Starting phenix.real_space_refine on Tue Sep 15 21:04:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6em4_3889/09_2026/6em4_3889.cif Found real_map, /net/cci-nas-00/data/ceres_data/6em4_3889/09_2026/6em4_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6em4_3889/09_2026/6em4_3889.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6em4_3889/09_2026/6em4_3889.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6em4_3889/09_2026/6em4_3889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6em4_3889/09_2026/6em4_3889.map" model { file = "/net/cci-nas-00/data/ceres_data/6em4_3889/09_2026/6em4_3889.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6em4_3889/09_2026/6em4_3889.cif" } 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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: 11961 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: {'RNAv2': 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: 1182 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: {'RNAv2': 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: 477 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: 9.66, per 1000 atoms: 0.21 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: 3.53 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 4.35 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: 10.13 Time building geometry restraints manager: 4.84 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: 65290 6.65 - 13.29: 88 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=" 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 angle pdb=" N ILE 3 120 " pdb=" CA ILE 3 120 " pdb=" C ILE 3 120 " ideal model delta sigma weight residual 112.83 106.06 6.77 9.90e-01 1.02e+00 4.67e+01 angle pdb=" N PRO A 104 " pdb=" CA PRO A 104 " pdb=" C PRO A 104 " ideal model delta sigma weight residual 110.70 118.42 -7.72 1.22e+00 6.72e-01 4.00e+01 ... (remaining 65375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.84: 22905 34.84 - 69.68: 2334 69.68 - 104.52: 199 104.52 - 139.36: 4 139.36 - 174.20: 15 Dihedral angle restraints: 25457 sinusoidal: 19503 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 36.35 -45.20 81.55 1 3.10e+00 1.04e-01 8.52e+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 36.34 -43.21 79.56 1 3.10e+00 1.04e-01 8.18e+02 dihedral pdb=" C4' C 6 7 " pdb=" C3' C 6 7 " pdb=" C2' C 6 7 " pdb=" C1' C 6 7 " ideal model delta sinusoidal sigma weight residual 36.35 -42.41 78.76 1 3.10e+00 1.04e-01 8.04e+02 ... (remaining 25454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 2986 0.107 - 0.215: 1718 0.215 - 0.322: 2381 0.322 - 0.430: 27 0.430 - 0.537: 4 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 -2.50 -1.96 -0.54 2.00e-01 2.50e+01 7.21e+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 -2.50 -2.00 -0.49 2.00e-01 2.50e+01 6.10e+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 -2.50 -2.04 -0.46 2.00e-01 2.50e+01 5.25e+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: 6.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.790 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 41.770 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.090 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5668 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= 0.562 Angle : 1.595 33.229 65380 Z= 0.891 Chirality : 0.168 0.537 7116 Planarity : 0.003 0.028 5954 Dihedral : 19.887 174.195 25457 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 are 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/Z covalent geometry : bond 0.00805 / 0.56 (47098) covalent geometry : angle 1.59464 / 0.89 (65380) hydrogen bonds : bond 0.26047 / 20.42 ( 1738) hydrogen bonds : angle 9.50381 / 7.41 ( 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 : 1.112 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1638 time to fit residues: 23.0485 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 : 1.246 ------------------------------------------------------------------------------- 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: 20.0000 chunk 265 optimal weight: 2.9990 chunk 523 optimal weight: 10.0000 chunk 497 optimal weight: 10.0000 chunk 414 optimal weight: 10.0000 chunk 310 optimal weight: 20.0000 chunk 488 optimal weight: 10.0000 chunk 366 optimal weight: 10.0000 chunk 597 optimal weight: 20.0000 overall best weight: 8.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.073454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.063128 restraints weight = 907732.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.062695 restraints weight = 1065809.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.062865 restraints weight = 974029.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.062819 restraints weight = 825258.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.062855 restraints weight = 792623.307| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3199 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 47098 Z= 0.317 Angle : 1.285 13.035 65380 Z= 0.527 Chirality : 0.074 0.572 7116 Planarity : 0.004 0.027 5954 Dihedral : 13.899 177.277 25457 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.67 % Favored : 94.03 % 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 : 0.02 % 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 are not related in a simple way. whole: -1.80 (0.10), residues: 5895 helix: -0.15 (0.11), residues: 2244 sheet: -1.77 (0.15), residues: 936 loop : -1.83 (0.11), residues: 2715 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.32 (47098) covalent geometry : angle 1.28482 / 0.53 (65380) hydrogen bonds : bond 0.04337 / 3.40 ( 1738) hydrogen bonds : angle 5.21026 / 4.07 ( 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 : 1.282 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1675 time to fit residues: 23.4109 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 : 1.263 ------------------------------------------------------------------------------- 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: 8.9990 chunk 449 optimal weight: 0.0060 chunk 584 optimal weight: 20.0000 chunk 695 optimal weight: 30.0000 chunk 65 optimal weight: 30.0000 chunk 611 optimal weight: 40.0000 chunk 175 optimal weight: 6.9990 chunk 492 optimal weight: 9.9990 chunk 550 optimal weight: 20.0000 overall best weight: 9.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.067632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.057806 restraints weight = 947456.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.057361 restraints weight = 792846.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.057278 restraints weight = 906955.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.057336 restraints weight = 807391.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.057336 restraints weight = 789279.177| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3354 moved from start: 0.8701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 47098 Z= 0.350 Angle : 1.370 14.733 65380 Z= 0.560 Chirality : 0.069 0.443 7116 Planarity : 0.003 0.056 5954 Dihedral : 14.633 179.491 25457 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.31 % Favored : 92.50 % 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 are not related in a simple way. whole: -1.11 (0.11), residues: 5895 helix: 0.72 (0.11), residues: 2294 sheet: -1.44 (0.17), residues: 849 loop : -1.77 (0.11), residues: 2752 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.35 (47098) covalent geometry : angle 1.36962 / 0.56 (65380) hydrogen bonds : bond 0.03897 / 3.06 ( 1738) hydrogen bonds : angle 5.14604 / 4.05 ( 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 : 1.340 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1728 time to fit residues: 24.1577 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 : 1.192 ------------------------------------------------------------------------------- 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: 0.4980 chunk 60 optimal weight: 40.0000 chunk 727 optimal weight: 50.0000 chunk 370 optimal weight: 50.0000 chunk 597 optimal weight: 9.9990 chunk 725 optimal weight: 50.0000 chunk 177 optimal weight: 50.0000 chunk 213 optimal weight: 50.0000 chunk 42 optimal weight: 10.0000 chunk 480 optimal weight: 10.0000 chunk 366 optimal weight: 40.0000 overall best weight: 14.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.063663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.053785 restraints weight = 962258.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.053701 restraints weight = 826740.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.053665 restraints weight = 744411.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.053676 restraints weight = 734311.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.053770 restraints weight = 724628.286| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3689 moved from start: 1.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 47098 Z= 0.411 Angle : 1.508 12.379 65380 Z= 0.618 Chirality : 0.074 0.466 7116 Planarity : 0.004 0.028 5954 Dihedral : 16.972 179.374 25457 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.60 % Favored : 91.11 % 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 : 0.03 % 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 are not related in a simple way. whole: -1.39 (0.11), residues: 5895 helix: 0.61 (0.11), residues: 2231 sheet: -1.77 (0.17), residues: 805 loop : -1.93 (0.11), residues: 2859 Details of bonding type rmsd/Z covalent geometry : bond 0.00738 / 0.41 (47098) covalent geometry : angle 1.50807 / 0.62 (65380) hydrogen bonds : bond 0.04439 / 3.50 ( 1738) hydrogen bonds : angle 6.00792 / 4.72 ( 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 : 1.303 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1697 time to fit residues: 24.0226 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 : 1.220 ------------------------------------------------------------------------------- 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: 10.0000 chunk 113 optimal weight: 40.0000 chunk 445 optimal weight: 40.0000 chunk 236 optimal weight: 7.9990 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: 14.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.077933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.066193 restraints weight = 832610.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.065733 restraints weight = 849295.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.065612 restraints weight = 931251.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.065605 restraints weight = 918133.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.065593 restraints weight = 906847.680| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3726 moved from start: 1.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 47098 Z= 0.401 Angle : 1.495 15.362 65380 Z= 0.608 Chirality : 0.078 0.444 7116 Planarity : 0.004 0.026 5954 Dihedral : 17.773 178.277 25457 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.03 % Favored : 89.72 % 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 : 0.03 % 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 are not related in a simple way. whole: -1.38 (0.11), residues: 5895 helix: 0.75 (0.11), residues: 2234 sheet: -1.71 (0.19), residues: 716 loop : -2.09 (0.11), residues: 2945 Details of bonding type rmsd/Z covalent geometry : bond 0.00730 / 0.40 (47098) covalent geometry : angle 1.49463 / 0.61 (65380) hydrogen bonds : bond 0.04188 / 3.30 ( 1738) hydrogen bonds : angle 5.84096 / 4.60 ( 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 : 1.176 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1732 time to fit residues: 23.6732 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 : 1.197 ------------------------------------------------------------------------------- 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: 10.0000 chunk 20 optimal weight: 40.0000 chunk 102 optimal weight: 50.0000 chunk 609 optimal weight: 20.0000 chunk 506 optimal weight: 10.0000 chunk 232 optimal weight: 30.0000 chunk 66 optimal weight: 50.0000 chunk 612 optimal weight: 50.0000 chunk 262 optimal weight: 0.5980 overall best weight: 14.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.079101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.067232 restraints weight = 818509.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.066777 restraints weight = 836737.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.066661 restraints weight = 884470.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.066647 restraints weight = 904362.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.066632 restraints weight = 896710.224| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3915 moved from start: 1.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 47098 Z= 0.372 Angle : 1.435 14.167 65380 Z= 0.584 Chirality : 0.078 0.431 7116 Planarity : 0.003 0.027 5954 Dihedral : 18.128 179.581 25457 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.09 % Favored : 88.62 % 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 : 0.03 % 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 are not related in a simple way. whole: -1.43 (0.11), residues: 5895 helix: 0.83 (0.11), residues: 2244 sheet: -2.03 (0.19), residues: 698 loop : -2.16 (0.11), residues: 2953 Details of bonding type rmsd/Z covalent geometry : bond 0.00674 / 0.37 (47098) covalent geometry : angle 1.43526 / 0.58 (65380) hydrogen bonds : bond 0.04186 / 3.29 ( 1738) hydrogen bonds : angle 6.00007 / 4.72 ( 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 : 1.048 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1580 time to fit residues: 22.0264 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 : 1.125 ------------------------------------------------------------------------------- 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: 20.0000 chunk 672 optimal weight: 50.0000 chunk 152 optimal weight: 40.0000 chunk 325 optimal weight: 50.0000 chunk 501 optimal weight: 9.9990 chunk 264 optimal weight: 2.9990 chunk 34 optimal weight: 40.0000 chunk 45 optimal weight: 9.9990 chunk 635 optimal weight: 50.0000 chunk 238 optimal weight: 20.0000 overall best weight: 10.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.078817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.066912 restraints weight = 833220.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.066348 restraints weight = 916300.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.066201 restraints weight = 1018242.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.066177 restraints weight = 1033126.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.066164 restraints weight = 1008950.240| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3888 moved from start: 1.6020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 47098 Z= 0.289 Angle : 1.180 12.497 65380 Z= 0.479 Chirality : 0.069 0.385 7116 Planarity : 0.003 0.023 5954 Dihedral : 17.770 179.049 25457 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.89 % Favored : 88.92 % 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 : 0.00 % 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 are not related in a simple way. whole: -1.13 (0.11), residues: 5895 helix: 1.26 (0.11), residues: 2251 sheet: -1.97 (0.19), residues: 721 loop : -2.14 (0.12), residues: 2923 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.29 (47098) covalent geometry : angle 1.18029 / 0.48 (65380) hydrogen bonds : bond 0.03455 / 2.71 ( 1738) hydrogen bonds : angle 5.38156 / 4.24 ( 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 : 1.020 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1704 time to fit residues: 24.2440 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 : 1.218 ------------------------------------------------------------------------------- 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: 40.0000 chunk 436 optimal weight: 40.0000 chunk 294 optimal weight: 20.0000 chunk 268 optimal weight: 2.9990 chunk 311 optimal weight: 20.0000 chunk 533 optimal weight: 30.0000 chunk 673 optimal weight: 40.0000 chunk 666 optimal weight: 50.0000 chunk 360 optimal weight: 40.0000 chunk 306 optimal weight: 50.0000 overall best weight: 22.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.056029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.050738 restraints weight = 926667.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.050899 restraints weight = 791513.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.051018 restraints weight = 696411.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.051129 restraints weight = 637720.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.051205 restraints weight = 596378.767| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6326 moved from start: 1.8119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.127 47098 Z= 0.542 Angle : 1.967 19.240 65380 Z= 0.802 Chirality : 0.100 0.513 7116 Planarity : 0.005 0.032 5954 Dihedral : 18.865 179.385 25457 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.27 % Allowed : 16.03 % Favored : 83.70 % 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 : 0.03 % 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 are not related in a simple way. whole: -2.62 (0.10), residues: 5895 helix: -0.27 (0.11), residues: 2179 sheet: -2.28 (0.20), residues: 598 loop : -2.82 (0.10), residues: 3118 Details of bonding type rmsd/Z covalent geometry : bond 0.00990 / 0.54 (47098) covalent geometry : angle 1.96747 / 0.80 (65380) hydrogen bonds : bond 0.05931 / 4.68 ( 1738) hydrogen bonds : angle 7.76549 / 6.11 ( 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 : 1.367 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1731 time to fit residues: 24.4055 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 : 1.247 ------------------------------------------------------------------------------- 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: 9.9990 chunk 95 optimal weight: 0.9980 chunk 629 optimal weight: 10.0000 chunk 604 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 10 optimal weight: 0.0470 chunk 256 optimal weight: 0.0980 chunk 154 optimal weight: 40.0000 chunk 432 optimal weight: 9.9990 overall best weight: 3.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.074409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.053892 restraints weight = 407365.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.054379 restraints weight = 295129.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.054379 restraints weight = 238279.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.054379 restraints weight = 238279.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.054379 restraints weight = 238279.811| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 1.7396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 47098 Z= 0.169 Angle : 1.000 13.271 65380 Z= 0.395 Chirality : 0.066 0.427 7116 Planarity : 0.002 0.017 5954 Dihedral : 17.797 177.717 25457 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.28 % Favored : 91.60 % 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 : 0.00 % 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 are not related in a simple way. whole: -1.12 (0.11), residues: 5895 helix: 1.53 (0.11), residues: 2241 sheet: -2.12 (0.19), residues: 704 loop : -2.32 (0.11), residues: 2950 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.17 (47098) covalent geometry : angle 1.00010 / 0.40 (65380) hydrogen bonds : bond 0.02827 / 2.21 ( 1738) hydrogen bonds : angle 5.03904 / 3.99 ( 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 : 1.183 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1748 time to fit residues: 24.3129 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 : 1.303 ------------------------------------------------------------------------------- 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: 50.0000 chunk 548 optimal weight: 10.0000 chunk 40 optimal weight: 30.0000 chunk 495 optimal weight: 10.0000 chunk 622 optimal weight: 9.9990 chunk 324 optimal weight: 30.0000 chunk 204 optimal weight: 50.0000 chunk 111 optimal weight: 8.9990 chunk 5 optimal weight: 40.0000 chunk 344 optimal weight: 30.0000 chunk 288 optimal weight: 40.0000 overall best weight: 13.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.072596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.051665 restraints weight = 415957.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.052095 restraints weight = 322064.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.052394 restraints weight = 248037.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.052534 restraints weight = 204298.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.052622 restraints weight = 195508.717| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 1.7996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 47098 Z= 0.343 Angle : 1.329 13.875 65380 Z= 0.536 Chirality : 0.076 0.398 7116 Planarity : 0.003 0.026 5954 Dihedral : 17.959 177.919 25457 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 14.79 % Favored : 85.09 % 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 : 0.00 % 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 are not related in a simple way. whole: -1.45 (0.11), residues: 5895 helix: 1.22 (0.11), residues: 2233 sheet: -2.12 (0.20), residues: 642 loop : -2.52 (0.11), residues: 3020 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.34 (47098) covalent geometry : angle 1.32903 / 0.54 (65380) hydrogen bonds : bond 0.03897 / 3.07 ( 1738) hydrogen bonds : angle 5.87032 / 4.62 ( 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 : 1.330 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1568 time to fit residues: 21.8724 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 : 0.969 ------------------------------------------------------------------------------- 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: 40.0000 chunk 306 optimal weight: 50.0000 chunk 366 optimal weight: 50.0000 chunk 428 optimal weight: 40.0000 chunk 25 optimal weight: 0.9980 chunk 451 optimal weight: 30.0000 chunk 119 optimal weight: 30.0000 chunk 588 optimal weight: 40.0000 chunk 509 optimal weight: 9.9990 chunk 320 optimal weight: 40.0000 chunk 12 optimal weight: 40.0000 overall best weight: 22.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.054394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.045829 restraints weight = 715464.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.046065 restraints weight = 594620.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.046200 restraints weight = 525069.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.046312 restraints weight = 486369.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.046391 restraints weight = 455091.698| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 1.9698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.136 47098 Z= 0.564 Angle : 2.007 17.178 65380 Z= 0.815 Chirality : 0.104 0.640 7116 Planarity : 0.005 0.032 5954 Dihedral : 19.041 179.751 25457 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 17.42 % Favored : 82.43 % 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 are not related in a simple way. whole: -2.99 (0.10), residues: 5895 helix: -0.45 (0.10), residues: 2170 sheet: -2.32 (0.22), residues: 543 loop : -3.18 (0.10), residues: 3182 Details of bonding type rmsd/Z covalent geometry : bond 0.01034 / 0.56 (47098) covalent geometry : angle 2.00737 / 0.82 (65380) hydrogen bonds : bond 0.05866 / 4.61 ( 1738) hydrogen bonds : angle 7.83279 / 6.14 ( 5013) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9113.73 seconds wall clock time: 156 minutes 26.62 seconds (9386.62 seconds total)