n 18 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG n 23 " --> pdb=" O SER n 19 " (cutoff:3.500A) Processing helix chain 'n' and resid 28 through 40 removed outlier: 3.835A pdb=" N PHE n 38 " --> pdb=" O ARG n 34 " (cutoff:3.500A) Processing helix chain 'n' and resid 64 through 72 Processing helix chain 'n' and resid 74 through 97 removed outlier: 3.741A pdb=" N ALA n 78 " --> pdb=" O GLU n 74 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS n 79 " --> pdb=" O PRO n 75 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG n 81 " --> pdb=" O LEU n 77 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA n 93 " --> pdb=" O LYS n 89 " (cutoff:3.500A) Processing helix chain 'n' and resid 98 through 108 removed outlier: 3.585A pdb=" N LEU n 105 " --> pdb=" O SER n 101 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU n 106 " --> pdb=" O ALA n 102 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU n 107 " --> pdb=" O LYS n 103 " (cutoff:3.500A) Processing helix chain 'n' and resid 114 through 118 Processing helix chain 'n' and resid 124 through 129 Processing helix chain 'n' and resid 131 through 144 removed outlier: 3.723A pdb=" N ALA n 135 " --> pdb=" O ASP n 131 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU n 141 " --> pdb=" O ASN n 137 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER n 143 " --> pdb=" O LEU n 139 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASN n 144 " --> pdb=" O PHE n 140 " (cutoff:3.500A) Processing helix chain 'n' and resid 152 through 173 removed outlier: 3.618A pdb=" N TYR n 169 " --> pdb=" O GLN n 165 " (cutoff:3.500A) Processing helix chain 'n' and resid 216 through 239 removed outlier: 3.844A pdb=" N THR n 227 " --> pdb=" O GLU n 223 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU n 228 " --> pdb=" O PHE n 224 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE n 231 " --> pdb=" O THR n 227 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL n 232 " --> pdb=" O LEU n 228 " (cutoff:3.500A) Processing helix chain 'n' and resid 249 through 256 removed outlier: 3.895A pdb=" N ILE n 255 " --> pdb=" O LYS n 251 " (cutoff:3.500A) Processing helix chain 'n' and resid 376 through 384 removed outlier: 3.719A pdb=" N ILE n 380 " --> pdb=" O LEU n 376 " (cutoff:3.500A) Processing helix chain 'n' and resid 429 through 437 Processing helix chain 'o' and resid 103 through 113 removed outlier: 3.826A pdb=" N GLN o 113 " --> pdb=" O LYS o 109 " (cutoff:3.500A) Processing helix chain 'o' and resid 141 through 153 removed outlier: 4.091A pdb=" N MET o 146 " --> pdb=" O LYS o 142 " (cutoff:3.500A) Processing helix chain 'o' and resid 195 through 208 removed outlier: 4.067A pdb=" N ASN o 199 " --> pdb=" O GLN o 195 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU o 205 " --> pdb=" O LYS o 201 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE o 208 " --> pdb=" O HIS o 204 " (cutoff:3.500A) Processing helix chain 'o' and resid 208 through 214 removed outlier: 3.743A pdb=" N ALA o 212 " --> pdb=" O ILE o 208 " (cutoff:3.500A) Processing helix chain 't' and resid 57 through 87 removed outlier: 3.993A pdb=" N ILE t 61 " --> pdb=" O ARG t 57 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL t 62 " --> pdb=" O ALA t 58 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU t 73 " --> pdb=" O SER t 69 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS t 76 " --> pdb=" O LYS t 72 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG t 77 " --> pdb=" O GLU t 73 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP t 83 " --> pdb=" O SER t 79 " (cutoff:3.500A) Processing helix chain 't' and resid 156 through 166 removed outlier: 4.093A pdb=" N ILE t 162 " --> pdb=" O LYS t 158 " (cutoff:3.500A) Processing helix chain 't' and resid 182 through 188 removed outlier: 4.378A pdb=" N LEU t 186 " --> pdb=" O ASN t 182 " (cutoff:3.500A) Processing helix chain 't' and resid 200 through 209 removed outlier: 3.521A pdb=" N LEU t 207 " --> pdb=" O SER t 203 " (cutoff:3.500A) Processing helix chain 't' and resid 233 through 238 Processing helix chain 't' and resid 246 through 256 removed outlier: 3.505A pdb=" N ILE t 251 " --> pdb=" O VAL t 247 " (cutoff:3.500A) Processing helix chain 't' and resid 260 through 266 Processing helix chain 't' and resid 281 through 299 removed outlier: 3.672A pdb=" N LEU t 286 " --> pdb=" O SER t 282 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU t 293 " --> pdb=" O ILE t 289 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA t 294 " --> pdb=" O LYS t 290 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER t 296 " --> pdb=" O ARG t 292 " (cutoff:3.500A) Processing helix chain 't' and resid 313 through 322 removed outlier: 3.595A pdb=" N LEU t 317 " --> pdb=" O ASP t 313 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS t 320 " --> pdb=" O SER t 316 " (cutoff:3.500A) Processing helix chain 'H' and resid 262 through 266 Processing helix chain 'H' and resid 269 through 286 Processing helix chain 'H' and resid 290 through 301 removed outlier: 3.516A pdb=" N LYS H 300 " --> pdb=" O GLU H 296 " (cutoff:3.500A) Processing helix chain 'H' and resid 341 through 345 Processing helix chain 'H' and resid 347 through 357 removed outlier: 4.104A pdb=" N GLU H 352 " --> pdb=" O PRO H 348 " (cutoff:3.500A) Processing helix chain 'H' and resid 383 through 396 removed outlier: 3.720A pdb=" N ARG H 387 " --> pdb=" O SER H 383 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU H 392 " --> pdb=" O PHE H 388 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP H 393 " --> pdb=" O GLU H 389 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR H 395 " --> pdb=" O SER H 391 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'x' and resid 120 through 124 removed outlier: 6.584A pdb=" N ILE x 95 " --> pdb=" O THR x 122 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL x 124 " --> pdb=" O ILE x 95 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU x 97 " --> pdb=" O VAL x 124 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY x 159 " --> pdb=" O ASN x 151 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'x' and resid 196 through 197 removed outlier: 3.869A pdb=" N ARG x 253 " --> pdb=" O LYS x 249 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 205 through 206 removed outlier: 4.439A pdb=" N SER F 113 " --> pdb=" O ARG F 88 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL F 134 " --> pdb=" O GLY F 230 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ARG F 232 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N TYR F 136 " --> pdb=" O ARG F 232 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 153 through 155 Processing sheet with id=AA5, first strand: chain '3' and resid 18 through 20 Processing sheet with id=AA6, first strand: chain '3' and resid 50 through 55 Processing sheet with id=AA7, first strand: chain '3' and resid 135 through 136 Processing sheet with id=AA8, first strand: chain '5' and resid 34 through 38 removed outlier: 6.851A pdb=" N ARG 5 2 " --> pdb=" O LEU 5 410 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE 5 406 " --> pdb=" O SER 5 6 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '5' and resid 47 through 52 removed outlier: 6.875A pdb=" N ALA 5 61 " --> pdb=" O ASP 5 48 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N MET 5 50 " --> pdb=" O ILE 5 59 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE 5 59 " --> pdb=" O MET 5 50 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL 5 52 " --> pdb=" O GLU 5 57 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N GLU 5 57 " --> pdb=" O VAL 5 52 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER 5 112 " --> pdb=" O LEU 5 69 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LYS 5 71 " --> pdb=" O ILE 5 110 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE 5 110 " --> pdb=" O LYS 5 71 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N SER 5 73 " --> pdb=" O PHE 5 108 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N PHE 5 108 " --> pdb=" O SER 5 73 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N HIS 5 75 " --> pdb=" O SER 5 106 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N SER 5 106 " --> pdb=" O HIS 5 75 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '5' and resid 140 through 145 removed outlier: 6.744A pdb=" N ALA 5 158 " --> pdb=" O VAL 5 141 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU 5 143 " --> pdb=" O VAL 5 156 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL 5 156 " --> pdb=" O LEU 5 143 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU 5 163 " --> pdb=" O THR 5 159 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU 5 164 " --> pdb=" O SER 5 180 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER 5 180 " --> pdb=" O LEU 5 164 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE 5 166 " --> pdb=" O LEU 5 178 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '5' and resid 189 through 192 removed outlier: 6.853A pdb=" N PHE 5 205 " --> pdb=" O LEU 5 216 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LEU 5 216 " --> pdb=" O PHE 5 205 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR 5 207 " --> pdb=" O ILE 5 214 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE 5 214 " --> pdb=" O TYR 5 207 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE 5 214 " --> pdb=" O GLU 5 231 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLU 5 231 " --> pdb=" O ILE 5 214 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU 5 216 " --> pdb=" O ILE 5 229 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '5' and resid 248 through 253 removed outlier: 6.803A pdb=" N ILE 5 273 " --> pdb=" O MET 5 249 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU 5 251 " --> pdb=" O ALA 5 271 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA 5 271 " --> pdb=" O LEU 5 251 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N PHE 5 253 " --> pdb=" O GLN 5 269 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N GLN 5 269 " --> pdb=" O PHE 5 253 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N HIS 5 278 " --> pdb=" O THR 5 274 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA 5 292 " --> pdb=" O LYS 5 281 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '5' and resid 303 through 309 removed outlier: 5.260A pdb=" N GLN 5 305 " --> pdb=" O THR 5 336 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N THR 5 336 " --> pdb=" O GLN 5 305 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASN 5 332 " --> pdb=" O PHE 5 309 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '5' and resid 366 through 370 removed outlier: 6.466A pdb=" N VAL 5 384 " --> pdb=" O LYS 5 397 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS 5 397 " --> pdb=" O VAL 5 384 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE 5 386 " --> pdb=" O LEU 5 395 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 35 through 37 removed outlier: 3.603A pdb=" N VAL A 86 " --> pdb=" O SER A 102 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 102 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 99 " --> pdb=" O PHE A 112 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A 101 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 110 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 134 through 137 removed outlier: 6.572A pdb=" N ARG A 134 " --> pdb=" O HIS A 175 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N MET A 177 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL A 136 " --> pdb=" O MET A 177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 181 through 182 Processing sheet with id=AB9, first strand: chain 'u' and resid 4 through 5 removed outlier: 3.581A pdb=" N TYR u 4 " --> pdb=" O CYS u 13 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'u' and resid 28 through 30 removed outlier: 3.769A pdb=" N TYR V 94 " --> pdb=" O MET u 20 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL u 22 " --> pdb=" O TYR V 94 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'y' and resid 4 through 5 Processing sheet with id=AC3, first strand: chain 'y' and resid 17 through 19 removed outlier: 6.860A pdb=" N CYS y 24 " --> pdb=" O VAL y 49 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'y' and resid 64 through 65 removed outlier: 6.402A pdb=" N LEU y 70 " --> pdb=" O GLN y 95 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'y' and resid 109 through 110 Processing sheet with id=AC6, first strand: chain 'y' and resid 152 through 154 Processing sheet with id=AC7, first strand: chain 'B' and resid 355 through 359 removed outlier: 6.268A pdb=" N LEU B 356 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASP B 59 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B 57 " --> pdb=" O TRP B 358 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N VAL B 220 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ILE B 215 " --> pdb=" O ASN B 279 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N MET B 323 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL B 285 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE B 321 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL B 72 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL B 57 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLU B 74 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N THR B 55 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL B 76 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N MET B 53 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL B 78 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 98 through 106 removed outlier: 7.236A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TRP B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N VAL B 87 " --> pdb=" O TRP B 106 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N VAL B 86 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N HIS B 163 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 98 through 106 removed outlier: 7.236A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TRP B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N VAL B 87 " --> pdb=" O TRP B 106 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 15 through 20 removed outlier: 5.759A pdb=" N ASN C 18 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL C 8 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL C 151 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU C 150 " --> pdb=" O TRP C 250 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU C 206 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N THR C 251 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL C 208 " --> pdb=" O THR C 251 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 62 through 63 Processing sheet with id=AD3, first strand: chain 'C' and resid 186 through 187 Processing sheet with id=AD4, first strand: chain 'e' and resid 72 through 76 removed outlier: 6.405A pdb=" N LYS e 72 " --> pdb=" O ALA e 93 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLU e 95 " --> pdb=" O LYS e 72 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N PHE e 74 " --> pdb=" O GLU e 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'E' and resid 77 through 80 removed outlier: 6.657A pdb=" N SER E 66 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N TYR E 54 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR E 38 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N VAL E 39 " --> pdb=" O THR E 87 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'f' and resid 8 through 18 removed outlier: 3.582A pdb=" N SER f 15 " --> pdb=" O LEU f 29 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL f 27 " --> pdb=" O GLN f 17 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ASN f 26 " --> pdb=" O PHE f 85 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE f 85 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG f 73 " --> pdb=" O ARG f 82 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N THR f 84 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL f 71 " --> pdb=" O THR f 84 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ARG f 48 " --> pdb=" O PHE f 101 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL f 52 " --> pdb=" O SER f 97 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N SER f 97 " --> pdb=" O VAL f 52 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA f 96 " --> pdb=" O HIS f 13 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 177 through 180 removed outlier: 6.104A pdb=" N VAL G 151 " --> pdb=" O ALA G 178 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL G 180 " --> pdb=" O VAL G 151 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ILE G 153 " --> pdb=" O VAL G 180 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU G 150 " --> pdb=" O LEU G 200 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'h' and resid 116 through 118 removed outlier: 3.697A pdb=" N ALA h 117 " --> pdb=" O ILE L 124 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'j' and resid 16 through 17 Processing sheet with id=AE1, first strand: chain 'L' and resid 23 through 25 Processing sheet with id=AE2, first strand: chain 'L' and resid 57 through 59 Processing sheet with id=AE3, first strand: chain 'M' and resid 14 through 15 Processing sheet with id=AE4, first strand: chain 'M' and resid 53 through 59 removed outlier: 5.225A pdb=" N GLY M 48 " --> pdb=" O PRO M 54 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LYS M 43 " --> pdb=" O ILE M 38 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ILE M 38 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU M 45 " --> pdb=" O VAL M 36 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N VAL M 20 " --> pdb=" O THR M 66 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.207A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN N 117 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL N 135 " --> pdb=" O VAL N 115 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL N 115 " --> pdb=" O VAL N 135 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.207A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN N 122 " --> pdb=" O TYR N 129 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N GLU N 131 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP N 120 " --> pdb=" O GLU N 131 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 9 through 10 removed outlier: 6.991A pdb=" N ILE O 9 " --> pdb=" O VAL O 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'P' and resid 14 through 22 removed outlier: 4.015A pdb=" N TYR P 21 " --> pdb=" O SER P 144 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N THR P 151 " --> pdb=" O VAL P 114 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N VAL P 114 " --> pdb=" O THR P 151 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'P' and resid 58 through 59 Processing sheet with id=AF1, first strand: chain 'Q' and resid 62 through 63 removed outlier: 6.703A pdb=" N VAL Q 62 " --> pdb=" O THR Q 88 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL Q 81 " --> pdb=" O ALA Q 102 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N LEU Q 104 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N VAL Q 83 " --> pdb=" O LEU Q 104 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N PHE Q 106 " --> pdb=" O VAL Q 83 " (cutoff:3.500A) removed outlier: 11.788A pdb=" N GLY Q 85 " --> pdb=" O PHE Q 106 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL Q 101 " --> pdb=" O ILE Q 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'Q' and resid 62 through 63 removed outlier: 6.703A pdb=" N VAL Q 62 " --> pdb=" O THR Q 88 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU Q 138 " --> pdb=" O THR Q 80 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL Q 84 " --> pdb=" O LEU Q 140 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'S' and resid 25 through 31 removed outlier: 3.546A pdb=" N GLY S 11 " --> pdb=" O PHE S 25 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER S 60 " --> pdb=" O ILE S 10 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'S' and resid 88 through 96 removed outlier: 3.614A pdb=" N TYR S 81 " --> pdb=" O HIS S 88 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ASN S 74 " --> pdb=" O GLU S 128 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLU S 128 " --> pdb=" O ASN S 74 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLY S 76 " --> pdb=" O VAL S 126 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N VAL S 126 " --> pdb=" O GLY S 76 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N TRP S 78 " --> pdb=" O LEU S 124 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'V' and resid 17 through 18 Processing sheet with id=AF6, first strand: chain 'V' and resid 22 through 25 removed outlier: 7.000A pdb=" N MET V 59 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N VAL V 39 " --> pdb=" O MET V 57 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N MET V 57 " --> pdb=" O VAL V 39 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET V 74 " --> pdb=" O ALA V 60 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL V 78 " --> pdb=" O VAL V 101 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N VAL V 101 " --> pdb=" O VAL V 78 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLY V 100 " --> pdb=" O ILE V 22 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ASN V 24 " --> pdb=" O GLY V 100 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ILE V 102 " --> pdb=" O ASN V 24 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'V' and resid 114 through 118 removed outlier: 6.138A pdb=" N SER V 133 " --> pdb=" O ILE V 114 " (cutoff:3.500A) removed outlier: 9.339A pdb=" N GLY V 116 " --> pdb=" O SER V 133 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL V 135 " --> pdb=" O GLY V 116 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Y' and resid 32 through 34 Processing sheet with id=AF9, first strand: chain 'Y' and resid 94 through 99 removed outlier: 7.358A pdb=" N VAL Y 85 " --> pdb=" O ILE Y 97 " (cutoff:3.500A) removed outlier: 10.802A pdb=" N LEU Y 99 " --> pdb=" O ASP Y 83 " (cutoff:3.500A) removed outlier: 10.506A pdb=" N ASP Y 83 " --> pdb=" O LEU Y 99 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER Y 72 " --> pdb=" O GLN Y 81 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ASP Y 83 " --> pdb=" O ILE Y 70 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ILE Y 70 " --> pdb=" O ASP Y 83 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N VAL Y 85 " --> pdb=" O GLY Y 68 " (cutoff:3.500A) removed outlier: 9.195A pdb=" N GLY Y 68 " --> pdb=" O VAL Y 85 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLU Y 55 " --> pdb=" O THR Y 107 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 316 through 318 removed outlier: 6.157A pdb=" N LEU D 317 " --> pdb=" O ILE D 344 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N THR D 346 " --> pdb=" O LEU D 317 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU D 343 " --> pdb=" O ILE D 292 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL D 294 " --> pdb=" O LEU D 343 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N CYS D 345 " --> pdb=" O VAL D 294 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 243 through 250 removed outlier: 6.519A pdb=" N GLN K 79 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU K 80 " --> pdb=" O LYS K 282 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER K 278 " --> pdb=" O ASN K 84 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE K 279 " --> pdb=" O LEU K 291 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 100 through 101 Processing sheet with id=AG4, first strand: chain 'K' and resid 153 through 155 removed outlier: 6.533A pdb=" N VAL K 123 " --> pdb=" O GLU K 153 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE K 155 " --> pdb=" O VAL K 123 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU K 125 " --> pdb=" O ILE K 155 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'n' and resid 178 through 181 Processing sheet with id=AG6, first strand: chain 'n' and resid 366 through 367 Processing sheet with id=AG7, first strand: chain 'o' and resid 117 through 120 removed outlier: 6.451A pdb=" N GLU o 138 " --> pdb=" O LYS o 118 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VAL o 120 " --> pdb=" O PHE o 136 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N PHE o 136 " --> pdb=" O VAL o 120 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU o 137 " --> pdb=" O ILE o 93 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE o 139 " --> pdb=" O GLY o 91 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N GLY o 91 " --> pdb=" O PHE o 139 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU o 167 " --> pdb=" O SER o 90 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE o 92 " --> pdb=" O ARG o 165 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ARG o 165 " --> pdb=" O ILE o 92 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N TYR o 94 " --> pdb=" O GLN o 163 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLN o 163 " --> pdb=" O TYR o 94 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 't' and resid 129 through 134 removed outlier: 6.952A pdb=" N PHE t 99 " --> pdb=" O VAL t 309 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLU t 311 " --> pdb=" O PHE t 99 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU t 101 " --> pdb=" O GLU t 311 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 't' and resid 174 through 179 1754 hydrogen bonds defined for protein. 5013 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.89 Time building geometry restraints manager: 4.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.24: 5867 1.24 - 1.34: 5884 1.34 - 1.44: 6827 1.44 - 1.54: 24770 1.54 - 1.64: 3750 Bond restraints: 47098 Sorted by residual: bond pdb=" C TYR o 110 " pdb=" O TYR o 110 " ideal model delta sigma weight residual 1.237 1.143 0.093 1.19e-02 7.06e+03 6.14e+01 bond pdb=" CA LEU n 94 " pdb=" C LEU n 94 " ideal model delta sigma weight residual 1.523 1.454 0.069 1.35e-02 5.49e+03 2.64e+01 bond pdb=" CA THR t 306 " pdb=" C THR t 306 " ideal model delta sigma weight residual 1.528 1.476 0.053 1.04e-02 9.25e+03 2.55e+01 bond pdb=" C ARG n 92 " pdb=" N ALA n 93 " ideal model delta sigma weight residual 1.334 1.274 0.059 1.23e-02 6.61e+03 2.33e+01 bond pdb=" N ALA t 58 " pdb=" CA ALA t 58 " ideal model delta sigma weight residual 1.458 1.518 -0.060 1.33e-02 5.65e+03 2.06e+01 ... (remaining 47093 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.65: 65297 6.65 - 13.29: 81 13.29 - 19.94: 1 19.94 - 26.58: 0 26.58 - 33.23: 1 Bond angle restraints: 65380 Sorted by residual: angle pdb=" N GLN 4 132 " pdb=" CA GLN 4 132 " pdb=" C GLN 4 132 " ideal model delta sigma weight residual 109.96 76.73 33.23 1.68e+00 3.54e-01 3.91e+02 angle pdb=" O3' A 11102 " pdb=" C3' A 11102 " pdb=" C2' A 11102 " ideal model delta sigma weight residual 113.70 125.88 -12.18 1.50e+00 4.44e-01 6.59e+01 angle pdb=" C4' U 11347 " pdb=" C3' U 11347 " pdb=" O3' U 11347 " ideal model delta sigma weight residual 113.00 124.90 -11.90 1.50e+00 4.44e-01 6.29e+01 angle pdb=" N LEU 4 133 " pdb=" CA LEU 4 133 " pdb=" C LEU 4 133 " ideal model delta sigma weight residual 110.80 94.06 16.74 2.13e+00 2.20e-01 6.18e+01 angle pdb=" C ASP 4 78 " pdb=" N PRO 4 79 " pdb=" CA PRO 4 79 " ideal model delta sigma weight residual 119.87 127.10 -7.23 1.04e+00 9.25e-01 4.83e+01 ... (remaining 65375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.84: 24185 34.84 - 69.68: 3536 69.68 - 104.52: 326 104.52 - 139.36: 7 139.36 - 174.20: 15 Dihedral angle restraints: 28069 sinusoidal: 22115 harmonic: 5954 Sorted by residual: dihedral pdb=" C4' U 6 33 " pdb=" C3' U 6 33 " pdb=" C2' U 6 33 " pdb=" C1' U 6 33 " ideal model delta sinusoidal sigma weight residual 36.00 -45.20 81.20 1 8.00e+00 1.56e-02 1.27e+02 dihedral pdb=" C4' A 6 55 " pdb=" C3' A 6 55 " pdb=" C2' A 6 55 " pdb=" C1' A 6 55 " ideal model delta sinusoidal sigma weight residual 36.00 -43.21 79.21 1 8.00e+00 1.56e-02 1.22e+02 dihedral pdb=" C5' A 6 55 " pdb=" C4' A 6 55 " pdb=" C3' A 6 55 " pdb=" O3' A 6 55 " ideal model delta sinusoidal sigma weight residual 82.00 160.61 -78.61 1 8.00e+00 1.56e-02 1.20e+02 ... (remaining 28066 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 4551 0.103 - 0.206: 1960 0.206 - 0.310: 573 0.310 - 0.413: 29 0.413 - 0.516: 3 Chirality restraints: 7116 Sorted by residual: chirality pdb=" C3' A 1 649 " pdb=" C4' A 1 649 " pdb=" O3' A 1 649 " pdb=" C2' A 1 649 " both_signs ideal model delta sigma weight residual False -2.48 -1.96 -0.52 2.00e-01 2.50e+01 6.66e+00 chirality pdb=" C3' A 11102 " pdb=" C4' A 11102 " pdb=" O3' A 11102 " pdb=" C2' A 11102 " both_signs ideal model delta sigma weight residual False -2.48 -2.00 -0.47 2.00e-01 2.50e+01 5.59e+00 chirality pdb=" C3' C 1 480 " pdb=" C4' C 1 480 " pdb=" O3' C 1 480 " pdb=" C2' C 1 480 " both_signs ideal model delta sigma weight residual False -2.48 -2.04 -0.44 2.00e-01 2.50e+01 4.77e+00 ... (remaining 7113 not shown) Planarity restraints: 5954 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP 4 78 " 0.013 2.00e-02 2.50e+03 2.83e-02 8.02e+00 pdb=" C ASP 4 78 " -0.049 2.00e-02 2.50e+03 pdb=" O ASP 4 78 " 0.019 2.00e-02 2.50e+03 pdb=" N PRO 4 79 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG H 287 " -0.011 2.00e-02 2.50e+03 2.35e-02 5.53e+00 pdb=" C ARG H 287 " 0.041 2.00e-02 2.50e+03 pdb=" O ARG H 287 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE H 288 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU t 59 " 0.011 2.00e-02 2.50e+03 2.29e-02 5.23e+00 pdb=" C GLU t 59 " -0.040 2.00e-02 2.50e+03 pdb=" O GLU t 59 " 0.015 2.00e-02 2.50e+03 pdb=" N SER t 60 " 0.013 2.00e-02 2.50e+03 ... (remaining 5951 not shown) Histogram of nonbonded interaction distances: 0.86 - 1.66: 8 1.66 - 2.47: 161 2.47 - 3.28: 40949 3.28 - 4.09: 81026 4.09 - 4.90: 114509 Warning: very small nonbonded interaction distances. Nonbonded interactions: 236653 Sorted by model distance: nonbonded pdb=" N PRO 4 61 " pdb=" OP2 G 1 466 " model vdw 0.855 3.120 nonbonded pdb=" C ARG 4 60 " pdb=" OP2 G 1 466 " model vdw 1.286 3.270 nonbonded pdb=" N ARG 4 60 " pdb=" OP1 G 1 466 " model vdw 1.446 3.120 nonbonded pdb=" O LEU B 99 " pdb=" O2' C 13004 " model vdw 1.510 3.040 nonbonded pdb=" O2' U 2 158 " pdb=" OP1 C 6 1 " model vdw 1.569 3.040 ... (remaining 236648 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 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: 5.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.060 Extract box with map and model: 0.870 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 42.120 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.150 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: 0.010 Load rotamer database and sin/cos tables:1.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5363 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 47098 Z= 0.617 Angle : 1.441 33.229 65380 Z= 1.007 Chirality : 0.117 0.516 7116 Planarity : 0.003 0.028 5954 Dihedral : 22.903 174.195 28069 Min Nonbonded Distance : 0.855 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 2.14 % Allowed : 7.46 % Favored : 90.40 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.71 (0.09), residues: 5895 helix: -2.66 (0.08), residues: 2114 sheet: -2.05 (0.16), residues: 768 loop : -2.38 (0.10), residues: 3013 Details of bonding type rmsd covalent geometry : bond 0.00844 (47098) covalent geometry : angle 1.44102 (65380) hydrogen bonds : bond 0.26047 ( 1738) hydrogen bonds : angle 9.50381 ( 5013) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11790 Ramachandran restraints generated. 5895 Oldfield, 0 Emsley, 5895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11790 Ramachandran restraints generated. 5895 Oldfield, 0 Emsley, 5895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 5222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.234 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1587 time to fit residues: 21.8311 Evaluate side-chains 68 residues out of total 5222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 394 optimal weight: 40.0000 chunk 430 optimal weight: 30.0000 chunk 41 optimal weight: 10.0000 chunk 265 optimal weight: 0.9990 chunk 523 optimal weight: 20.0000 chunk 497 optimal weight: 20.0000 chunk 414 optimal weight: 10.0000 chunk 310 optimal weight: 20.0000 chunk 488 optimal weight: 20.0000 chunk 366 optimal weight: 10.0000 chunk 597 optimal weight: 20.0000 overall best weight: 10.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.071826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.061210 restraints weight = 920414.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.060973 restraints weight = 1099490.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.061239 restraints weight = 937596.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.061036 restraints weight = 862229.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.061025 restraints weight = 939592.941| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3070 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 47098 Z= 0.317 Angle : 0.905 11.457 65380 Z= 0.503 Chirality : 0.041 0.479 7116 Planarity : 0.005 0.026 5954 Dihedral : 20.432 176.004 28069 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.04 % Favored : 93.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.10), residues: 5895 helix: -0.38 (0.10), residues: 2266 sheet: -1.73 (0.16), residues: 884 loop : -1.86 (0.11), residues: 2745 Details of bonding type rmsd covalent geometry : bond 0.00463 (47098) covalent geometry : angle 0.90467 (65380) hydrogen bonds : bond 0.05007 ( 1738) hydrogen bonds : angle 5.58263 ( 5013) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11790 Ramachandran restraints generated. 5895 Oldfield, 0 Emsley, 5895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11790 Ramachandran restraints generated. 5895 Oldfield, 0 Emsley, 5895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 5222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.310 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1691 time to fit residues: 23.4733 Evaluate side-chains 68 residues out of total 5222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 707 optimal weight: 50.0000 chunk 372 optimal weight: 40.0000 chunk 582 optimal weight: 40.0000 chunk 449 optimal weight: 30.0000 chunk 584 optimal weight: 40.0000 chunk 695 optimal weight: 30.0000 chunk 65 optimal weight: 30.0000 chunk 611 optimal weight: 50.0000 chunk 175 optimal weight: 50.0000 chunk 492 optimal weight: 30.0000 chunk 550 optimal weight: 50.0000 overall best weight: 32.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.079010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.066458 restraints weight = 840779.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.066084 restraints weight = 885555.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.066009 restraints weight = 952328.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.065988 restraints weight = 929046.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.065966 restraints weight = 973176.136| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3546 moved from start: 1.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.216 47098 Z= 0.742 Angle : 1.872 23.179 65380 Z= 0.996 Chirality : 0.087 0.513 7116 Planarity : 0.008 0.056 5954 Dihedral : 26.400 179.965 28069 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 26.60 Ramachandran Plot: Outliers : 0.66 % Allowed : 12.65 % Favored : 86.68 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.03 % Twisted Proline : 1.27 % Twisted General : 0.42 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.55 (0.09), residues: 5895 helix: -1.94 (0.09), residues: 2150 sheet: -2.00 (0.19), residues: 638 loop : -2.79 (0.10), residues: 3107 Details of bonding type rmsd covalent geometry : bond 0.01139 (47098) covalent geometry : angle 1.87190 (65380) hydrogen bonds : bond 0.08554 ( 1738) hydrogen bonds : angle 9.22215 ( 5013) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11790 Ramachandran restraints generated. 5895 Oldfield, 0 Emsley, 5895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11790 Ramachandran restraints generated. 5895 Oldfield, 0 Emsley, 5895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 5222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.186 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1774 time to fit residues: 24.6092 Evaluate side-chains 68 residues out of total 5222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 417 optimal weight: 0.0770 chunk 60 optimal weight: 30.0000 chunk 727 optimal weight: 50.0000 chunk 370 optimal weight: 40.0000 chunk 597 optimal weight: 20.0000 chunk 725 optimal weight: 20.0000 chunk 177 optimal weight: 50.0000 chunk 213 optimal weight: 40.0000 chunk 42 optimal weight: 7.9990 chunk 480 optimal weight: 9.9990 chunk 366 optimal weight: 10.0000 overall best weight: 9.6150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.078153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.066992 restraints weight = 814986.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.066274 restraints weight = 815367.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.066187 restraints weight = 884189.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.066154 restraints weight = 889683.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.066128 restraints weight = 922112.088| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3695 moved from start: 1.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 47098 Z= 0.240 Angle : 0.721 11.917 65380 Z= 0.400 Chirality : 0.033 0.264 7116 Planarity : 0.003 0.025 5954 Dihedral : 25.289 178.156 28069 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.01 % Favored : 90.74 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.03 % Twisted Proline : 0.42 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.08 (0.11), residues: 5895 helix: 0.09 (0.11), residues: 2208 sheet: -2.07 (0.18), residues: 715 loop : -2.42 (0.11), residues: 2972 Details of bonding type rmsd covalent geometry : bond 0.00356 (47098) covalent geometry : angle 0.72102 (65380) hydrogen bonds : bond 0.03747 ( 1738) hydrogen bonds : angle 5.89128 ( 5013) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11790 Ramachandran restraints generated. 5895 Oldfield, 0 Emsley, 5895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11790 Ramachandran restraints generated. 5895 Oldfield, 0 Emsley, 5895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 5222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.938 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1589 time to fit residues: 22.0749 Evaluate side-chains 68 residues out of total 5222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 723 optimal weight: 40.0000 chunk 404 optimal weight: 5.9990 chunk 413 optimal weight: 50.0000 chunk 253 optimal weight: 20.0000 chunk 113 optimal weight: 50.0000 chunk 445 optimal weight: 40.0000 chunk 236 optimal weight: 10.0000 chunk 338 optimal weight: 20.0000 chunk 687 optimal weight: 50.0000 chunk 435 optimal weight: 30.0000 chunk 451 optimal weight: 30.0000 overall best weight: 17.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.078283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.066050 restraints weight = 854720.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.065410 restraints weight = 920989.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.065303 restraints weight = 1014663.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.065265 restraints weight = 1013058.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.065234 restraints weight = 1031792.819| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3052 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3052 r_free = 0.3052 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3052 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3912 moved from start: 1.6300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 47098 Z= 0.419 Angle : 1.122 15.671 65380 Z= 0.620 Chirality : 0.054 0.390 7116 Planarity : 0.004 0.028 5954 Dihedral : 26.216 177.383 28069 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.27 % Allowed : 14.57 % Favored : 85.16 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.03 % Twisted Proline : 0.42 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.43 (0.10), residues: 5895 helix: -0.23 (0.11), residues: 2204 sheet: -2.05 (0.21), residues: 611 loop : -2.66 (0.11), residues: 3080 Details of bonding type rmsd covalent geometry : bond 0.00632 (47098) covalent geometry : angle 1.12172 (65380) hydrogen bonds : bond 0.05515 ( 1738) hydrogen bonds : angle 7.11417 ( 5013) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11790 Ramachandran restraints generated. 5895 Oldfield, 0 Emsley, 5895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11790 Ramachandran restraints generated. 5895 Oldfield, 0 Emsley, 5895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 5222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.224 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1593 time to fit residues: 22.3336 Evaluate side-chains 68 residues out of total 5222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 103 optimal weight: 50.0000 chunk 649 optimal weight: 50.0000 chunk 371 optimal weight: 9.9990 chunk 20 optimal weight: 50.0000 chunk 102 optimal weight: 30.0000 chunk 609 optimal weight: 40.0000 chunk 506 optimal weight: 20.0000 chunk 232 optimal weight: 30.0000 chunk 66 optimal weight: 50.0000 chunk 612 optimal weight: 50.0000 chunk 262 optimal weight: 40.0000 overall best weight: 25.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.055473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.050233 restraints weight = 921066.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.050392 restraints weight = 772782.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.050506 restraints weight = 672927.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.050626 restraints weight = 618116.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.050631 restraints weight = 574790.264| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6397 moved from start: 1.8562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.123 47098 Z= 0.541 Angle : 1.345 17.192 65380 Z= 0.728 Chirality : 0.066 0.444 7116 Planarity : 0.006 0.033 5954 Dihedral : 26.853 178.926 28069 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 20.93 Ramachandran Plot: Outliers : 0.24 % Allowed : 15.25 % Favored : 84.51 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.03 % Twisted Proline : 0.42 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.54 (0.10), residues: 5895 helix: -1.26 (0.10), residues: 2170 sheet: -2.43 (0.21), residues: 588 loop : -3.26 (0.10), residues: 3137 Details of bonding type rmsd covalent geometry : bond 0.00820 (47098) covalent geometry : angle 1.34538 (65380) hydrogen bonds : bond 0.05923 ( 1738) hydrogen bonds : angle 8.07622 ( 5013) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11790 Ramachandran restraints generated. 5895 Oldfield, 0 Emsley, 5895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11790 Ramachandran restraints generated. 5895 Oldfield, 0 Emsley, 5895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 5222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.338 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1751 time to fit residues: 24.3963 Evaluate side-chains 68 residues out of total 5222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 483 optimal weight: 9.9990 chunk 601 optimal weight: 30.0000 chunk 672 optimal weight: 50.0000 chunk 152 optimal weight: 50.0000 chunk 325 optimal weight: 30.0000 chunk 501 optimal weight: 20.0000 chunk 264 optimal weight: 7.9990 chunk 34 optimal weight: 20.0000 chunk 45 optimal weight: 40.0000 chunk 635 optimal weight: 40.0000 chunk 238 optimal weight: 6.9990 overall best weight: 12.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.071837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.051090 restraints weight = 409210.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.051460 restraints weight = 300966.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.051693 restraints weight = 253500.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.051747 restraints weight = 199918.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.051840 restraints weight = 200598.285| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 1.8411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 47098 Z= 0.277 Angle : 0.767 12.965 65380 Z= 0.428 Chirality : 0.037 0.297 7116 Planarity : 0.003 0.025 5954 Dihedral : 26.052 177.548 28069 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.72 % Favored : 86.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.03 % Twisted Proline : 0.42 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.52 (0.11), residues: 5895 helix: 0.02 (0.11), residues: 2203 sheet: -2.46 (0.20), residues: 611 loop : -2.91 (0.11), residues: 3081 Details of bonding type rmsd covalent geometry : bond 0.00415 (47098) covalent geometry : angle 0.76701 (65380) hydrogen bonds : bond 0.03858 ( 1738) hydrogen bonds : angle 6.30678 ( 5013) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11790 Ramachandran restraints generated. 5895 Oldfield, 0 Emsley, 5895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11790 Ramachandran restraints generated. 5895 Oldfield, 0 Emsley, 5895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 5222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.259 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1642 time to fit residues: 23.1907 Evaluate side-chains 68 residues out of total 5222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 170 optimal weight: 50.0000 chunk 252 optimal weight: 30.0000 chunk 436 optimal weight: 50.0000 chunk 294 optimal weight: 20.0000 chunk 268 optimal weight: 40.0000 chunk 311 optimal weight: 20.0000 chunk 533 optimal weight: 50.0000 chunk 673 optimal weight: 90.0000 chunk 666 optimal weight: 50.0000 chunk 360 optimal weight: 40.0000 chunk 306 optimal weight: 50.0000 overall best weight: 30.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.053617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.045234 restraints weight = 728669.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.045442 restraints weight = 596732.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.045613 restraints weight = 503820.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.045658 restraints weight = 429558.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.045665 restraints weight = 410251.283| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 2.0015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.161 47098 Z= 0.626 Angle : 1.520 17.891 65380 Z= 0.822 Chirality : 0.073 0.414 7116 Planarity : 0.006 0.034 5954 Dihedral : 27.344 179.828 28069 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 27.18 Ramachandran Plot: Outliers : 0.32 % Allowed : 20.36 % Favored : 79.32 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.03 % Twisted Proline : 0.42 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.92 (0.10), residues: 5895 helix: -1.56 (0.10), residues: 2163 sheet: -2.63 (0.22), residues: 484 loop : -3.48 (0.10), residues: 3248 Details of bonding type rmsd covalent geometry : bond 0.00949 (47098) covalent geometry : angle 1.51984 (65380) hydrogen bonds : bond 0.06772 ( 1738) hydrogen bonds : angle 8.79532 ( 5013) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11790 Ramachandran restraints generated. 5895 Oldfield, 0 Emsley, 5895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11790 Ramachandran restraints generated. 5895 Oldfield, 0 Emsley, 5895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 5222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.223 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1712 time to fit residues: 23.5209 Evaluate side-chains 68 residues out of total 5222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 305 optimal weight: 40.0000 chunk 359 optimal weight: 30.0000 chunk 626 optimal weight: 30.0000 chunk 95 optimal weight: 30.0000 chunk 629 optimal weight: 20.0000 chunk 604 optimal weight: 30.0000 chunk 36 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 256 optimal weight: 9.9990 chunk 154 optimal weight: 0.8980 chunk 432 optimal weight: 9.9990 overall best weight: 10.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.055032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.049848 restraints weight = 897282.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.050032 restraints weight = 765674.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.050158 restraints weight = 668625.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.050258 restraints weight = 601111.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.050326 restraints weight = 558464.266| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3142 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3142 r_free = 0.3142 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3142 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 moved from start: 1.9553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 47098 Z= 0.247 Angle : 0.724 12.438 65380 Z= 0.408 Chirality : 0.035 0.302 7116 Planarity : 0.003 0.023 5954 Dihedral : 26.259 177.422 28069 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.45 % Favored : 86.41 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.03 % Twisted Proline : 0.42 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.78 (0.11), residues: 5895 helix: -0.06 (0.11), residues: 2209 sheet: -2.58 (0.20), residues: 605 loop : -3.19 (0.11), residues: 3081 Details of bonding type rmsd covalent geometry : bond 0.00372 (47098) covalent geometry : angle 0.72366 (65380) hydrogen bonds : bond 0.03729 ( 1738) hydrogen bonds : angle 6.36351 ( 5013) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11790 Ramachandran restraints generated. 5895 Oldfield, 0 Emsley, 5895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11790 Ramachandran restraints generated. 5895 Oldfield, 0 Emsley, 5895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 5222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.261 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1445 time to fit residues: 19.9341 Evaluate side-chains 68 residues out of total 5222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 179 optimal weight: 30.0000 chunk 548 optimal weight: 30.0000 chunk 40 optimal weight: 30.0000 chunk 495 optimal weight: 20.0000 chunk 622 optimal weight: 30.0000 chunk 324 optimal weight: 30.0000 chunk 204 optimal weight: 50.0000 chunk 111 optimal weight: 40.0000 chunk 5 optimal weight: 30.0000 chunk 344 optimal weight: 40.0000 chunk 288 optimal weight: 40.0000 overall best weight: 28.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.053095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.044675 restraints weight = 722821.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.044917 restraints weight = 587878.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.045033 restraints weight = 508583.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.045175 restraints weight = 470167.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.045233 restraints weight = 440659.595| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 2.0480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.147 47098 Z= 0.563 Angle : 1.339 15.732 65380 Z= 0.727 Chirality : 0.063 0.416 7116 Planarity : 0.006 0.032 5954 Dihedral : 27.076 178.105 28069 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 22.76 Ramachandran Plot: Outliers : 0.25 % Allowed : 21.54 % Favored : 78.20 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.03 % Twisted Proline : 0.42 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.86 (0.10), residues: 5895 helix: -1.31 (0.10), residues: 2185 sheet: -2.67 (0.21), residues: 547 loop : -3.62 (0.10), residues: 3163 Details of bonding type rmsd covalent geometry : bond 0.00859 (47098) covalent geometry : angle 1.33923 (65380) hydrogen bonds : bond 0.06181 ( 1738) hydrogen bonds : angle 8.24307 ( 5013) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11790 Ramachandran restraints generated. 5895 Oldfield, 0 Emsley, 5895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11790 Ramachandran restraints generated. 5895 Oldfield, 0 Emsley, 5895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 5222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.342 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1754 time to fit residues: 24.6260 Evaluate side-chains 68 residues out of total 5222 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 762 random chunks: chunk 722 optimal weight: 7.9990 chunk 306 optimal weight: 20.0000 chunk 366 optimal weight: 50.0000 chunk 428 optimal weight: 0.9990 chunk 25 optimal weight: 20.0000 chunk 451 optimal weight: 30.0000 chunk 119 optimal weight: 50.0000 chunk 588 optimal weight: 50.0000 chunk 509 optimal weight: 10.0000 chunk 320 optimal weight: 30.0000 chunk 12 optimal weight: 20.0000 overall best weight: 11.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.054420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.049311 restraints weight = 927417.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.049496 restraints weight = 772164.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.049646 restraints weight = 669757.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.049751 restraints weight = 605741.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.049845 restraints weight = 565063.121| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 2.0173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 47098 Z= 0.262 Angle : 0.754 12.791 65380 Z= 0.421 Chirality : 0.036 0.301 7116 Planarity : 0.003 0.023 5954 Dihedral : 26.248 179.870 28069 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 14.39 % Favored : 85.48 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.80 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.91 (0.11), residues: 5895 helix: -0.12 (0.11), residues: 2220 sheet: -2.61 (0.20), residues: 607 loop : -3.33 (0.10), residues: 3068 Details of bonding type rmsd covalent geometry : bond 0.00395 (47098) covalent geometry : angle 0.75376 (65380) hydrogen bonds : bond 0.03789 ( 1738) hydrogen bonds : angle 6.32093 ( 5013) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9813.12 seconds wall clock time: 168 minutes 48.62 seconds (10128.62 seconds total)