Starting phenix.real_space_refine on Sat Feb 17 08:44:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w1y_32258/02_2024/7w1y_32258_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w1y_32258/02_2024/7w1y_32258.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w1y_32258/02_2024/7w1y_32258.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w1y_32258/02_2024/7w1y_32258.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w1y_32258/02_2024/7w1y_32258_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w1y_32258/02_2024/7w1y_32258_updated.pdb" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.115 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: 7 Type Number sf(0) Gaussians Zn 10 6.06 5 P 228 5.49 5 Mg 12 5.21 5 S 361 5.16 5 C 42402 2.51 5 N 12171 2.21 5 O 13471 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 ARG 183": "NH1" <-> "NH2" Residue "2 GLU 184": "OE1" <-> "OE2" Residue "2 ARG 198": "NH1" <-> "NH2" Residue "2 ARG 218": "NH1" <-> "NH2" Residue "2 ARG 240": "NH1" <-> "NH2" Residue "2 ARG 276": "NH1" <-> "NH2" Residue "2 GLU 293": "OE1" <-> "OE2" Residue "2 ARG 307": "NH1" <-> "NH2" Residue "2 GLU 346": "OE1" <-> "OE2" Residue "2 GLU 362": "OE1" <-> "OE2" Residue "2 GLU 411": "OE1" <-> "OE2" Residue "2 GLU 489": "OE1" <-> "OE2" Residue "2 ARG 514": "NH1" <-> "NH2" Residue "2 ARG 567": "NH1" <-> "NH2" Residue "2 GLU 602": "OE1" <-> "OE2" Residue "2 ARG 636": "NH1" <-> "NH2" Residue "2 PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 768": "OE1" <-> "OE2" Residue "2 ARG 820": "NH1" <-> "NH2" Residue "2 ARG 825": "NH1" <-> "NH2" Residue "2 ARG 826": "NH1" <-> "NH2" Residue "2 GLU 884": "OE1" <-> "OE2" Residue "3 ARG 13": "NH1" <-> "NH2" Residue "3 ARG 17": "NH1" <-> "NH2" Residue "3 ARG 56": "NH1" <-> "NH2" Residue "3 GLU 97": "OE1" <-> "OE2" Residue "3 ARG 114": "NH1" <-> "NH2" Residue "3 GLU 156": "OE1" <-> "OE2" Residue "3 ARG 157": "NH1" <-> "NH2" Residue "3 ARG 158": "NH1" <-> "NH2" Residue "3 GLU 179": "OE1" <-> "OE2" Residue "3 GLU 185": "OE1" <-> "OE2" Residue "3 ARG 234": "NH1" <-> "NH2" Residue "3 ARG 336": "NH1" <-> "NH2" Residue "3 ARG 391": "NH1" <-> "NH2" Residue "3 GLU 424": "OE1" <-> "OE2" Residue "3 ARG 430": "NH1" <-> "NH2" Residue "3 ARG 458": "NH1" <-> "NH2" Residue "3 GLU 496": "OE1" <-> "OE2" Residue "3 ARG 503": "NH1" <-> "NH2" Residue "3 ARG 508": "NH1" <-> "NH2" Residue "3 GLU 560": "OE1" <-> "OE2" Residue "3 ARG 598": "NH1" <-> "NH2" Residue "3 ARG 623": "NH1" <-> "NH2" Residue "4 ARG 343": "NH1" <-> "NH2" Residue "4 ARG 501": "NH1" <-> "NH2" Residue "4 ARG 554": "NH1" <-> "NH2" Residue "4 GLU 632": "OE1" <-> "OE2" Residue "4 ARG 701": "NH1" <-> "NH2" Residue "4 ARG 724": "NH1" <-> "NH2" Residue "4 ARG 739": "NH1" <-> "NH2" Residue "4 ARG 763": "NH1" <-> "NH2" Residue "4 GLU 767": "OE1" <-> "OE2" Residue "5 GLU 37": "OE1" <-> "OE2" Residue "5 ARG 40": "NH1" <-> "NH2" Residue "5 ARG 162": "NH1" <-> "NH2" Residue "5 ARG 167": "NH1" <-> "NH2" Residue "5 ARG 185": "NH1" <-> "NH2" Residue "5 ARG 195": "NH1" <-> "NH2" Residue "5 ARG 204": "NH1" <-> "NH2" Residue "5 TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 284": "NH1" <-> "NH2" Residue "5 ARG 290": "NH1" <-> "NH2" Residue "5 GLU 319": "OE1" <-> "OE2" Residue "5 GLU 320": "OE1" <-> "OE2" Residue "5 GLU 333": "OE1" <-> "OE2" Residue "5 ARG 362": "NH1" <-> "NH2" Residue "5 ARG 455": "NH1" <-> "NH2" Residue "5 ARG 494": "NH1" <-> "NH2" Residue "5 ARG 513": "NH1" <-> "NH2" Residue "5 ARG 585": "NH1" <-> "NH2" Residue "5 ARG 598": "NH1" <-> "NH2" Residue "5 ARG 674": "NH1" <-> "NH2" Residue "5 ARG 717": "NH1" <-> "NH2" Residue "5 ARG 718": "NH1" <-> "NH2" Residue "6 ARG 19": "NH1" <-> "NH2" Residue "6 ARG 92": "NH1" <-> "NH2" Residue "6 ARG 101": "NH1" <-> "NH2" Residue "6 ARG 124": "NH1" <-> "NH2" Residue "6 GLU 125": "OE1" <-> "OE2" Residue "6 ARG 143": "NH1" <-> "NH2" Residue "6 ARG 166": "NH1" <-> "NH2" Residue "6 ARG 207": "NH1" <-> "NH2" Residue "6 ARG 229": "NH1" <-> "NH2" Residue "6 GLU 277": "OE1" <-> "OE2" Residue "6 GLU 279": "OE1" <-> "OE2" Residue "6 ARG 282": "NH1" <-> "NH2" Residue "6 GLU 382": "OE1" <-> "OE2" Residue "6 GLU 411": "OE1" <-> "OE2" Residue "6 ARG 435": "NH1" <-> "NH2" Residue "6 GLU 437": "OE1" <-> "OE2" Residue "6 GLU 438": "OE1" <-> "OE2" Residue "6 ARG 468": "NH1" <-> "NH2" Residue "6 ARG 512": "NH1" <-> "NH2" Residue "6 ARG 529": "NH1" <-> "NH2" Residue "6 ARG 550": "NH1" <-> "NH2" Residue "6 ARG 604": "NH1" <-> "NH2" Residue "6 GLU 622": "OE1" <-> "OE2" Residue "6 GLU 757": "OE1" <-> "OE2" Residue "6 GLU 765": "OE1" <-> "OE2" Residue "7 GLU 11": "OE1" <-> "OE2" Residue "7 ARG 43": "NH1" <-> "NH2" Residue "7 GLU 68": "OE1" <-> "OE2" Residue "7 ARG 72": "NH1" <-> "NH2" Residue "7 ARG 106": "NH1" <-> "NH2" Residue "7 ARG 112": "NH1" <-> "NH2" Residue "7 ARG 164": "NH1" <-> "NH2" Residue "7 ARG 169": "NH1" <-> "NH2" Residue "7 ARG 215": "NH1" <-> "NH2" Residue "7 GLU 234": "OE1" <-> "OE2" Residue "7 GLU 295": "OE1" <-> "OE2" Residue "7 GLU 299": "OE1" <-> "OE2" Residue "7 ARG 372": "NH1" <-> "NH2" Residue "7 ARG 396": "NH1" <-> "NH2" Residue "7 ARG 407": "NH1" <-> "NH2" Residue "7 GLU 446": "OE1" <-> "OE2" Residue "7 GLU 452": "OE1" <-> "OE2" Residue "7 ARG 481": "NH1" <-> "NH2" Residue "7 ARG 498": "NH1" <-> "NH2" Residue "7 ARG 499": "NH1" <-> "NH2" Residue "7 ARG 611": "NH1" <-> "NH2" Residue "7 GLU 626": "OE1" <-> "OE2" Residue "7 GLU 628": "OE1" <-> "OE2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A ARG 218": "NH1" <-> "NH2" Residue "A GLU 235": "OE1" <-> "OE2" Residue "A ARG 240": "NH1" <-> "NH2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "A GLU 265": "OE1" <-> "OE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A GLU 366": "OE1" <-> "OE2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A ARG 514": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 636": "NH1" <-> "NH2" Residue "A ARG 765": "NH1" <-> "NH2" Residue "A GLU 800": "OE1" <-> "OE2" Residue "A ARG 820": "NH1" <-> "NH2" Residue "A ARG 825": "NH1" <-> "NH2" Residue "A ARG 826": "NH1" <-> "NH2" Residue "B GLU 11": "OE1" <-> "OE2" Residue "B ARG 13": "NH1" <-> "NH2" Residue "B GLU 14": "OE1" <-> "OE2" Residue "B ARG 17": "NH1" <-> "NH2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B ARG 114": "NH1" <-> "NH2" Residue "B ARG 157": "NH1" <-> "NH2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 234": "NH1" <-> "NH2" Residue "B ARG 291": "NH1" <-> "NH2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 391": "NH1" <-> "NH2" Residue "B ARG 392": "NH1" <-> "NH2" Residue "B ARG 430": "NH1" <-> "NH2" Residue "B ARG 458": "NH1" <-> "NH2" Residue "B GLU 467": "OE1" <-> "OE2" Residue "B ARG 503": "NH1" <-> "NH2" Residue "B ARG 508": "NH1" <-> "NH2" Residue "B ARG 598": "NH1" <-> "NH2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B ARG 623": "NH1" <-> "NH2" Residue "C ARG 248": "NH1" <-> "NH2" Residue "C GLU 316": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ARG 343": "NH1" <-> "NH2" Residue "C ARG 395": "NH1" <-> "NH2" Residue "C GLU 460": "OE1" <-> "OE2" Residue "C ARG 501": "NH1" <-> "NH2" Residue "C ARG 554": "NH1" <-> "NH2" Residue "C ARG 701": "NH1" <-> "NH2" Residue "C GLU 704": "OE1" <-> "OE2" Residue "C ARG 724": "NH1" <-> "NH2" Residue "C ARG 739": "NH1" <-> "NH2" Residue "C ARG 763": "NH1" <-> "NH2" Residue "C ARG 777": "NH1" <-> "NH2" Residue "D GLU 37": "OE1" <-> "OE2" Residue "D ARG 40": "NH1" <-> "NH2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D GLU 101": "OE1" <-> "OE2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D ARG 167": "NH1" <-> "NH2" Residue "D ARG 251": "NH1" <-> "NH2" Residue "D ARG 290": "NH1" <-> "NH2" Residue "D GLU 333": "OE1" <-> "OE2" Residue "D ARG 362": "NH1" <-> "NH2" Residue "D GLU 446": "OE1" <-> "OE2" Residue "D ARG 455": "NH1" <-> "NH2" Residue "D ARG 513": "NH1" <-> "NH2" Residue "D ARG 528": "NH1" <-> "NH2" Residue "D ARG 598": "NH1" <-> "NH2" Residue "D GLU 634": "OE1" <-> "OE2" Residue "D GLU 638": "OE1" <-> "OE2" Residue "D ARG 682": "NH1" <-> "NH2" Residue "D GLU 705": "OE1" <-> "OE2" Residue "D ARG 717": "NH1" <-> "NH2" Residue "D ARG 718": "NH1" <-> "NH2" Residue "D ARG 724": "NH1" <-> "NH2" Residue "D ARG 727": "NH1" <-> "NH2" Residue "D ARG 732": "NH1" <-> "NH2" Residue "E GLU 82": "OE1" <-> "OE2" Residue "E ARG 92": "NH1" <-> "NH2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E ARG 124": "NH1" <-> "NH2" Residue "E ARG 143": "NH1" <-> "NH2" Residue "E ARG 166": "NH1" <-> "NH2" Residue "E PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 207": "NH1" <-> "NH2" Residue "E GLU 210": "OE1" <-> "OE2" Residue "E ARG 229": "NH1" <-> "NH2" Residue "E GLU 265": "OE1" <-> "OE2" Residue "E GLU 277": "OE1" <-> "OE2" Residue "E ARG 282": "NH1" <-> "NH2" Residue "E ARG 309": "NH1" <-> "NH2" Residue "E ARG 435": "NH1" <-> "NH2" Residue "E GLU 441": "OE1" <-> "OE2" Residue "E ARG 468": "NH1" <-> "NH2" Residue "E ARG 512": "NH1" <-> "NH2" Residue "E ARG 529": "NH1" <-> "NH2" Residue "E ARG 550": "NH1" <-> "NH2" Residue "E ARG 604": "NH1" <-> "NH2" Residue "E ARG 732": "NH1" <-> "NH2" Residue "F ARG 43": "NH1" <-> "NH2" Residue "F GLU 44": "OE1" <-> "OE2" Residue "F GLU 90": "OE1" <-> "OE2" Residue "F ARG 106": "NH1" <-> "NH2" Residue "F GLU 110": "OE1" <-> "OE2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F ARG 164": "NH1" <-> "NH2" Residue "F ARG 169": "NH1" <-> "NH2" Residue "F ARG 215": "NH1" <-> "NH2" Residue "F GLU 295": "OE1" <-> "OE2" Residue "F GLU 348": "OE1" <-> "OE2" Residue "F ARG 372": "NH1" <-> "NH2" Residue "F ARG 396": "NH1" <-> "NH2" Residue "F ARG 407": "NH1" <-> "NH2" Residue "F ARG 481": "NH1" <-> "NH2" Residue "F ARG 498": "NH1" <-> "NH2" Residue "F ARG 499": "NH1" <-> "NH2" Residue "F GLU 552": "OE1" <-> "OE2" Residue "F ARG 590": "NH1" <-> "NH2" Residue "F GLU 591": "OE1" <-> "OE2" Residue "F ARG 611": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 68655 Number of models: 1 Model: "" Number of chains: 26 Chain: "2" Number of atoms: 5591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 5591 Classifications: {'peptide': 706} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 29, 'TRANS': 676} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "3" Number of atoms: 5080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 650, 5080 Classifications: {'peptide': 650} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 24, 'TRANS': 625} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "4" Number of atoms: 5187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5187 Classifications: {'peptide': 653} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 30, 'TRANS': 622} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "5" Number of atoms: 5500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 5500 Classifications: {'peptide': 710} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 681} Chain breaks: 4 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 7, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 62 Chain: "6" Number of atoms: 5726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 5726 Classifications: {'peptide': 716} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 23, 'TRANS': 692} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'TYR:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "7" Number of atoms: 5065 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 636, 5057 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 29, 'TRANS': 606} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 636, 5057 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 29, 'TRANS': 606} Chain breaks: 1 bond proxies already assigned to first conformer: 5128 Chain: "A" Number of atoms: 5556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5556 Classifications: {'peptide': 702} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 29, 'TRANS': 672} Chain breaks: 2 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 5100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5100 Classifications: {'peptide': 651} Link IDs: {'PTRANS': 24, 'TRANS': 626} Chain breaks: 1 Chain: "C" Number of atoms: 5184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5184 Classifications: {'peptide': 651} Link IDs: {'PTRANS': 30, 'TRANS': 620} Chain breaks: 2 Chain: "D" Number of atoms: 5474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 705, 5474 Classifications: {'peptide': 705} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 676} Chain breaks: 5 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'HIS:plan': 1, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 61 Chain: "E" Number of atoms: 5694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5694 Classifications: {'peptide': 711} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 687} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 5102 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 643, 5094 Classifications: {'peptide': 643} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 29, 'TRANS': 613} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 643, 5094 Classifications: {'peptide': 643} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 29, 'TRANS': 613} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 5166 Chain: "O" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 49, 1029 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Conformer: "B" Number of residues, atoms: 49, 980 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain: "S" Number of atoms: 2009 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 49, 980 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Conformer: "B" Number of residues, atoms: 49, 1029 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain: "2" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "3" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "5" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "6" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "7" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1242 SG CYS 2 329 59.172 81.251 127.233 1.00 29.59 S ATOM 1265 SG CYS 2 332 56.240 81.338 129.649 1.00 31.17 S ATOM 1416 SG CYS 2 352 58.966 84.155 129.457 1.00 29.37 S ATOM 1438 SG CYS 2 355 59.943 81.105 130.897 1.00 31.45 S ATOM 12152 SG CYS 4 306 100.364 100.699 122.005 1.00 43.02 S ATOM 12174 SG CYS 4 309 102.905 103.251 123.003 1.00 48.60 S ATOM 12320 SG CYS 4 328 103.736 99.659 123.316 1.00 48.74 S ATOM 12341 SG CYS 4 331 101.061 101.130 125.682 1.00 54.41 S ATOM 17176 SG CYS 5 172 69.007 61.956 130.200 1.00 33.68 S ATOM 17199 SG CYS 5 175 67.092 60.010 132.502 1.00 36.36 S ATOM 17370 SG CYS 5 197 66.270 63.604 132.391 1.00 40.44 S ATOM 17444 SG CYS 5 207 69.850 62.702 133.642 1.00 40.96 S ATOM 22553 SG CYS 6 158 83.952 94.789 125.607 1.00 39.93 S ATOM 22575 SG CYS 6 161 84.514 97.018 128.632 1.00 42.23 S ATOM 22736 SG CYS 6 180 87.105 96.686 126.367 1.00 38.97 S ATOM 22775 SG CYS 6 185 86.107 93.505 128.472 1.00 39.86 S ATOM 28592 SG CYS 7 184 110.796 73.886 121.444 1.00 30.39 S ATOM 28615 SG CYS 7 187 112.942 70.769 122.763 1.00 34.73 S ATOM 28761 SG CYS 7 206 109.112 71.020 122.961 1.00 31.36 S ATOM 28798 SG CYS 7 211 110.911 72.968 125.106 1.00 33.71 S ATOM 33378 SG CYS A 329 93.530 81.059 130.880 1.00 33.22 S ATOM 33401 SG CYS A 332 96.311 80.992 128.260 1.00 34.17 S ATOM 33552 SG CYS A 352 94.347 84.166 128.841 1.00 32.97 S ATOM 33574 SG CYS A 355 92.558 81.086 127.383 1.00 34.83 S ATOM 44294 SG CYS C 306 52.719 100.800 135.781 1.00 44.55 S ATOM 44316 SG CYS C 309 50.052 103.418 135.022 1.00 52.52 S ATOM 44462 SG CYS C 328 49.825 99.762 133.385 1.00 50.77 S ATOM 44483 SG CYS C 331 52.035 101.760 132.197 1.00 53.05 S ATOM 49307 SG CYS D 172 83.333 61.806 128.149 1.00 32.78 S ATOM 49330 SG CYS D 175 85.197 59.774 125.611 1.00 36.31 S ATOM 49501 SG CYS D 197 86.002 63.391 126.056 1.00 37.14 S ATOM 49569 SG CYS D 207 82.561 62.540 124.612 1.00 38.36 S ATOM 54648 SG CYS E 158 68.689 94.973 132.395 1.00 41.73 S ATOM 54670 SG CYS E 161 68.345 97.205 129.309 1.00 43.76 S ATOM 54831 SG CYS E 180 65.569 96.848 131.440 1.00 39.54 S ATOM 54870 SG CYS E 185 66.720 93.735 129.363 1.00 39.19 S ATOM 60657 SG CYS F 184 41.633 74.349 136.766 1.00 30.40 S ATOM 60680 SG CYS F 187 39.566 71.264 135.589 1.00 33.85 S ATOM 60826 SG CYS F 206 43.454 71.794 135.232 1.00 32.93 S ATOM 60863 SG CYS F 211 41.707 73.589 133.080 1.00 34.39 S Residues with excluded nonbonded symmetry interactions: 100 residue: pdb=" N AASN 7 95 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN 7 95 " occ=0.50 residue: pdb=" N AASN F 95 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN F 95 " occ=0.50 residue group: pdb=" P A DA O 1 " occ=0.50 ... (39 atoms not shown) pdb=" C6 B DT O 1 " occ=0.50 residue group: pdb=" P A DA O 2 " occ=0.50 ... (39 atoms not shown) pdb=" C6 B DT O 2 " occ=0.50 residue group: pdb=" P A DA O 3 " occ=0.50 ... (39 atoms not shown) pdb=" C6 B DT O 3 " occ=0.50 residue group: pdb=" P A DA O 4 " occ=0.50 ... (39 atoms not shown) pdb=" C6 B DT O 4 " occ=0.50 residue group: pdb=" P A DA O 5 " occ=0.50 ... (39 atoms not shown) pdb=" C6 B DT O 5 " occ=0.50 residue group: pdb=" P A DA O 6 " occ=0.50 ... (39 atoms not shown) pdb=" C6 B DT O 6 " occ=0.50 residue group: pdb=" P A DA O 7 " occ=0.50 ... (39 atoms not shown) pdb=" C6 B DT O 7 " occ=0.50 residue group: pdb=" P A DA O 8 " occ=0.50 ... (39 atoms not shown) pdb=" C6 B DT O 8 " occ=0.50 residue group: pdb=" P A DA O 9 " occ=0.50 ... (39 atoms not shown) pdb=" C6 B DT O 9 " occ=0.50 residue group: pdb=" P A DA O 10 " occ=0.50 ... (39 atoms not shown) pdb=" C6 B DT O 10 " occ=0.50 ... (remaining 88 not shown) Time building chain proxies: 29.57, per 1000 atoms: 0.43 Number of scatterers: 68655 At special positions: 0 Unit cell: (153.7, 145.22, 260.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 10 29.99 S 361 16.00 P 228 15.00 Mg 12 11.99 O 13471 8.00 N 12171 7.00 C 42402 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 24.27 Conformation dependent library (CDL) restraints added in 11.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 21001 " pdb="ZN ZN 21001 " - pdb=" SG CYS 2 329 " pdb="ZN ZN 21001 " - pdb=" SG CYS 2 355 " pdb="ZN ZN 21001 " - pdb=" SG CYS 2 332 " pdb="ZN ZN 21001 " - pdb=" SG CYS 2 352 " pdb=" ZN 4 901 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 309 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 306 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 328 " pdb="ZN ZN 4 901 " - pdb=" SG CYS 4 331 " pdb=" ZN 5 801 " pdb="ZN ZN 5 801 " - pdb=" SG CYS 5 175 " pdb="ZN ZN 5 801 " - pdb=" SG CYS 5 172 " pdb="ZN ZN 5 801 " - pdb=" SG CYS 5 197 " pdb="ZN ZN 5 801 " - pdb=" SG CYS 5 207 " pdb=" ZN 6 901 " pdb="ZN ZN 6 901 " - pdb=" SG CYS 6 180 " pdb="ZN ZN 6 901 " - pdb=" SG CYS 6 161 " pdb="ZN ZN 6 901 " - pdb=" SG CYS 6 158 " pdb="ZN ZN 6 901 " - pdb=" SG CYS 6 185 " pdb=" ZN 7 801 " pdb="ZN ZN 7 801 " - pdb=" SG CYS 7 206 " pdb="ZN ZN 7 801 " - pdb=" SG CYS 7 211 " pdb="ZN ZN 7 801 " - pdb=" SG CYS 7 187 " pdb="ZN ZN 7 801 " - pdb=" SG CYS 7 184 " pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 329 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 355 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 332 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 352 " pdb=" ZN C 901 " pdb="ZN ZN C 901 " - pdb=" SG CYS C 309 " pdb="ZN ZN C 901 " - pdb=" SG CYS C 331 " pdb="ZN ZN C 901 " - pdb=" SG CYS C 328 " pdb="ZN ZN C 901 " - pdb=" SG CYS C 306 " pdb=" ZN D 801 " pdb="ZN ZN D 801 " - pdb=" SG CYS D 175 " pdb="ZN ZN D 801 " - pdb=" SG CYS D 172 " pdb="ZN ZN D 801 " - pdb=" SG CYS D 197 " pdb="ZN ZN D 801 " - pdb=" SG CYS D 207 " pdb=" ZN E 901 " pdb="ZN ZN E 901 " - pdb=" SG CYS E 180 " pdb="ZN ZN E 901 " - pdb=" SG CYS E 161 " pdb="ZN ZN E 901 " - pdb=" SG CYS E 158 " pdb="ZN ZN E 901 " - pdb=" SG CYS E 185 " pdb=" ZN F 801 " pdb="ZN ZN F 801 " - pdb=" SG CYS F 206 " pdb="ZN ZN F 801 " - pdb=" SG CYS F 211 " pdb="ZN ZN F 801 " - pdb=" SG CYS F 184 " pdb="ZN ZN F 801 " - pdb=" SG CYS F 187 " Number of angles added : 60 16132 Ramachandran restraints generated. 8066 Oldfield, 0 Emsley, 8066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15412 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 320 helices and 94 sheets defined 38.1% alpha, 16.0% beta 31 base pairs and 83 stacking pairs defined. Time for finding SS restraints: 24.26 Creating SS restraints... Processing helix chain '2' and resid 182 through 187 Processing helix chain '2' and resid 189 through 205 Processing helix chain '2' and resid 214 through 224 Processing helix chain '2' and resid 234 through 240 Processing helix chain '2' and resid 242 through 250 Proline residue: 2 249 - end of helix Processing helix chain '2' and resid 252 through 270 Processing helix chain '2' and resid 272 through 276 removed outlier: 3.649A pdb=" N ASP 2 275 " --> pdb=" O PRO 2 272 " (cutoff:3.500A) Processing helix chain '2' and resid 294 through 296 No H-bonds generated for 'chain '2' and resid 294 through 296' Processing helix chain '2' and resid 299 through 301 No H-bonds generated for 'chain '2' and resid 299 through 301' Processing helix chain '2' and resid 382 through 384 No H-bonds generated for 'chain '2' and resid 382 through 384' Processing helix chain '2' and resid 461 through 470 removed outlier: 4.091A pdb=" N ASP 2 470 " --> pdb=" O SER 2 466 " (cutoff:3.500A) Processing helix chain '2' and resid 473 through 480 Processing helix chain '2' and resid 489 through 500 Processing helix chain '2' and resid 529 through 539 Processing helix chain '2' and resid 575 through 578 No H-bonds generated for 'chain '2' and resid 575 through 578' Processing helix chain '2' and resid 589 through 591 No H-bonds generated for 'chain '2' and resid 589 through 591' Processing helix chain '2' and resid 594 through 606 Processing helix chain '2' and resid 633 through 635 No H-bonds generated for 'chain '2' and resid 633 through 635' Processing helix chain '2' and resid 643 through 645 No H-bonds generated for 'chain '2' and resid 643 through 645' Processing helix chain '2' and resid 651 through 656 removed outlier: 3.980A pdb=" N ARG 2 656 " --> pdb=" O PRO 2 652 " (cutoff:3.500A) Processing helix chain '2' and resid 669 through 685 Processing helix chain '2' and resid 688 through 690 No H-bonds generated for 'chain '2' and resid 688 through 690' Processing helix chain '2' and resid 720 through 728 Processing helix chain '2' and resid 741 through 756 Processing helix chain '2' and resid 764 through 780 Processing helix chain '2' and resid 788 through 804 Processing helix chain '2' and resid 808 through 817 Processing helix chain '2' and resid 819 through 822 No H-bonds generated for 'chain '2' and resid 819 through 822' Processing helix chain '2' and resid 828 through 850 removed outlier: 4.050A pdb=" N ARG 2 850 " --> pdb=" O TYR 2 846 " (cutoff:3.500A) Processing helix chain '2' and resid 862 through 871 Processing helix chain '2' and resid 878 through 882 Processing helix chain '2' and resid 884 through 888 Processing helix chain '3' and resid 10 through 23 Processing helix chain '3' and resid 31 through 42 Processing helix chain '3' and resid 51 through 57 Processing helix chain '3' and resid 59 through 67 Processing helix chain '3' and resid 69 through 87 Processing helix chain '3' and resid 89 through 94 Processing helix chain '3' and resid 118 through 120 No H-bonds generated for 'chain '3' and resid 118 through 120' Processing helix chain '3' and resid 169 through 172 Processing helix chain '3' and resid 226 through 228 No H-bonds generated for 'chain '3' and resid 226 through 228' Processing helix chain '3' and resid 278 through 290 Processing helix chain '3' and resid 295 through 301 Processing helix chain '3' and resid 311 through 322 Processing helix chain '3' and resid 351 through 361 Processing helix chain '3' and resid 375 through 377 No H-bonds generated for 'chain '3' and resid 375 through 377' Processing helix chain '3' and resid 397 through 400 No H-bonds generated for 'chain '3' and resid 397 through 400' Processing helix chain '3' and resid 411 through 413 No H-bonds generated for 'chain '3' and resid 411 through 413' Processing helix chain '3' and resid 416 through 428 removed outlier: 3.975A pdb=" N HIS 3 423 " --> pdb=" O ARG 3 419 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLU 3 424 " --> pdb=" O THR 3 420 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL 3 425 " --> pdb=" O ALA 3 421 " (cutoff:3.500A) Processing helix chain '3' and resid 465 through 468 No H-bonds generated for 'chain '3' and resid 465 through 468' Processing helix chain '3' and resid 473 through 478 removed outlier: 3.558A pdb=" N ARG 3 478 " --> pdb=" O SER 3 474 " (cutoff:3.500A) Processing helix chain '3' and resid 491 through 506 Processing helix chain '3' and resid 532 through 534 No H-bonds generated for 'chain '3' and resid 532 through 534' Processing helix chain '3' and resid 565 through 577 removed outlier: 3.999A pdb=" N ILE 3 577 " --> pdb=" O HIS 3 573 " (cutoff:3.500A) Processing helix chain '3' and resid 584 through 597 Processing helix chain '3' and resid 600 through 602 No H-bonds generated for 'chain '3' and resid 600 through 602' Processing helix chain '3' and resid 615 through 631 Processing helix chain '3' and resid 639 through 652 Processing helix chain '4' and resid 116 through 118 No H-bonds generated for 'chain '4' and resid 116 through 118' Processing helix chain '4' and resid 159 through 171 Processing helix chain '4' and resid 192 through 203 Processing helix chain '4' and resid 212 through 218 Processing helix chain '4' and resid 220 through 228 Processing helix chain '4' and resid 230 through 247 Proline residue: 4 235 - end of helix Processing helix chain '4' and resid 271 through 273 No H-bonds generated for 'chain '4' and resid 271 through 273' Processing helix chain '4' and resid 276 through 278 No H-bonds generated for 'chain '4' and resid 276 through 278' Processing helix chain '4' and resid 341 through 343 No H-bonds generated for 'chain '4' and resid 341 through 343' Processing helix chain '4' and resid 432 through 436 Processing helix chain '4' and resid 443 through 453 Processing helix chain '4' and resid 458 through 464 Processing helix chain '4' and resid 474 through 485 Processing helix chain '4' and resid 516 through 524 Processing helix chain '4' and resid 540 through 544 Processing helix chain '4' and resid 562 through 565 No H-bonds generated for 'chain '4' and resid 562 through 565' Processing helix chain '4' and resid 581 through 593 removed outlier: 4.073A pdb=" N VAL 4 586 " --> pdb=" O SER 4 582 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LEU 4 587 " --> pdb=" O THR 4 583 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N HIS 4 588 " --> pdb=" O ARG 4 584 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU 4 589 " --> pdb=" O SER 4 585 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL 4 590 " --> pdb=" O VAL 4 586 " (cutoff:3.500A) Processing helix chain '4' and resid 620 through 622 No H-bonds generated for 'chain '4' and resid 620 through 622' Processing helix chain '4' and resid 630 through 634 Processing helix chain '4' and resid 638 through 643 Processing helix chain '4' and resid 656 through 670 removed outlier: 3.576A pdb=" N TYR 4 670 " --> pdb=" O LEU 4 666 " (cutoff:3.500A) Processing helix chain '4' and resid 684 through 697 removed outlier: 3.809A pdb=" N ASP 4 689 " --> pdb=" O ALA 4 685 " (cutoff:3.500A) Processing helix chain '4' and resid 704 through 721 Processing helix chain '4' and resid 731 through 747 Processing helix chain '4' and resid 755 through 767 Processing helix chain '5' and resid 28 through 41 Processing helix chain '5' and resid 54 through 65 Processing helix chain '5' and resid 74 through 80 Processing helix chain '5' and resid 82 through 90 Processing helix chain '5' and resid 92 through 111 removed outlier: 3.588A pdb=" N GLN 5 97 " --> pdb=" O ALA 5 93 " (cutoff:3.500A) Processing helix chain '5' and resid 142 through 144 No H-bonds generated for 'chain '5' and resid 142 through 144' Processing helix chain '5' and resid 216 through 218 No H-bonds generated for 'chain '5' and resid 216 through 218' Processing helix chain '5' and resid 233 through 235 No H-bonds generated for 'chain '5' and resid 233 through 235' Processing helix chain '5' and resid 316 through 326 Processing helix chain '5' and resid 331 through 337 Processing helix chain '5' and resid 347 through 358 Processing helix chain '5' and resid 387 through 397 Processing helix chain '5' and resid 433 through 436 No H-bonds generated for 'chain '5' and resid 433 through 436' Processing helix chain '5' and resid 452 through 463 removed outlier: 3.947A pdb=" N GLU 5 463 " --> pdb=" O HIS 5 459 " (cutoff:3.500A) Processing helix chain '5' and resid 497 through 499 No H-bonds generated for 'chain '5' and resid 497 through 499' Processing helix chain '5' and resid 508 through 511 No H-bonds generated for 'chain '5' and resid 508 through 511' Processing helix chain '5' and resid 530 through 540 Processing helix chain '5' and resid 556 through 569 Processing helix chain '5' and resid 576 through 600 Processing helix chain '5' and resid 610 through 627 removed outlier: 3.787A pdb=" N LYS 5 627 " --> pdb=" O LEU 5 623 " (cutoff:3.500A) Processing helix chain '5' and resid 634 through 651 removed outlier: 3.861A pdb=" N SER 5 647 " --> pdb=" O LEU 5 643 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ASP 5 650 " --> pdb=" O VAL 5 646 " (cutoff:3.500A) Processing helix chain '5' and resid 653 through 674 removed outlier: 3.970A pdb=" N THR 5 664 " --> pdb=" O VAL 5 660 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU 5 670 " --> pdb=" O GLN 5 666 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET 5 671 " --> pdb=" O GLU 5 667 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU 5 672 " --> pdb=" O ASP 5 668 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER 5 673 " --> pdb=" O GLN 5 669 " (cutoff:3.500A) Processing helix chain '5' and resid 689 through 697 removed outlier: 3.634A pdb=" N ILE 5 695 " --> pdb=" O GLU 5 691 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP 5 697 " --> pdb=" O SER 5 693 " (cutoff:3.500A) Processing helix chain '5' and resid 705 through 716 removed outlier: 3.703A pdb=" N LYS 5 710 " --> pdb=" O HIS 5 706 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL 5 711 " --> pdb=" O ALA 5 707 " (cutoff:3.500A) Processing helix chain '5' and resid 722 through 733 removed outlier: 4.214A pdb=" N ARG 5 727 " --> pdb=" O HIS 5 723 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL 5 729 " --> pdb=" O MET 5 725 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR 5 731 " --> pdb=" O ARG 5 727 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ARG 5 732 " --> pdb=" O LYS 5 728 " (cutoff:3.500A) Processing helix chain '6' and resid 21 through 36 Processing helix chain '6' and resid 45 through 54 removed outlier: 4.035A pdb=" N GLU 6 52 " --> pdb=" O GLN 6 48 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU 6 53 " --> pdb=" O LEU 6 49 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE 6 54 " --> pdb=" O ALA 6 50 " (cutoff:3.500A) Processing helix chain '6' and resid 65 through 71 Processing helix chain '6' and resid 73 through 81 Processing helix chain '6' and resid 83 through 99 Proline residue: 6 88 - end of helix Processing helix chain '6' and resid 123 through 125 No H-bonds generated for 'chain '6' and resid 123 through 125' Processing helix chain '6' and resid 195 through 197 No H-bonds generated for 'chain '6' and resid 195 through 197' Processing helix chain '6' and resid 212 through 214 No H-bonds generated for 'chain '6' and resid 212 through 214' Processing helix chain '6' and resid 280 through 286 Processing helix chain '6' and resid 322 through 328 Processing helix chain '6' and resid 331 through 341 Processing helix chain '6' and resid 346 through 354 Processing helix chain '6' and resid 362 through 373 Processing helix chain '6' and resid 402 through 412 Processing helix chain '6' and resid 426 through 429 No H-bonds generated for 'chain '6' and resid 426 through 429' Processing helix chain '6' and resid 448 through 451 No H-bonds generated for 'chain '6' and resid 448 through 451' Processing helix chain '6' and resid 462 through 464 No H-bonds generated for 'chain '6' and resid 462 through 464' Processing helix chain '6' and resid 467 through 479 removed outlier: 4.274A pdb=" N ALA 6 472 " --> pdb=" O ARG 6 468 " (cutoff:3.500A) Processing helix chain '6' and resid 524 through 529 removed outlier: 3.970A pdb=" N ARG 6 529 " --> pdb=" O PRO 6 525 " (cutoff:3.500A) Processing helix chain '6' and resid 542 through 557 Processing helix chain '6' and resid 569 through 581 removed outlier: 4.125A pdb=" N GLN 6 581 " --> pdb=" O LEU 6 577 " (cutoff:3.500A) Processing helix chain '6' and resid 588 through 605 removed outlier: 3.694A pdb=" N ASP 6 605 " --> pdb=" O LEU 6 601 " (cutoff:3.500A) Processing helix chain '6' and resid 618 through 634 Processing helix chain '6' and resid 642 through 655 Processing helix chain '6' and resid 722 through 739 removed outlier: 4.012A pdb=" N VAL 6 728 " --> pdb=" O SER 6 724 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU 6 738 " --> pdb=" O VAL 6 734 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ASP 6 739 " --> pdb=" O GLU 6 735 " (cutoff:3.500A) Processing helix chain '6' and resid 746 through 758 Processing helix chain '6' and resid 763 through 779 removed outlier: 4.056A pdb=" N ARG 6 779 " --> pdb=" O LYS 6 775 " (cutoff:3.500A) Processing helix chain '7' and resid 6 through 19 Processing helix chain '7' and resid 32 through 41 removed outlier: 3.806A pdb=" N GLN 7 36 " --> pdb=" O LYS 7 32 " (cutoff:3.500A) Processing helix chain '7' and resid 52 through 56 Processing helix chain '7' and resid 60 through 68 Processing helix chain '7' and resid 70 through 88 Proline residue: 7 86 - end of helix Processing helix chain '7' and resid 98 through 112 Processing helix chain '7' and resid 128 through 131 Processing helix chain '7' and resid 149 through 151 No H-bonds generated for 'chain '7' and resid 149 through 151' Processing helix chain '7' and resid 154 through 156 No H-bonds generated for 'chain '7' and resid 154 through 156' Processing helix chain '7' and resid 209 through 213 Processing helix chain '7' and resid 241 through 243 No H-bonds generated for 'chain '7' and resid 241 through 243' Processing helix chain '7' and resid 259 through 261 No H-bonds generated for 'chain '7' and resid 259 through 261' Processing helix chain '7' and resid 307 through 309 No H-bonds generated for 'chain '7' and resid 307 through 309' Processing helix chain '7' and resid 321 through 328 Processing helix chain '7' and resid 332 through 338 Processing helix chain '7' and resid 348 through 359 Processing helix chain '7' and resid 387 through 397 Processing helix chain '7' and resid 411 through 413 No H-bonds generated for 'chain '7' and resid 411 through 413' Processing helix chain '7' and resid 433 through 436 No H-bonds generated for 'chain '7' and resid 433 through 436' Processing helix chain '7' and resid 447 through 449 No H-bonds generated for 'chain '7' and resid 447 through 449' Processing helix chain '7' and resid 452 through 464 Processing helix chain '7' and resid 509 through 514 Processing helix chain '7' and resid 527 through 543 Processing helix chain '7' and resid 556 through 567 Processing helix chain '7' and resid 578 through 594 Processing helix chain '7' and resid 603 through 620 Processing helix chain '7' and resid 627 through 641 removed outlier: 4.301A pdb=" N LYS 7 641 " --> pdb=" O MET 7 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 189 through 204 Processing helix chain 'A' and resid 214 through 225 Processing helix chain 'A' and resid 234 through 240 Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 252 through 270 Processing helix chain 'A' and resid 272 through 276 removed outlier: 4.084A pdb=" N ASP A 275 " --> pdb=" O PRO A 272 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG A 276 " --> pdb=" O LYS A 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 272 through 276' Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 461 through 470 removed outlier: 3.634A pdb=" N ASP A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 480 Processing helix chain 'A' and resid 489 through 500 Processing helix chain 'A' and resid 529 through 539 Processing helix chain 'A' and resid 589 through 591 No H-bonds generated for 'chain 'A' and resid 589 through 591' Processing helix chain 'A' and resid 594 through 606 Processing helix chain 'A' and resid 633 through 635 No H-bonds generated for 'chain 'A' and resid 633 through 635' Processing helix chain 'A' and resid 644 through 646 No H-bonds generated for 'chain 'A' and resid 644 through 646' Processing helix chain 'A' and resid 651 through 656 removed outlier: 3.660A pdb=" N ARG A 656 " --> pdb=" O PRO A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 685 Processing helix chain 'A' and resid 720 through 728 Processing helix chain 'A' and resid 740 through 756 Processing helix chain 'A' and resid 764 through 780 Processing helix chain 'A' and resid 788 through 804 Processing helix chain 'A' and resid 808 through 822 removed outlier: 5.478A pdb=" N ARG A 820 " --> pdb=" O LYS A 816 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TYR A 821 " --> pdb=" O THR A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 850 removed outlier: 3.935A pdb=" N ASN A 849 " --> pdb=" O THR A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 872 Processing helix chain 'A' and resid 878 through 882 Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'B' and resid 10 through 24 Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 51 through 57 Processing helix chain 'B' and resid 59 through 67 Processing helix chain 'B' and resid 69 through 87 Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 118 through 120 No H-bonds generated for 'chain 'B' and resid 118 through 120' Processing helix chain 'B' and resid 169 through 172 Processing helix chain 'B' and resid 226 through 228 No H-bonds generated for 'chain 'B' and resid 226 through 228' Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 278 through 290 Processing helix chain 'B' and resid 295 through 301 Processing helix chain 'B' and resid 311 through 322 Processing helix chain 'B' and resid 351 through 361 Processing helix chain 'B' and resid 375 through 377 No H-bonds generated for 'chain 'B' and resid 375 through 377' Processing helix chain 'B' and resid 397 through 400 No H-bonds generated for 'chain 'B' and resid 397 through 400' Processing helix chain 'B' and resid 416 through 428 removed outlier: 4.431A pdb=" N GLU B 424 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 468 No H-bonds generated for 'chain 'B' and resid 465 through 468' Processing helix chain 'B' and resid 473 through 478 removed outlier: 3.959A pdb=" N ARG B 478 " --> pdb=" O SER B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 504 Processing helix chain 'B' and resid 525 through 528 No H-bonds generated for 'chain 'B' and resid 525 through 528' Processing helix chain 'B' and resid 565 through 577 removed outlier: 3.915A pdb=" N ILE B 577 " --> pdb=" O HIS B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 598 Processing helix chain 'B' and resid 600 through 602 No H-bonds generated for 'chain 'B' and resid 600 through 602' Processing helix chain 'B' and resid 615 through 632 Processing helix chain 'B' and resid 639 through 653 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 159 through 171 Processing helix chain 'C' and resid 193 through 202 Processing helix chain 'C' and resid 212 through 218 Processing helix chain 'C' and resid 220 through 228 Processing helix chain 'C' and resid 230 through 247 Proline residue: C 235 - end of helix Processing helix chain 'C' and resid 271 through 273 No H-bonds generated for 'chain 'C' and resid 271 through 273' Processing helix chain 'C' and resid 276 through 278 No H-bonds generated for 'chain 'C' and resid 276 through 278' Processing helix chain 'C' and resid 341 through 343 No H-bonds generated for 'chain 'C' and resid 341 through 343' Processing helix chain 'C' and resid 432 through 435 No H-bonds generated for 'chain 'C' and resid 432 through 435' Processing helix chain 'C' and resid 443 through 453 Processing helix chain 'C' and resid 458 through 465 Processing helix chain 'C' and resid 474 through 485 Processing helix chain 'C' and resid 493 through 495 No H-bonds generated for 'chain 'C' and resid 493 through 495' Processing helix chain 'C' and resid 516 through 524 Processing helix chain 'C' and resid 535 through 537 No H-bonds generated for 'chain 'C' and resid 535 through 537' Processing helix chain 'C' and resid 540 through 544 Processing helix chain 'C' and resid 562 through 565 No H-bonds generated for 'chain 'C' and resid 562 through 565' Processing helix chain 'C' and resid 581 through 593 removed outlier: 4.116A pdb=" N VAL C 586 " --> pdb=" O SER C 582 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU C 587 " --> pdb=" O THR C 583 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N HIS C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU C 589 " --> pdb=" O SER C 585 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL C 590 " --> pdb=" O VAL C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 634 Processing helix chain 'C' and resid 638 through 643 removed outlier: 3.690A pdb=" N SER C 642 " --> pdb=" O HIS C 638 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG C 643 " --> pdb=" O THR C 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 638 through 643' Processing helix chain 'C' and resid 656 through 670 removed outlier: 3.712A pdb=" N TYR C 670 " --> pdb=" O LEU C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 697 Processing helix chain 'C' and resid 704 through 721 Processing helix chain 'C' and resid 731 through 747 removed outlier: 3.709A pdb=" N GLU C 735 " --> pdb=" O PRO C 731 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 767 Processing helix chain 'D' and resid 28 through 41 Processing helix chain 'D' and resid 54 through 64 Processing helix chain 'D' and resid 74 through 80 Processing helix chain 'D' and resid 82 through 90 Processing helix chain 'D' and resid 92 through 111 Processing helix chain 'D' and resid 137 through 139 No H-bonds generated for 'chain 'D' and resid 137 through 139' Processing helix chain 'D' and resid 142 through 144 No H-bonds generated for 'chain 'D' and resid 142 through 144' Processing helix chain 'D' and resid 316 through 326 Processing helix chain 'D' and resid 331 through 338 Processing helix chain 'D' and resid 347 through 358 Processing helix chain 'D' and resid 387 through 397 Processing helix chain 'D' and resid 433 through 436 No H-bonds generated for 'chain 'D' and resid 433 through 436' Processing helix chain 'D' and resid 452 through 461 removed outlier: 3.995A pdb=" N GLU D 460 " --> pdb=" O VAL D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 499 No H-bonds generated for 'chain 'D' and resid 497 through 499' Processing helix chain 'D' and resid 508 through 513 removed outlier: 3.554A pdb=" N ARG D 513 " --> pdb=" O THR D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 543 removed outlier: 5.439A pdb=" N ALA D 543 " --> pdb=" O LEU D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 569 Processing helix chain 'D' and resid 576 through 599 Processing helix chain 'D' and resid 610 through 626 Processing helix chain 'D' and resid 634 through 648 Processing helix chain 'D' and resid 652 through 679 removed outlier: 4.010A pdb=" N THR D 664 " --> pdb=" O VAL D 660 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER D 673 " --> pdb=" O GLN D 669 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ARG D 674 " --> pdb=" O GLU D 670 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS D 677 " --> pdb=" O SER D 673 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLN D 678 " --> pdb=" O ARG D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 698 Processing helix chain 'D' and resid 705 through 718 removed outlier: 3.536A pdb=" N LEU D 712 " --> pdb=" O ILE D 708 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG D 717 " --> pdb=" O GLN D 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 727 No H-bonds generated for 'chain 'D' and resid 724 through 727' Processing helix chain 'E' and resid 21 through 36 Processing helix chain 'E' and resid 45 through 54 removed outlier: 3.709A pdb=" N GLU E 52 " --> pdb=" O GLN E 48 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE E 54 " --> pdb=" O ALA E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 71 Processing helix chain 'E' and resid 73 through 81 Processing helix chain 'E' and resid 83 through 100 Proline residue: E 88 - end of helix removed outlier: 3.644A pdb=" N ASP E 100 " --> pdb=" O THR E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 125 No H-bonds generated for 'chain 'E' and resid 123 through 125' Processing helix chain 'E' and resid 280 through 287 Processing helix chain 'E' and resid 322 through 327 Processing helix chain 'E' and resid 331 through 341 Processing helix chain 'E' and resid 346 through 354 Processing helix chain 'E' and resid 362 through 373 Processing helix chain 'E' and resid 402 through 412 Processing helix chain 'E' and resid 448 through 451 No H-bonds generated for 'chain 'E' and resid 448 through 451' Processing helix chain 'E' and resid 462 through 464 No H-bonds generated for 'chain 'E' and resid 462 through 464' Processing helix chain 'E' and resid 467 through 479 removed outlier: 4.066A pdb=" N ALA E 472 " --> pdb=" O ARG E 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 506 through 508 No H-bonds generated for 'chain 'E' and resid 506 through 508' Processing helix chain 'E' and resid 516 through 519 No H-bonds generated for 'chain 'E' and resid 516 through 519' Processing helix chain 'E' and resid 524 through 529 Processing helix chain 'E' and resid 542 through 557 Processing helix chain 'E' and resid 569 through 581 removed outlier: 4.039A pdb=" N GLN E 581 " --> pdb=" O LEU E 577 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 605 removed outlier: 4.311A pdb=" N ASP E 605 " --> pdb=" O LEU E 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 635 removed outlier: 3.639A pdb=" N HIS E 635 " --> pdb=" O MET E 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 642 through 655 Processing helix chain 'E' and resid 720 through 735 removed outlier: 3.815A pdb=" N ILE E 723 " --> pdb=" O TYR E 720 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU E 731 " --> pdb=" O VAL E 728 " (cutoff:3.500A) Processing helix chain 'E' and resid 746 through 757 removed outlier: 3.886A pdb=" N ASN E 750 " --> pdb=" O SER E 746 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLU E 757 " --> pdb=" O LEU E 753 " (cutoff:3.500A) Processing helix chain 'E' and resid 765 through 778 Processing helix chain 'F' and resid 6 through 19 Processing helix chain 'F' and resid 32 through 41 removed outlier: 4.017A pdb=" N GLN F 36 " --> pdb=" O LYS F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 57 Processing helix chain 'F' and resid 60 through 69 Processing helix chain 'F' and resid 72 through 88 Proline residue: F 86 - end of helix Processing helix chain 'F' and resid 99 through 112 Processing helix chain 'F' and resid 128 through 131 Processing helix chain 'F' and resid 149 through 151 No H-bonds generated for 'chain 'F' and resid 149 through 151' Processing helix chain 'F' and resid 154 through 156 No H-bonds generated for 'chain 'F' and resid 154 through 156' Processing helix chain 'F' and resid 209 through 213 Processing helix chain 'F' and resid 241 through 243 No H-bonds generated for 'chain 'F' and resid 241 through 243' Processing helix chain 'F' and resid 259 through 261 No H-bonds generated for 'chain 'F' and resid 259 through 261' Processing helix chain 'F' and resid 312 through 315 No H-bonds generated for 'chain 'F' and resid 312 through 315' Processing helix chain 'F' and resid 321 through 328 Processing helix chain 'F' and resid 330 through 338 removed outlier: 4.404A pdb=" N TYR F 333 " --> pdb=" O GLU F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 348 through 359 Processing helix chain 'F' and resid 387 through 397 Processing helix chain 'F' and resid 411 through 413 No H-bonds generated for 'chain 'F' and resid 411 through 413' Processing helix chain 'F' and resid 433 through 436 No H-bonds generated for 'chain 'F' and resid 433 through 436' Processing helix chain 'F' and resid 447 through 449 No H-bonds generated for 'chain 'F' and resid 447 through 449' Processing helix chain 'F' and resid 452 through 464 Processing helix chain 'F' and resid 501 through 505 Processing helix chain 'F' and resid 509 through 513 Processing helix chain 'F' and resid 527 through 543 Processing helix chain 'F' and resid 556 through 567 Processing helix chain 'F' and resid 575 through 594 removed outlier: 4.794A pdb=" N ASP F 579 " --> pdb=" O SER F 576 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA F 594 " --> pdb=" O GLU F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 603 through 620 Processing helix chain 'F' and resid 627 through 644 removed outlier: 4.212A pdb=" N LYS F 641 " --> pdb=" O MET F 637 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N SER F 643 " --> pdb=" O MET F 639 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU F 644 " --> pdb=" O SER F 640 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '2' and resid 229 through 233 removed outlier: 6.048A pdb=" N HIS 2 282 " --> pdb=" O LEU 2 230 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL 2 232 " --> pdb=" O HIS 2 282 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ARG 2 284 " --> pdb=" O VAL 2 232 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain '2' and resid 411 through 418 removed outlier: 3.979A pdb=" N GLN 2 304 " --> pdb=" O TYR 2 418 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG 2 377 " --> pdb=" O THR 2 313 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N CYS 2 315 " --> pdb=" O ARG 2 375 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG 2 375 " --> pdb=" O CYS 2 315 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU 2 399 " --> pdb=" O ALA 2 441 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N HIS 2 443 " --> pdb=" O LEU 2 399 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR 2 415 " --> pdb=" O ASN 2 442 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL 2 444 " --> pdb=" O GLU 2 413 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLU 2 413 " --> pdb=" O VAL 2 444 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '2' and resid 326 through 329 removed outlier: 4.644A pdb=" N LYS 2 326 " --> pdb=" O ASN 2 364 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '2' and resid 659 through 663 Processing sheet with id= E, first strand: chain '2' and resid 559 through 562 Processing sheet with id= F, first strand: chain '2' and resid 608 through 612 Processing sheet with id= G, first strand: chain '2' and resid 858 through 861 removed outlier: 3.526A pdb=" N ILE 2 858 " --> pdb=" O GLN 2 902 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '2' and resid 319 through 324 removed outlier: 6.782A pdb=" N ILE 2 369 " --> pdb=" O SER 2 323 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '3' and resid 46 through 50 removed outlier: 6.524A pdb=" N TYR 3 99 " --> pdb=" O LEU 3 47 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL 3 49 " --> pdb=" O TYR 3 99 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLY 3 101 " --> pdb=" O VAL 3 49 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain '3' and resid 110 through 112 removed outlier: 7.680A pdb=" N VAL 3 111 " --> pdb=" O VAL 3 124 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N CYS 3 126 " --> pdb=" O VAL 3 111 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N THR 3 240 " --> pdb=" O ALA 3 262 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ALA 3 262 " --> pdb=" O THR 3 240 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ARG 3 242 " --> pdb=" O LEU 3 260 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU 3 260 " --> pdb=" O ARG 3 242 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N LEU 3 244 " --> pdb=" O THR 3 258 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N THR 3 258 " --> pdb=" O LEU 3 244 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '3' and resid 153 through 158 removed outlier: 3.505A pdb=" N LYS 3 153 " --> pdb=" O CYS 3 148 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL 3 145 " --> pdb=" O GLU 3 187 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '3' and resid 216 through 222 removed outlier: 3.859A pdb=" N LYS 3 133 " --> pdb=" O THR 3 200 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLN 3 202 " --> pdb=" O VAL 3 131 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL 3 131 " --> pdb=" O GLN 3 202 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '3' and resid 481 through 485 removed outlier: 6.507A pdb=" N GLY 3 404 " --> pdb=" O SER 3 447 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU 3 449 " --> pdb=" O GLY 3 404 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL 3 406 " --> pdb=" O LEU 3 449 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ALA 3 451 " --> pdb=" O VAL 3 406 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE 3 408 " --> pdb=" O ALA 3 451 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N ASN 3 453 " --> pdb=" O ILE 3 408 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '3' and resid 381 through 384 Processing sheet with id= O, first strand: chain '3' and resid 430 through 435 Processing sheet with id= P, first strand: chain '3' and resid 607 through 609 Processing sheet with id= Q, first strand: chain '3' and resid 138 through 143 removed outlier: 6.462A pdb=" N VAL 3 192 " --> pdb=" O VAL 3 142 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain '4' and resid 207 through 211 removed outlier: 6.445A pdb=" N GLN 4 259 " --> pdb=" O LEU 4 208 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL 4 210 " --> pdb=" O GLN 4 259 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ARG 4 261 " --> pdb=" O VAL 4 210 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain '4' and resid 369 through 375 removed outlier: 6.191A pdb=" N GLN 4 355 " --> pdb=" O VAL 4 289 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N VAL 4 289 " --> pdb=" O GLN 4 355 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE 4 393 " --> pdb=" O VAL 4 418 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N VAL 4 418 " --> pdb=" O ILE 4 393 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ARG 4 395 " --> pdb=" O ILE 4 416 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ILE 4 416 " --> pdb=" O ARG 4 395 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL 4 397 " --> pdb=" O THR 4 414 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N THR 4 414 " --> pdb=" O VAL 4 397 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain '4' and resid 312 through 316 removed outlier: 4.460A pdb=" N PHE 4 303 " --> pdb=" O ILE 4 340 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain '4' and resid 646 through 650 Processing sheet with id= V, first strand: chain '4' and resid 545 through 549 Processing sheet with id= W, first strand: chain '4' and resid 595 through 599 Processing sheet with id= X, first strand: chain '4' and resid 296 through 301 removed outlier: 6.604A pdb=" N LEU 4 345 " --> pdb=" O GLN 4 300 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain '5' and resid 43 through 46 Processing sheet with id= Z, first strand: chain '5' and resid 69 through 73 removed outlier: 6.334A pdb=" N GLN 5 125 " --> pdb=" O ILE 5 70 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N VAL 5 72 " --> pdb=" O GLN 5 125 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N MET 5 127 " --> pdb=" O VAL 5 72 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain '5' and resid 244 through 249 removed outlier: 3.549A pdb=" N GLN 5 225 " --> pdb=" O CYS 5 249 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA 5 157 " --> pdb=" O LYS 5 228 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN 5 230 " --> pdb=" O ILE 5 155 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ILE 5 155 " --> pdb=" O GLN 5 230 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE 5 268 " --> pdb=" O VAL 5 296 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N VAL 5 296 " --> pdb=" O ILE 5 268 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N SER 5 270 " --> pdb=" O ILE 5 294 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ILE 5 294 " --> pdb=" O SER 5 270 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain '5' and resid 170 through 172 Processing sheet with id= AC, first strand: chain '5' and resid 516 through 520 Processing sheet with id= AD, first strand: chain '5' and resid 417 through 420 Processing sheet with id= AE, first strand: chain '5' and resid 466 through 470 Processing sheet with id= AF, first strand: chain '5' and resid 164 through 167 removed outlier: 6.492A pdb=" N LYS 5 220 " --> pdb=" O THR 5 166 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain '6' and resid 60 through 64 removed outlier: 6.532A pdb=" N TYR 6 111 " --> pdb=" O LEU 6 61 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL 6 63 " --> pdb=" O TYR 6 111 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ALA 6 113 " --> pdb=" O VAL 6 63 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain '6' and resid 241 through 247 removed outlier: 6.612A pdb=" N ARG 6 207 " --> pdb=" O VAL 6 142 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N THR 6 144 " --> pdb=" O LYS 6 205 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LYS 6 205 " --> pdb=" O THR 6 144 " (cutoff:3.500A) removed outlier: 14.374A pdb=" N TYR 6 294 " --> pdb=" O SER 6 223 " (cutoff:3.500A) removed outlier: 12.028A pdb=" N GLU 6 225 " --> pdb=" O TYR 6 294 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N LEU 6 296 " --> pdb=" O GLU 6 225 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N ILE 6 227 " --> pdb=" O LEU 6 296 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N PHE 6 298 " --> pdb=" O ILE 6 227 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR 6 245 " --> pdb=" O CYS 6 301 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL 6 303 " --> pdb=" O ASP 6 243 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ASP 6 243 " --> pdb=" O VAL 6 303 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain '6' and resid 155 through 158 removed outlier: 4.601A pdb=" N THR 6 155 " --> pdb=" O ASP 6 194 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain '6' and resid 532 through 536 removed outlier: 3.553A pdb=" N GLY 6 396 " --> pdb=" O ALA 6 503 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLY 6 455 " --> pdb=" O SER 6 498 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU 6 500 " --> pdb=" O GLY 6 455 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N CYS 6 457 " --> pdb=" O LEU 6 500 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ALA 6 502 " --> pdb=" O CYS 6 457 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE 6 459 " --> pdb=" O ALA 6 502 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N ASN 6 504 " --> pdb=" O ILE 6 459 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain '6' and resid 431 through 435 Processing sheet with id= AL, first strand: chain '6' and resid 481 through 486 Processing sheet with id= AM, first strand: chain '6' and resid 147 through 153 removed outlier: 7.065A pdb=" N ARG 6 199 " --> pdb=" O VAL 6 152 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain '7' and resid 47 through 51 removed outlier: 6.341A pdb=" N GLU 7 135 " --> pdb=" O LEU 7 48 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL 7 50 " --> pdb=" O GLU 7 135 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR 7 137 " --> pdb=" O VAL 7 50 " (cutoff:3.500A) No H-bonds generated for sheet with id= AN Processing sheet with id= AO, first strand: chain '7' and resid 252 through 258 removed outlier: 3.656A pdb=" N ARG 7 169 " --> pdb=" O LYS 7 236 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLN 7 238 " --> pdb=" O VAL 7 167 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N VAL 7 167 " --> pdb=" O GLN 7 238 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE 7 276 " --> pdb=" O ALA 7 300 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ALA 7 300 " --> pdb=" O ILE 7 276 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU 7 278 " --> pdb=" O LEU 7 298 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU 7 298 " --> pdb=" O LEU 7 278 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE 7 280 " --> pdb=" O THR 7 296 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N THR 7 296 " --> pdb=" O ILE 7 280 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain '7' and resid 190 through 194 removed outlier: 4.397A pdb=" N THR 7 181 " --> pdb=" O GLN 7 223 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain '7' and resid 517 through 521 Processing sheet with id= AR, first strand: chain '7' and resid 416 through 420 Processing sheet with id= AS, first strand: chain '7' and resid 466 through 470 Processing sheet with id= AT, first strand: chain '7' and resid 174 through 179 removed outlier: 6.707A pdb=" N ARG 7 228 " --> pdb=" O VAL 7 178 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'A' and resid 229 through 233 removed outlier: 6.136A pdb=" N HIS A 282 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL A 232 " --> pdb=" O HIS A 282 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ARG A 284 " --> pdb=" O VAL A 232 " (cutoff:3.500A) No H-bonds generated for sheet with id= AU Processing sheet with id= AV, first strand: chain 'A' and resid 393 through 399 removed outlier: 3.556A pdb=" N SER A 314 " --> pdb=" O ARG A 377 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLN A 379 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N VAL A 312 " --> pdb=" O GLN A 379 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN A 304 " --> pdb=" O TYR A 418 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE A 417 " --> pdb=" O ALA A 441 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ALA A 441 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N HIS A 419 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ILE A 439 " --> pdb=" O HIS A 419 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'A' and resid 327 through 329 Processing sheet with id= AX, first strand: chain 'A' and resid 505 through 507 removed outlier: 3.656A pdb=" N HIS A 511 " --> pdb=" O PRO A 507 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'A' and resid 659 through 663 Processing sheet with id= AZ, first strand: chain 'A' and resid 559 through 562 Processing sheet with id= BA, first strand: chain 'A' and resid 608 through 612 Processing sheet with id= BB, first strand: chain 'A' and resid 858 through 861 Processing sheet with id= BC, first strand: chain 'A' and resid 319 through 324 removed outlier: 6.797A pdb=" N ILE A 369 " --> pdb=" O SER A 323 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'B' and resid 46 through 50 removed outlier: 6.644A pdb=" N TYR B 99 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N VAL B 49 " --> pdb=" O TYR B 99 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLY B 101 " --> pdb=" O VAL B 49 " (cutoff:3.500A) No H-bonds generated for sheet with id= BD Processing sheet with id= BE, first strand: chain 'B' and resid 110 through 112 removed outlier: 8.018A pdb=" N VAL B 111 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N CYS B 126 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N THR B 240 " --> pdb=" O ALA B 262 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ALA B 262 " --> pdb=" O THR B 240 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ARG B 242 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LEU B 260 " --> pdb=" O ARG B 242 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'B' and resid 154 through 158 Processing sheet with id= BG, first strand: chain 'B' and resid 216 through 221 removed outlier: 3.907A pdb=" N LYS B 133 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLN B 202 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N VAL B 131 " --> pdb=" O GLN B 202 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'B' and resid 481 through 485 removed outlier: 6.605A pdb=" N GLY B 404 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N LEU B 449 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL B 406 " --> pdb=" O LEU B 449 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ALA B 451 " --> pdb=" O VAL B 406 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE B 408 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N ASN B 453 " --> pdb=" O ILE B 408 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'B' and resid 381 through 384 Processing sheet with id= BJ, first strand: chain 'B' and resid 430 through 434 Processing sheet with id= BK, first strand: chain 'B' and resid 607 through 609 Processing sheet with id= BL, first strand: chain 'B' and resid 138 through 143 removed outlier: 6.406A pdb=" N VAL B 192 " --> pdb=" O VAL B 142 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'C' and resid 126 through 128 Processing sheet with id= BN, first strand: chain 'C' and resid 207 through 211 removed outlier: 6.509A pdb=" N GLN C 259 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N VAL C 210 " --> pdb=" O GLN C 259 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ARG C 261 " --> pdb=" O VAL C 210 " (cutoff:3.500A) No H-bonds generated for sheet with id= BN Processing sheet with id= BO, first strand: chain 'C' and resid 369 through 375 removed outlier: 6.057A pdb=" N GLN C 355 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N VAL C 289 " --> pdb=" O GLN C 355 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE C 393 " --> pdb=" O VAL C 418 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N VAL C 418 " --> pdb=" O ILE C 393 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ARG C 395 " --> pdb=" O ILE C 416 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ILE C 416 " --> pdb=" O ARG C 395 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL C 397 " --> pdb=" O THR C 414 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N THR C 414 " --> pdb=" O VAL C 397 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'C' and resid 312 through 316 Processing sheet with id= BQ, first strand: chain 'C' and resid 646 through 650 Processing sheet with id= BR, first strand: chain 'C' and resid 545 through 550 removed outlier: 3.615A pdb=" N GLN C 555 " --> pdb=" O ASP C 550 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'C' and resid 595 through 599 Processing sheet with id= BT, first strand: chain 'C' and resid 296 through 301 removed outlier: 6.545A pdb=" N LEU C 345 " --> pdb=" O GLN C 300 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'D' and resid 44 through 46 Processing sheet with id= BV, first strand: chain 'D' and resid 69 through 73 removed outlier: 6.238A pdb=" N GLN D 125 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL D 72 " --> pdb=" O GLN D 125 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET D 127 " --> pdb=" O VAL D 72 " (cutoff:3.500A) No H-bonds generated for sheet with id= BV Processing sheet with id= BW, first strand: chain 'D' and resid 244 through 250 removed outlier: 3.669A pdb=" N ALA D 157 " --> pdb=" O LYS D 228 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLN D 230 " --> pdb=" O ILE D 155 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N ILE D 155 " --> pdb=" O GLN D 230 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE D 268 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N VAL D 296 " --> pdb=" O ILE D 268 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER D 270 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ILE D 294 " --> pdb=" O SER D 270 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'D' and resid 170 through 172 Processing sheet with id= BY, first strand: chain 'D' and resid 516 through 520 removed outlier: 6.684A pdb=" N GLY D 440 " --> pdb=" O SER D 483 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N LEU D 485 " --> pdb=" O GLY D 440 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL D 442 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ALA D 487 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE D 444 " --> pdb=" O ALA D 487 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N ASN D 489 " --> pdb=" O ILE D 444 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'D' and resid 417 through 420 Processing sheet with id= CA, first strand: chain 'D' and resid 466 through 470 Processing sheet with id= CB, first strand: chain 'D' and resid 162 through 167 removed outlier: 6.663A pdb=" N LYS D 220 " --> pdb=" O THR D 166 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'E' and resid 60 through 64 removed outlier: 6.391A pdb=" N TYR E 111 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N VAL E 63 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ALA E 113 " --> pdb=" O VAL E 63 " (cutoff:3.500A) No H-bonds generated for sheet with id= CC Processing sheet with id= CD, first strand: chain 'E' and resid 241 through 247 removed outlier: 6.555A pdb=" N ARG E 207 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N THR E 144 " --> pdb=" O LYS E 205 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LYS E 205 " --> pdb=" O THR E 144 " (cutoff:3.500A) removed outlier: 14.300A pdb=" N TYR E 294 " --> pdb=" O SER E 223 " (cutoff:3.500A) removed outlier: 11.966A pdb=" N GLU E 225 " --> pdb=" O TYR E 294 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N LEU E 296 " --> pdb=" O GLU E 225 " (cutoff:3.500A) removed outlier: 8.732A pdb=" N ILE E 227 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N PHE E 298 " --> pdb=" O ILE E 227 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N THR E 245 " --> pdb=" O CYS E 301 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N VAL E 303 " --> pdb=" O ASP E 243 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASP E 243 " --> pdb=" O VAL E 303 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'E' and resid 155 through 158 removed outlier: 4.647A pdb=" N THR E 155 " --> pdb=" O ASP E 194 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'E' and resid 532 through 536 removed outlier: 3.636A pdb=" N GLY E 396 " --> pdb=" O ALA E 503 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain 'E' and resid 431 through 435 Processing sheet with id= CH, first strand: chain 'E' and resid 481 through 486 Processing sheet with id= CI, first strand: chain 'E' and resid 148 through 153 removed outlier: 7.239A pdb=" N ARG E 199 " --> pdb=" O VAL E 152 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 'F' and resid 47 through 51 removed outlier: 6.561A pdb=" N GLU F 135 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL F 50 " --> pdb=" O GLU F 135 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TYR F 137 " --> pdb=" O VAL F 50 " (cutoff:3.500A) No H-bonds generated for sheet with id= CJ Processing sheet with id= CK, first strand: chain 'F' and resid 252 through 258 removed outlier: 6.474A pdb=" N GLN F 238 " --> pdb=" O VAL F 167 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL F 167 " --> pdb=" O GLN F 238 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE F 276 " --> pdb=" O ALA F 300 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ALA F 300 " --> pdb=" O ILE F 276 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU F 278 " --> pdb=" O LEU F 298 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU F 298 " --> pdb=" O LEU F 278 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILE F 280 " --> pdb=" O THR F 296 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N THR F 296 " --> pdb=" O ILE F 280 " (cutoff:3.500A) Processing sheet with id= CL, first strand: chain 'F' and resid 190 through 194 removed outlier: 4.375A pdb=" N THR F 181 " --> pdb=" O GLN F 223 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain 'F' and resid 517 through 521 Processing sheet with id= CN, first strand: chain 'F' and resid 416 through 420 Processing sheet with id= CO, first strand: chain 'F' and resid 466 through 470 Processing sheet with id= CP, first strand: chain 'F' and resid 174 through 179 removed outlier: 6.576A pdb=" N ARG F 228 " --> pdb=" O VAL F 178 " (cutoff:3.500A) 2426 hydrogen bonds defined for protein. 7038 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 62 basepair parallelities 166 stacking parallelities Total time for adding SS restraints: 30.75 Time building geometry restraints manager: 26.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 13635 1.32 - 1.44: 16546 1.44 - 1.57: 39018 1.57 - 1.69: 426 1.69 - 1.82: 574 Bond restraints: 70199 Sorted by residual: bond pdb=" O3'A DA O 16 " pdb=" P A DA O 17 " ideal model delta sigma weight residual 1.607 1.412 0.195 1.50e-02 4.44e+03 1.70e+02 bond pdb=" O3'B DT O 16 " pdb=" P B DT O 17 " ideal model delta sigma weight residual 1.607 1.412 0.195 1.50e-02 4.44e+03 1.70e+02 bond pdb=" C4 ATP 31101 " pdb=" C5 ATP 31101 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.94e+01 bond pdb=" C4 ATP 4 903 " pdb=" C5 ATP 4 903 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.82e+01 bond pdb=" C4 ATP 7 803 " pdb=" C5 ATP 7 803 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.70e+01 ... (remaining 70194 not shown) Histogram of bond angle deviations from ideal: 93.68 - 103.00: 894 103.00 - 112.33: 37387 112.33 - 121.66: 41711 121.66 - 130.98: 15355 130.98 - 140.31: 334 Bond angle restraints: 95681 Sorted by residual: angle pdb=" PB ATP A1003 " pdb=" O3B ATP A1003 " pdb=" PG ATP A1003 " ideal model delta sigma weight residual 139.87 121.71 18.16 1.00e+00 1.00e+00 3.30e+02 angle pdb=" PB ATP 31101 " pdb=" O3B ATP 31101 " pdb=" PG ATP 31101 " ideal model delta sigma weight residual 139.87 123.12 16.75 1.00e+00 1.00e+00 2.81e+02 angle pdb=" PB ATP B1101 " pdb=" O3B ATP B1101 " pdb=" PG ATP B1101 " ideal model delta sigma weight residual 139.87 124.20 15.67 1.00e+00 1.00e+00 2.45e+02 angle pdb=" PA ATP A1003 " pdb=" O3A ATP A1003 " pdb=" PB ATP A1003 " ideal model delta sigma weight residual 136.83 121.81 15.02 1.00e+00 1.00e+00 2.25e+02 angle pdb=" PB ATP C 903 " pdb=" O3B ATP C 903 " pdb=" PG ATP C 903 " ideal model delta sigma weight residual 139.87 125.47 14.40 1.00e+00 1.00e+00 2.07e+02 ... (remaining 95676 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 41352 35.92 - 71.85: 1602 71.85 - 107.77: 78 107.77 - 143.69: 14 143.69 - 179.61: 12 Dihedral angle restraints: 43058 sinusoidal: 19300 harmonic: 23758 Sorted by residual: dihedral pdb=" CA ARG E 229 " pdb=" C ARG E 229 " pdb=" N ALA E 230 " pdb=" CA ALA E 230 " ideal model delta harmonic sigma weight residual -180.00 -141.42 -38.58 0 5.00e+00 4.00e-02 5.95e+01 dihedral pdb=" CA HIS E 782 " pdb=" C HIS E 782 " pdb=" N TYR E 783 " pdb=" CA TYR E 783 " ideal model delta harmonic sigma weight residual 180.00 141.94 38.06 0 5.00e+00 4.00e-02 5.80e+01 dihedral pdb=" CA ARG 6 229 " pdb=" C ARG 6 229 " pdb=" N ALA 6 230 " pdb=" CA ALA 6 230 " ideal model delta harmonic sigma weight residual 180.00 -144.59 -35.41 0 5.00e+00 4.00e-02 5.02e+01 ... (remaining 43055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 10295 0.120 - 0.239: 507 0.239 - 0.359: 17 0.359 - 0.478: 3 0.478 - 0.598: 1 Chirality restraints: 10823 Sorted by residual: chirality pdb=" CB VAL E 226 " pdb=" CA VAL E 226 " pdb=" CG1 VAL E 226 " pdb=" CG2 VAL E 226 " both_signs ideal model delta sigma weight residual False -2.63 -2.03 -0.60 2.00e-01 2.50e+01 8.93e+00 chirality pdb=" CB VAL 6 206 " pdb=" CA VAL 6 206 " pdb=" CG1 VAL 6 206 " pdb=" CG2 VAL 6 206 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.23e+00 chirality pdb=" CB VAL 6 226 " pdb=" CA VAL 6 226 " pdb=" CG1 VAL 6 226 " pdb=" CG2 VAL 6 226 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.90e+00 ... (remaining 10820 not shown) Planarity restraints: 11700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1'A DT S -36 " -0.038 2.00e-02 2.50e+03 6.59e-02 1.09e+02 pdb=" N1 A DT S -36 " 0.022 2.00e-02 2.50e+03 pdb=" C2 A DT S -36 " -0.061 2.00e-02 2.50e+03 pdb=" O2 A DT S -36 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A DT S -36 " 0.095 2.00e-02 2.50e+03 pdb=" C4 A DT S -36 " 0.106 2.00e-02 2.50e+03 pdb=" O4 A DT S -36 " -0.131 2.00e-02 2.50e+03 pdb=" C5 A DT S -36 " 0.009 2.00e-02 2.50e+03 pdb=" C7 A DT S -36 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A DT S -36 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 3 76 " -0.056 2.00e-02 2.50e+03 5.73e-02 5.75e+01 pdb=" CG PHE 3 76 " 0.132 2.00e-02 2.50e+03 pdb=" CD1 PHE 3 76 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 PHE 3 76 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE 3 76 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE 3 76 " -0.019 2.00e-02 2.50e+03 pdb=" CZ PHE 3 76 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1'A DA O 3 " 0.007 2.00e-02 2.50e+03 4.07e-02 4.55e+01 pdb=" N9 A DA O 3 " -0.006 2.00e-02 2.50e+03 pdb=" C8 A DA O 3 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A DA O 3 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A DA O 3 " -0.002 2.00e-02 2.50e+03 pdb=" C6 A DA O 3 " -0.078 2.00e-02 2.50e+03 pdb=" N6 A DA O 3 " 0.075 2.00e-02 2.50e+03 pdb=" N1 A DA O 3 " -0.057 2.00e-02 2.50e+03 pdb=" C2 A DA O 3 " 0.056 2.00e-02 2.50e+03 pdb=" N3 A DA O 3 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A DA O 3 " 0.000 2.00e-02 2.50e+03 ... (remaining 11697 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 292 2.42 - 3.04: 44025 3.04 - 3.66: 107211 3.66 - 4.28: 170965 4.28 - 4.90: 275600 Nonbonded interactions: 598093 Sorted by model distance: nonbonded pdb=" OG SER 3 352 " pdb="MG MG 31100 " model vdw 1.800 2.170 nonbonded pdb=" OG SER B 352 " pdb="MG MG B1100 " model vdw 1.807 2.170 nonbonded pdb="MG MG 7 802 " pdb=" O1B ATP 7 803 " model vdw 1.823 2.170 nonbonded pdb=" OG SER 4 517 " pdb="MG MG 4 902 " model vdw 1.836 2.170 nonbonded pdb=" OG SER C 517 " pdb="MG MG C 902 " model vdw 1.845 2.170 ... (remaining 598088 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '2' and (resid 176 through 272 or (resid 273 and (name N or name CA or na \ me C or name O or name CB )) or resid 274 or (resid 275 through 276 and (name N \ or name CA or name C or name O or name CB )) or resid 277 through 449 or resid 4 \ 56 through 690 or resid 713 through 826 or (resid 827 through 828 and (name N or \ name CA or name C or name O or name CB )) or resid 829 through 904 or resid 100 \ 1 through 1003)) selection = (chain 'A' and (resid 176 through 449 or resid 456 through 904 or resid 1001 thr \ ough 1003)) } ncs_group { reference = chain '3' selection = (chain 'B' and (resid 2 through 269 or (resid 270 and (name N or name CA or name \ C or name O or name CB )) or resid 271 through 536 or resid 545 through 557 or \ (resid 558 through 559 and (name N or name CA or name C or name O or name CB )) \ or resid 560 through 659 or resid 1100 through 1101)) } ncs_group { reference = (chain '4' and (resid 107 through 672 or resid 682 through 783 or resid 901 thro \ ugh 903)) selection = (chain 'C' and (resid 107 through 178 or (resid 179 through 180 and (name N or n \ ame CA or name C or name O or name CB )) or resid 181 through 781 or (resid 782 \ and (name N or name CA or name C or name O or name CB )) or resid 783 or resid 9 \ 01 through 903)) } ncs_group { reference = (chain '5' and (resid 2 through 203 or (resid 204 and (name N or name CA or name \ C or name O or name CB )) or resid 205 through 280 or resid 285 through 311 or \ resid 314 through 495 or (resid 496 through 497 and (name N or name CA or name C \ or name O or name CB )) or resid 498 through 673 or (resid 674 and (name N or n \ ame CA or name C or name O or name CB )) or resid 675 or (resid 676 and (name N \ or name CA or name C or name O or name CB )) or resid 677 through 678 or (resid \ 679 and (name N or name CA or name C or name O or name CB )) or resid 680 throug \ h 721 or (resid 722 and (name N or name CA or name C or name O or name CB )) or \ resid 723 through 734 or resid 801 through 803)) selection = (chain 'D' and (resid 2 through 600 or (resid 601 through 603 and (name N or nam \ e CA or name C or name O or name CB )) or resid 604 through 681 or (resid 682 an \ d (name N or name CA or name C or name O or name CB )) or resid 683 through 684 \ or (resid 685 and (name N or name CA or name C or name O or name CB )) or resid \ 686 through 698 or resid 704 through 723 or (resid 724 through 725 and (name N o \ r name CA or name C or name O or name CB )) or resid 726 or (resid 727 through 7 \ 28 and (name N or name CA or name C or name O or name CB )) or resid 729 through \ 731 or (resid 732 and (name N or name CA or name C or name O or name CB )) or r \ esid 733 through 734 or resid 801 through 803)) } ncs_group { reference = (chain '6' and (resid 16 through 314 or resid 319 through 662 or resid 719 throu \ gh 737 or resid 744 through 787 or resid 901 through 903)) selection = (chain 'E' and (resid 16 through 314 or resid 319 through 719 or (resid 720 and \ (name N or name CA or name C or name O or name CB )) or resid 721 through 787 or \ resid 901 through 903)) } ncs_group { reference = (chain '7' and (resid 3 through 24 or (resid 25 and (name N or name CA or name C \ or name O or name CB )) or resid 26 through 27 or (resid 28 and (name N or name \ CA or name C or name O or name CB )) or resid 29 through 94 or resid 96 through \ 645 or resid 801 through 803)) selection = (chain 'F' and (resid 3 through 94 or resid 96 through 311 or resid 319 through \ 645 or resid 801 through 803)) } 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=0.00 max=1.00 mean=0.97 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.720 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: 0.050 Extract box with map and model: 15.530 Check model and map are aligned: 0.740 Set scattering table: 0.480 Process input model: 179.170 Find NCS groups from input model: 5.960 Set up NCS constraints: 0.490 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:10.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 216.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 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 : 0.013 0.195 70199 Z= 0.873 Angle : 1.037 21.360 95681 Z= 0.589 Chirality : 0.061 0.598 10823 Planarity : 0.006 0.130 11700 Dihedral : 17.988 179.614 27646 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.01 % Allowed : 0.58 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.09), residues: 8066 helix: 0.04 (0.09), residues: 3188 sheet: -0.73 (0.13), residues: 1397 loop : -1.21 (0.10), residues: 3481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.005 TRP 6 614 HIS 0.026 0.002 HIS 7 301 PHE 0.132 0.004 PHE 3 76 TYR 0.051 0.003 TYR 6 347 ARG 0.024 0.001 ARG F 372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16132 Ramachandran restraints generated. 8066 Oldfield, 0 Emsley, 8066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16132 Ramachandran restraints generated. 8066 Oldfield, 0 Emsley, 8066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 7109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 720 time to evaluate : 5.710 Fit side-chains revert: symmetry clash REVERT: 2 621 GLN cc_start: 0.8727 (pt0) cc_final: 0.8522 (pt0) REVERT: 2 843 GLN cc_start: 0.7454 (tm-30) cc_final: 0.7137 (tm-30) REVERT: 3 493 GLN cc_start: 0.7670 (tt0) cc_final: 0.7434 (tt0) REVERT: 5 245 MET cc_start: 0.8839 (tpp) cc_final: 0.8610 (tpp) REVERT: 5 595 GLN cc_start: 0.8610 (tp-100) cc_final: 0.8169 (tp-100) REVERT: A 798 MET cc_start: 0.8958 (tmm) cc_final: 0.8694 (tmm) REVERT: B 178 ASP cc_start: 0.7698 (t70) cc_final: 0.7481 (t70) REVERT: C 606 GLN cc_start: 0.8416 (mt0) cc_final: 0.8171 (mt0) REVERT: D 215 MET cc_start: 0.9083 (mtp) cc_final: 0.8741 (mtp) outliers start: 1 outliers final: 1 residues processed: 721 average time/residue: 1.7939 time to fit residues: 1629.7538 Evaluate side-chains 539 residues out of total 7109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 538 time to evaluate : 5.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 502 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 818 random chunks: chunk 690 optimal weight: 0.9980 chunk 620 optimal weight: 2.9990 chunk 344 optimal weight: 0.9980 chunk 211 optimal weight: 6.9990 chunk 418 optimal weight: 5.9990 chunk 331 optimal weight: 0.9990 chunk 641 optimal weight: 0.2980 chunk 248 optimal weight: 6.9990 chunk 389 optimal weight: 0.9980 chunk 477 optimal weight: 0.2980 chunk 742 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 197 HIS 2 419 HIS ** 2 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 33 GLN 4 130 GLN 4 402 ASN ** 5 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 785 HIS 7 465 GLN 7 529 ASN A 549 GLN B 468 ASN C 126 GLN ** C 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 ASN C 593 GLN C 608 ASN D 524 HIS D 596 HIS E 440 HIS E 725 ASN F 196 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 70199 Z= 0.197 Angle : 0.643 16.076 95681 Z= 0.339 Chirality : 0.043 0.174 10823 Planarity : 0.004 0.052 11700 Dihedral : 18.293 179.518 11595 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.93 % Favored : 95.06 % Rotamer: Outliers : 0.99 % Allowed : 8.48 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.09), residues: 8066 helix: 0.71 (0.09), residues: 3165 sheet: -0.58 (0.13), residues: 1445 loop : -1.09 (0.10), residues: 3456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 593 HIS 0.013 0.001 HIS 5 540 PHE 0.037 0.001 PHE 3 76 TYR 0.021 0.001 TYR 6 347 ARG 0.009 0.000 ARG F 590 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16132 Ramachandran restraints generated. 8066 Oldfield, 0 Emsley, 8066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16132 Ramachandran restraints generated. 8066 Oldfield, 0 Emsley, 8066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 7109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 627 time to evaluate : 5.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 588 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7932 (mm-30) REVERT: 2 843 GLN cc_start: 0.7420 (tm-30) cc_final: 0.7039 (tm-30) REVERT: 2 882 ASP cc_start: 0.7673 (m-30) cc_final: 0.7234 (p0) REVERT: 2 888 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8004 (ttt) REVERT: 4 699 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7383 (mpp) REVERT: 5 245 MET cc_start: 0.8804 (tpp) cc_final: 0.8598 (tpp) REVERT: 5 504 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.8001 (pp) REVERT: A 224 LYS cc_start: 0.8666 (mtpm) cc_final: 0.8345 (mttp) REVERT: A 481 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8513 (pt) REVERT: A 838 GLN cc_start: 0.8871 (tm-30) cc_final: 0.8658 (tm-30) REVERT: B 195 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7849 (p0) REVERT: B 547 LYS cc_start: 0.8445 (ttmm) cc_final: 0.8214 (tppp) REVERT: D 215 MET cc_start: 0.8913 (mtp) cc_final: 0.8644 (mtp) REVERT: D 449 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8104 (mtpt) REVERT: D 502 ASP cc_start: 0.8061 (t70) cc_final: 0.7834 (t0) REVERT: E 466 ASP cc_start: 0.6826 (t0) cc_final: 0.6608 (t0) REVERT: E 478 GLU cc_start: 0.7898 (pp20) cc_final: 0.7676 (tp30) outliers start: 70 outliers final: 19 residues processed: 664 average time/residue: 1.6402 time to fit residues: 1402.3097 Evaluate side-chains 565 residues out of total 7109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 540 time to evaluate : 5.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 428 THR Chi-restraints excluded: chain 2 residue 752 LYS Chi-restraints excluded: chain 2 residue 888 MET Chi-restraints excluded: chain 3 residue 473 ASP Chi-restraints excluded: chain 3 residue 639 LEU Chi-restraints excluded: chain 3 residue 647 GLU Chi-restraints excluded: chain 4 residue 187 ASP Chi-restraints excluded: chain 4 residue 699 MET Chi-restraints excluded: chain 5 residue 44 VAL Chi-restraints excluded: chain 5 residue 430 GLU Chi-restraints excluded: chain 5 residue 504 ILE Chi-restraints excluded: chain 6 residue 226 VAL Chi-restraints excluded: chain 6 residue 390 ILE Chi-restraints excluded: chain 6 residue 441 GLU Chi-restraints excluded: chain 7 residue 242 ASP Chi-restraints excluded: chain 7 residue 307 ASN Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 360 CYS Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain D residue 449 LYS Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain F residue 324 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 818 random chunks: chunk 412 optimal weight: 8.9990 chunk 230 optimal weight: 4.9990 chunk 618 optimal weight: 4.9990 chunk 505 optimal weight: 8.9990 chunk 204 optimal weight: 6.9990 chunk 744 optimal weight: 1.9990 chunk 803 optimal weight: 1.9990 chunk 662 optimal weight: 9.9990 chunk 737 optimal weight: 0.9990 chunk 253 optimal weight: 9.9990 chunk 597 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 419 HIS 2 563 HIS ** 2 843 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 474 HIS 6 785 HIS ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN D 198 ASN D 524 HIS E 440 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 70199 Z= 0.349 Angle : 0.663 17.475 95681 Z= 0.345 Chirality : 0.045 0.246 10823 Planarity : 0.004 0.055 11700 Dihedral : 18.245 179.866 11593 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.58 % Favored : 94.40 % Rotamer: Outliers : 2.07 % Allowed : 11.48 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.09), residues: 8066 helix: 0.77 (0.09), residues: 3188 sheet: -0.62 (0.13), residues: 1474 loop : -1.02 (0.10), residues: 3404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 593 HIS 0.010 0.001 HIS 7 301 PHE 0.046 0.002 PHE 3 76 TYR 0.021 0.002 TYR 6 347 ARG 0.007 0.000 ARG F 590 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16132 Ramachandran restraints generated. 8066 Oldfield, 0 Emsley, 8066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16132 Ramachandran restraints generated. 8066 Oldfield, 0 Emsley, 8066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 7109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 582 time to evaluate : 5.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 620 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8480 (pp) REVERT: 2 843 GLN cc_start: 0.7435 (tm-30) cc_final: 0.7065 (tm-30) REVERT: 2 881 TYR cc_start: 0.7868 (m-80) cc_final: 0.7629 (m-80) REVERT: 2 882 ASP cc_start: 0.7690 (m-30) cc_final: 0.7222 (p0) REVERT: 3 417 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7304 (mmt) REVERT: 3 489 MET cc_start: 0.7814 (mtp) cc_final: 0.7601 (mtt) REVERT: 4 437 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6778 (pp20) REVERT: 4 461 ARG cc_start: 0.8236 (mtp85) cc_final: 0.8006 (mtt180) REVERT: 5 27 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7036 (mtp180) REVERT: 5 460 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7648 (tt0) REVERT: 5 504 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8050 (pp) REVERT: 5 531 MET cc_start: 0.7204 (tmm) cc_final: 0.6957 (tmm) REVERT: 5 671 MET cc_start: 0.4086 (mpt) cc_final: 0.3150 (ppp) REVERT: 7 125 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7787 (pm20) REVERT: 7 621 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7922 (mtt) REVERT: A 324 MET cc_start: 0.8411 (mmt) cc_final: 0.8178 (mmt) REVERT: A 838 GLN cc_start: 0.8810 (tm-30) cc_final: 0.8539 (tm-30) REVERT: B 195 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7524 (p0) REVERT: D 215 MET cc_start: 0.8988 (mtp) cc_final: 0.8692 (mtp) REVERT: D 449 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8059 (mtpt) REVERT: D 453 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7345 (p0) REVERT: D 502 ASP cc_start: 0.8065 (t70) cc_final: 0.7773 (t0) REVERT: E 73 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7779 (tm-30) REVERT: E 466 ASP cc_start: 0.7012 (t0) cc_final: 0.6739 (t0) REVERT: F 528 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7538 (m-30) outliers start: 146 outliers final: 63 residues processed: 670 average time/residue: 1.6310 time to fit residues: 1410.0864 Evaluate side-chains 610 residues out of total 7109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 534 time to evaluate : 5.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 291 VAL Chi-restraints excluded: chain 2 residue 352 CYS Chi-restraints excluded: chain 2 residue 461 VAL Chi-restraints excluded: chain 2 residue 620 LEU Chi-restraints excluded: chain 2 residue 752 LYS Chi-restraints excluded: chain 2 residue 833 LEU Chi-restraints excluded: chain 2 residue 839 LEU Chi-restraints excluded: chain 3 residue 11 GLU Chi-restraints excluded: chain 3 residue 195 ASP Chi-restraints excluded: chain 3 residue 224 ASP Chi-restraints excluded: chain 3 residue 417 MET Chi-restraints excluded: chain 3 residue 473 ASP Chi-restraints excluded: chain 3 residue 553 HIS Chi-restraints excluded: chain 3 residue 562 MET Chi-restraints excluded: chain 3 residue 603 MET Chi-restraints excluded: chain 3 residue 639 LEU Chi-restraints excluded: chain 3 residue 647 GLU Chi-restraints excluded: chain 4 residue 157 VAL Chi-restraints excluded: chain 4 residue 187 ASP Chi-restraints excluded: chain 4 residue 399 ILE Chi-restraints excluded: chain 4 residue 401 VAL Chi-restraints excluded: chain 4 residue 437 GLU Chi-restraints excluded: chain 5 residue 27 ARG Chi-restraints excluded: chain 5 residue 44 VAL Chi-restraints excluded: chain 5 residue 199 THR Chi-restraints excluded: chain 5 residue 430 GLU Chi-restraints excluded: chain 5 residue 460 GLU Chi-restraints excluded: chain 5 residue 504 ILE Chi-restraints excluded: chain 5 residue 532 LEU Chi-restraints excluded: chain 5 residue 568 VAL Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain 6 residue 206 VAL Chi-restraints excluded: chain 6 residue 226 VAL Chi-restraints excluded: chain 6 residue 254 VAL Chi-restraints excluded: chain 6 residue 278 THR Chi-restraints excluded: chain 6 residue 354 LEU Chi-restraints excluded: chain 6 residue 390 ILE Chi-restraints excluded: chain 6 residue 489 VAL Chi-restraints excluded: chain 6 residue 590 SER Chi-restraints excluded: chain 6 residue 661 THR Chi-restraints excluded: chain 7 residue 125 GLN Chi-restraints excluded: chain 7 residue 242 ASP Chi-restraints excluded: chain 7 residue 405 THR Chi-restraints excluded: chain 7 residue 621 MET Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 360 CYS Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 638 HIS Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 449 LYS Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 384 THR Chi-restraints excluded: chain E residue 766 LEU Chi-restraints excluded: chain E residue 788 ILE Chi-restraints excluded: chain F residue 235 MET Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain F residue 528 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 818 random chunks: chunk 735 optimal weight: 4.9990 chunk 559 optimal weight: 0.0040 chunk 386 optimal weight: 0.4980 chunk 82 optimal weight: 0.3980 chunk 355 optimal weight: 0.8980 chunk 499 optimal weight: 3.9990 chunk 746 optimal weight: 0.9980 chunk 790 optimal weight: 4.9990 chunk 390 optimal weight: 0.8980 chunk 707 optimal weight: 0.9990 chunk 213 optimal weight: 2.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 355 GLN ** 5 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 785 HIS 7 223 GLN ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN D 198 ASN D 524 HIS E 209 GLN E 212 GLN E 440 HIS E 725 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 70199 Z= 0.166 Angle : 0.581 14.747 95681 Z= 0.305 Chirality : 0.042 0.193 10823 Planarity : 0.004 0.048 11700 Dihedral : 17.994 179.952 11593 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.69 % Favored : 95.30 % Rotamer: Outliers : 1.97 % Allowed : 13.14 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.09), residues: 8066 helix: 1.04 (0.09), residues: 3180 sheet: -0.50 (0.13), residues: 1471 loop : -0.96 (0.10), residues: 3415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 614 HIS 0.009 0.001 HIS 5 540 PHE 0.026 0.001 PHE D 393 TYR 0.015 0.001 TYR 2 535 ARG 0.007 0.000 ARG 7 325 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16132 Ramachandran restraints generated. 8066 Oldfield, 0 Emsley, 8066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16132 Ramachandran restraints generated. 8066 Oldfield, 0 Emsley, 8066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 7109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 598 time to evaluate : 5.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 481 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8158 (pt) REVERT: 2 620 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8355 (pp) REVERT: 2 671 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8398 (mp10) REVERT: 2 820 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7313 (ppt-90) REVERT: 2 837 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7991 (mtpt) REVERT: 2 843 GLN cc_start: 0.7437 (tm-30) cc_final: 0.7037 (tm-30) REVERT: 2 881 TYR cc_start: 0.7920 (m-80) cc_final: 0.7553 (m-80) REVERT: 2 882 ASP cc_start: 0.7663 (m-30) cc_final: 0.7215 (p0) REVERT: 3 257 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.7321 (mtp-110) REVERT: 3 417 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.7174 (mmt) REVERT: 3 489 MET cc_start: 0.7609 (mtp) cc_final: 0.7304 (mtt) REVERT: 4 437 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6730 (pp20) REVERT: 5 504 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8032 (pp) REVERT: 5 531 MET cc_start: 0.7264 (tmm) cc_final: 0.7013 (tmm) REVERT: 6 771 ARG cc_start: 0.5786 (OUTLIER) cc_final: 0.4423 (tmt90) REVERT: 7 125 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7830 (pm20) REVERT: 7 561 ARG cc_start: 0.8146 (mtp180) cc_final: 0.7872 (mtp-110) REVERT: 7 621 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7858 (mtt) REVERT: A 224 LYS cc_start: 0.8633 (mtpm) cc_final: 0.8202 (mttp) REVERT: A 481 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8540 (pt) REVERT: A 651 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7244 (mm-30) REVERT: A 812 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7628 (ttp80) REVERT: A 838 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8501 (tm-30) REVERT: B 547 LYS cc_start: 0.8464 (ttmm) cc_final: 0.8180 (tppp) REVERT: C 591 MET cc_start: 0.9058 (mtp) cc_final: 0.8507 (mtm) REVERT: C 600 LYS cc_start: 0.6274 (ptpt) cc_final: 0.4963 (mptm) REVERT: D 215 MET cc_start: 0.8897 (mtp) cc_final: 0.8596 (mtp) REVERT: D 449 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8033 (mtpt) REVERT: D 502 ASP cc_start: 0.8059 (t70) cc_final: 0.7771 (t0) REVERT: F 528 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7534 (m-30) outliers start: 139 outliers final: 56 residues processed: 694 average time/residue: 1.6028 time to fit residues: 1451.8993 Evaluate side-chains 611 residues out of total 7109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 539 time to evaluate : 5.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 291 VAL Chi-restraints excluded: chain 2 residue 347 VAL Chi-restraints excluded: chain 2 residue 352 CYS Chi-restraints excluded: chain 2 residue 428 THR Chi-restraints excluded: chain 2 residue 481 ILE Chi-restraints excluded: chain 2 residue 620 LEU Chi-restraints excluded: chain 2 residue 621 GLN Chi-restraints excluded: chain 2 residue 671 GLN Chi-restraints excluded: chain 2 residue 820 ARG Chi-restraints excluded: chain 2 residue 833 LEU Chi-restraints excluded: chain 2 residue 837 LYS Chi-restraints excluded: chain 2 residue 888 MET Chi-restraints excluded: chain 3 residue 11 GLU Chi-restraints excluded: chain 3 residue 257 ARG Chi-restraints excluded: chain 3 residue 273 GLN Chi-restraints excluded: chain 3 residue 386 GLN Chi-restraints excluded: chain 3 residue 417 MET Chi-restraints excluded: chain 3 residue 473 ASP Chi-restraints excluded: chain 3 residue 639 LEU Chi-restraints excluded: chain 3 residue 647 GLU Chi-restraints excluded: chain 4 residue 157 VAL Chi-restraints excluded: chain 4 residue 187 ASP Chi-restraints excluded: chain 4 residue 399 ILE Chi-restraints excluded: chain 4 residue 401 VAL Chi-restraints excluded: chain 4 residue 437 GLU Chi-restraints excluded: chain 5 residue 44 VAL Chi-restraints excluded: chain 5 residue 430 GLU Chi-restraints excluded: chain 5 residue 504 ILE Chi-restraints excluded: chain 5 residue 532 LEU Chi-restraints excluded: chain 5 residue 721 ILE Chi-restraints excluded: chain 6 residue 106 LEU Chi-restraints excluded: chain 6 residue 168 VAL Chi-restraints excluded: chain 6 residue 206 VAL Chi-restraints excluded: chain 6 residue 226 VAL Chi-restraints excluded: chain 6 residue 278 THR Chi-restraints excluded: chain 6 residue 390 ILE Chi-restraints excluded: chain 6 residue 771 ARG Chi-restraints excluded: chain 7 residue 125 GLN Chi-restraints excluded: chain 7 residue 242 ASP Chi-restraints excluded: chain 7 residue 307 ASN Chi-restraints excluded: chain 7 residue 405 THR Chi-restraints excluded: chain 7 residue 590 ARG Chi-restraints excluded: chain 7 residue 621 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 812 ARG Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 638 HIS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 449 LYS Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 782 HIS Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain F residue 528 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 818 random chunks: chunk 658 optimal weight: 0.7980 chunk 448 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 588 optimal weight: 4.9990 chunk 326 optimal weight: 4.9990 chunk 674 optimal weight: 0.3980 chunk 546 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 403 optimal weight: 0.9980 chunk 709 optimal weight: 1.9990 chunk 199 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 419 HIS ** 5 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 750 ASN 6 785 HIS ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 ASN D 198 ASN D 525 ASN E 440 HIS F 18 GLN F 87 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 70199 Z= 0.179 Angle : 0.574 13.971 95681 Z= 0.300 Chirality : 0.042 0.200 10823 Planarity : 0.004 0.047 11700 Dihedral : 17.857 178.335 11593 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.74 % Favored : 95.25 % Rotamer: Outliers : 2.13 % Allowed : 14.15 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.09), residues: 8066 helix: 1.14 (0.09), residues: 3185 sheet: -0.47 (0.13), residues: 1488 loop : -0.90 (0.10), residues: 3393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 614 HIS 0.013 0.001 HIS D 524 PHE 0.025 0.001 PHE D 393 TYR 0.015 0.001 TYR 2 535 ARG 0.007 0.000 ARG E 468 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16132 Ramachandran restraints generated. 8066 Oldfield, 0 Emsley, 8066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16132 Ramachandran restraints generated. 8066 Oldfield, 0 Emsley, 8066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 7109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 585 time to evaluate : 6.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 481 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8137 (pt) REVERT: 2 620 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8327 (pp) REVERT: 2 752 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.6615 (mmpt) REVERT: 2 820 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7313 (ppt-90) REVERT: 2 843 GLN cc_start: 0.7448 (tm-30) cc_final: 0.7039 (tm-30) REVERT: 2 882 ASP cc_start: 0.7704 (m-30) cc_final: 0.7261 (p0) REVERT: 2 888 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7913 (mmm) REVERT: 3 257 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7340 (mtp-110) REVERT: 4 461 ARG cc_start: 0.8291 (mtp85) cc_final: 0.8085 (mtt180) REVERT: 4 754 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: 5 27 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7529 (mtp85) REVERT: 5 504 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.7984 (pp) REVERT: 5 671 MET cc_start: 0.3983 (mpt) cc_final: 0.2666 (ppp) REVERT: 6 771 ARG cc_start: 0.5782 (OUTLIER) cc_final: 0.4537 (tmt90) REVERT: 7 125 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7840 (pm20) REVERT: 7 242 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7795 (p0) REVERT: A 224 LYS cc_start: 0.8698 (mtpm) cc_final: 0.8354 (mttt) REVERT: A 812 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7601 (ttp80) REVERT: A 838 GLN cc_start: 0.8801 (tm-30) cc_final: 0.8486 (tm-30) REVERT: C 591 MET cc_start: 0.9067 (mtp) cc_final: 0.8586 (mtm) REVERT: D 215 MET cc_start: 0.8887 (mtp) cc_final: 0.8600 (mtp) REVERT: D 653 LEU cc_start: 0.6650 (OUTLIER) cc_final: 0.5679 (mm) REVERT: D 715 MET cc_start: 0.6654 (tpp) cc_final: 0.6041 (pp-130) REVERT: F 528 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7528 (m-30) REVERT: F 565 MET cc_start: 0.8466 (ptp) cc_final: 0.8192 (ptm) outliers start: 150 outliers final: 62 residues processed: 686 average time/residue: 1.5514 time to fit residues: 1388.9061 Evaluate side-chains 625 residues out of total 7109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 548 time to evaluate : 5.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 291 VAL Chi-restraints excluded: chain 2 residue 347 VAL Chi-restraints excluded: chain 2 residue 352 CYS Chi-restraints excluded: chain 2 residue 428 THR Chi-restraints excluded: chain 2 residue 481 ILE Chi-restraints excluded: chain 2 residue 565 VAL Chi-restraints excluded: chain 2 residue 620 LEU Chi-restraints excluded: chain 2 residue 752 LYS Chi-restraints excluded: chain 2 residue 820 ARG Chi-restraints excluded: chain 2 residue 833 LEU Chi-restraints excluded: chain 2 residue 888 MET Chi-restraints excluded: chain 3 residue 226 VAL Chi-restraints excluded: chain 3 residue 257 ARG Chi-restraints excluded: chain 3 residue 273 GLN Chi-restraints excluded: chain 3 residue 386 GLN Chi-restraints excluded: chain 3 residue 473 ASP Chi-restraints excluded: chain 3 residue 555 THR Chi-restraints excluded: chain 3 residue 639 LEU Chi-restraints excluded: chain 4 residue 157 VAL Chi-restraints excluded: chain 4 residue 187 ASP Chi-restraints excluded: chain 4 residue 327 VAL Chi-restraints excluded: chain 4 residue 399 ILE Chi-restraints excluded: chain 4 residue 401 VAL Chi-restraints excluded: chain 4 residue 754 GLU Chi-restraints excluded: chain 5 residue 27 ARG Chi-restraints excluded: chain 5 residue 44 VAL Chi-restraints excluded: chain 5 residue 430 GLU Chi-restraints excluded: chain 5 residue 504 ILE Chi-restraints excluded: chain 5 residue 721 ILE Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain 6 residue 168 VAL Chi-restraints excluded: chain 6 residue 206 VAL Chi-restraints excluded: chain 6 residue 226 VAL Chi-restraints excluded: chain 6 residue 233 VAL Chi-restraints excluded: chain 6 residue 278 THR Chi-restraints excluded: chain 6 residue 354 LEU Chi-restraints excluded: chain 6 residue 390 ILE Chi-restraints excluded: chain 6 residue 489 VAL Chi-restraints excluded: chain 6 residue 771 ARG Chi-restraints excluded: chain 7 residue 125 GLN Chi-restraints excluded: chain 7 residue 242 ASP Chi-restraints excluded: chain 7 residue 405 THR Chi-restraints excluded: chain 7 residue 590 ARG Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 812 ARG Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 638 HIS Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain D residue 653 LEU Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 782 HIS Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain F residue 528 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 818 random chunks: chunk 266 optimal weight: 8.9990 chunk 712 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 464 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 791 optimal weight: 3.9990 chunk 657 optimal weight: 4.9990 chunk 366 optimal weight: 1.9990 chunk 65 optimal weight: 0.0980 chunk 261 optimal weight: 3.9990 chunk 415 optimal weight: 8.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 671 GLN 2 829 ASN ** 5 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 785 HIS ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 ASN E 440 HIS ** F 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 70199 Z= 0.313 Angle : 0.630 15.738 95681 Z= 0.326 Chirality : 0.044 0.217 10823 Planarity : 0.004 0.049 11700 Dihedral : 17.917 179.842 11593 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.09 % Favored : 94.90 % Rotamer: Outliers : 2.49 % Allowed : 14.46 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.09), residues: 8066 helix: 1.08 (0.09), residues: 3186 sheet: -0.51 (0.13), residues: 1503 loop : -0.92 (0.10), residues: 3377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 614 HIS 0.019 0.001 HIS 5 540 PHE 0.032 0.002 PHE 3 76 TYR 0.017 0.002 TYR 3 32 ARG 0.008 0.000 ARG E 468 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16132 Ramachandran restraints generated. 8066 Oldfield, 0 Emsley, 8066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16132 Ramachandran restraints generated. 8066 Oldfield, 0 Emsley, 8066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 7109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 575 time to evaluate : 5.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 481 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8236 (pt) REVERT: 2 620 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8426 (pp) REVERT: 2 671 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8324 (mp-120) REVERT: 2 752 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.6621 (mmpt) REVERT: 2 820 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7314 (ppt-90) REVERT: 2 843 GLN cc_start: 0.7465 (tm-30) cc_final: 0.7035 (tm-30) REVERT: 2 882 ASP cc_start: 0.7730 (m-30) cc_final: 0.7265 (p0) REVERT: 3 33 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.7698 (tm130) REVERT: 3 257 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7375 (mtp-110) REVERT: 3 619 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7557 (mp0) REVERT: 4 754 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7755 (mp0) REVERT: 5 128 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8470 (mt) REVERT: 5 504 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8016 (pp) REVERT: 5 671 MET cc_start: 0.4153 (mpt) cc_final: 0.2985 (ppp) REVERT: 6 771 ARG cc_start: 0.5807 (OUTLIER) cc_final: 0.4523 (tmt90) REVERT: 7 125 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7800 (pm20) REVERT: 7 220 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8071 (pp) REVERT: A 324 MET cc_start: 0.8397 (mmt) cc_final: 0.8151 (mmt) REVERT: A 812 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7591 (ttp80) REVERT: A 838 GLN cc_start: 0.8809 (tm-30) cc_final: 0.8489 (tm-30) REVERT: B 38 GLU cc_start: 0.7406 (tp30) cc_final: 0.7099 (tp30) REVERT: C 288 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8617 (ttm) REVERT: C 591 MET cc_start: 0.9012 (mtp) cc_final: 0.8583 (mtm) REVERT: D 215 MET cc_start: 0.8969 (mtp) cc_final: 0.8642 (mtp) REVERT: D 453 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7297 (p0) REVERT: D 715 MET cc_start: 0.6708 (tpp) cc_final: 0.6076 (pp-130) REVERT: E 73 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7765 (tm-30) REVERT: F 172 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.6888 (mm-30) REVERT: F 528 ASP cc_start: 0.7843 (OUTLIER) cc_final: 0.7560 (m-30) REVERT: F 565 MET cc_start: 0.8494 (ptp) cc_final: 0.8206 (ptm) outliers start: 176 outliers final: 92 residues processed: 695 average time/residue: 1.6040 time to fit residues: 1446.7831 Evaluate side-chains 653 residues out of total 7109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 541 time to evaluate : 5.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 291 VAL Chi-restraints excluded: chain 2 residue 347 VAL Chi-restraints excluded: chain 2 residue 352 CYS Chi-restraints excluded: chain 2 residue 428 THR Chi-restraints excluded: chain 2 residue 481 ILE Chi-restraints excluded: chain 2 residue 524 ASP Chi-restraints excluded: chain 2 residue 565 VAL Chi-restraints excluded: chain 2 residue 620 LEU Chi-restraints excluded: chain 2 residue 621 GLN Chi-restraints excluded: chain 2 residue 671 GLN Chi-restraints excluded: chain 2 residue 752 LYS Chi-restraints excluded: chain 2 residue 820 ARG Chi-restraints excluded: chain 2 residue 833 LEU Chi-restraints excluded: chain 2 residue 839 LEU Chi-restraints excluded: chain 2 residue 860 VAL Chi-restraints excluded: chain 3 residue 33 GLN Chi-restraints excluded: chain 3 residue 39 LEU Chi-restraints excluded: chain 3 residue 93 LYS Chi-restraints excluded: chain 3 residue 226 VAL Chi-restraints excluded: chain 3 residue 257 ARG Chi-restraints excluded: chain 3 residue 339 ILE Chi-restraints excluded: chain 3 residue 361 THR Chi-restraints excluded: chain 3 residue 386 GLN Chi-restraints excluded: chain 3 residue 473 ASP Chi-restraints excluded: chain 3 residue 555 THR Chi-restraints excluded: chain 3 residue 562 MET Chi-restraints excluded: chain 3 residue 603 MET Chi-restraints excluded: chain 3 residue 619 GLU Chi-restraints excluded: chain 3 residue 639 LEU Chi-restraints excluded: chain 4 residue 157 VAL Chi-restraints excluded: chain 4 residue 187 ASP Chi-restraints excluded: chain 4 residue 295 LEU Chi-restraints excluded: chain 4 residue 399 ILE Chi-restraints excluded: chain 4 residue 401 VAL Chi-restraints excluded: chain 4 residue 754 GLU Chi-restraints excluded: chain 5 residue 44 VAL Chi-restraints excluded: chain 5 residue 94 GLU Chi-restraints excluded: chain 5 residue 109 GLU Chi-restraints excluded: chain 5 residue 128 LEU Chi-restraints excluded: chain 5 residue 199 THR Chi-restraints excluded: chain 5 residue 266 MET Chi-restraints excluded: chain 5 residue 430 GLU Chi-restraints excluded: chain 5 residue 504 ILE Chi-restraints excluded: chain 5 residue 568 VAL Chi-restraints excluded: chain 5 residue 670 GLU Chi-restraints excluded: chain 5 residue 721 ILE Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain 6 residue 168 VAL Chi-restraints excluded: chain 6 residue 206 VAL Chi-restraints excluded: chain 6 residue 226 VAL Chi-restraints excluded: chain 6 residue 233 VAL Chi-restraints excluded: chain 6 residue 278 THR Chi-restraints excluded: chain 6 residue 354 LEU Chi-restraints excluded: chain 6 residue 371 MET Chi-restraints excluded: chain 6 residue 390 ILE Chi-restraints excluded: chain 6 residue 489 VAL Chi-restraints excluded: chain 6 residue 661 THR Chi-restraints excluded: chain 6 residue 771 ARG Chi-restraints excluded: chain 7 residue 125 GLN Chi-restraints excluded: chain 7 residue 220 LEU Chi-restraints excluded: chain 7 residue 242 ASP Chi-restraints excluded: chain 7 residue 307 ASN Chi-restraints excluded: chain 7 residue 391 LEU Chi-restraints excluded: chain 7 residue 405 THR Chi-restraints excluded: chain 7 residue 590 ARG Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 812 ARG Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 360 CYS Chi-restraints excluded: chain B residue 417 MET Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 499 LYS Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 638 HIS Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain D residue 181 ASN Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 453 ASP Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 782 HIS Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 172 GLU Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain F residue 528 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 818 random chunks: chunk 763 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 450 optimal weight: 0.3980 chunk 577 optimal weight: 5.9990 chunk 447 optimal weight: 3.9990 chunk 666 optimal weight: 4.9990 chunk 441 optimal weight: 5.9990 chunk 788 optimal weight: 1.9990 chunk 493 optimal weight: 0.0270 chunk 480 optimal weight: 3.9990 chunk 364 optimal weight: 0.0770 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 671 GLN 2 829 ASN ** 2 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 130 GLN 4 654 GLN ** 5 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 785 HIS 7 223 GLN ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 ASN ** D 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 GLN E 440 HIS E 725 ASN F 18 GLN F 87 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 70199 Z= 0.173 Angle : 0.580 13.882 95681 Z= 0.303 Chirality : 0.042 0.224 10823 Planarity : 0.004 0.047 11700 Dihedral : 17.736 179.755 11593 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.73 % Favored : 95.26 % Rotamer: Outliers : 2.00 % Allowed : 15.51 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.09), residues: 8066 helix: 1.17 (0.09), residues: 3191 sheet: -0.45 (0.13), residues: 1475 loop : -0.86 (0.10), residues: 3400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 614 HIS 0.018 0.001 HIS 5 540 PHE 0.024 0.001 PHE D 393 TYR 0.018 0.001 TYR 2 881 ARG 0.010 0.000 ARG E 468 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16132 Ramachandran restraints generated. 8066 Oldfield, 0 Emsley, 8066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16132 Ramachandran restraints generated. 8066 Oldfield, 0 Emsley, 8066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 7109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 589 time to evaluate : 5.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 188 MET cc_start: 0.6554 (mtt) cc_final: 0.6063 (ptp) REVERT: 2 481 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8137 (pt) REVERT: 2 620 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8298 (pp) REVERT: 2 752 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.6614 (mmpt) REVERT: 2 820 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.7255 (ppt-90) REVERT: 2 843 GLN cc_start: 0.7501 (tm-30) cc_final: 0.7092 (tm-30) REVERT: 2 871 GLN cc_start: 0.7529 (mt0) cc_final: 0.7267 (mt0) REVERT: 2 882 ASP cc_start: 0.7661 (m-30) cc_final: 0.7216 (p0) REVERT: 3 33 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.7764 (tm130) REVERT: 4 754 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7720 (mp0) REVERT: 5 27 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7107 (mtp180) REVERT: 5 504 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.7985 (pp) REVERT: 5 671 MET cc_start: 0.4351 (mpt) cc_final: 0.3235 (ppp) REVERT: 6 771 ARG cc_start: 0.5789 (OUTLIER) cc_final: 0.4622 (tmt90) REVERT: 7 125 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7841 (pm20) REVERT: 7 220 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8121 (pt) REVERT: 7 446 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7936 (mm-30) REVERT: A 224 LYS cc_start: 0.8648 (mtpm) cc_final: 0.8297 (mttt) REVERT: A 838 GLN cc_start: 0.8805 (tm-30) cc_final: 0.8479 (tm-30) REVERT: B 38 GLU cc_start: 0.7501 (tp30) cc_final: 0.7206 (tp30) REVERT: C 591 MET cc_start: 0.9056 (mtp) cc_final: 0.8447 (mtm) REVERT: C 600 LYS cc_start: 0.6276 (ptpt) cc_final: 0.4976 (mptm) REVERT: D 215 MET cc_start: 0.8901 (mtp) cc_final: 0.8669 (mtp) REVERT: D 715 MET cc_start: 0.6829 (tpp) cc_final: 0.6219 (pp-130) REVERT: E 73 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7720 (tm-30) REVERT: F 565 MET cc_start: 0.8534 (ptp) cc_final: 0.8242 (ptm) outliers start: 141 outliers final: 82 residues processed: 694 average time/residue: 1.7282 time to fit residues: 1538.3623 Evaluate side-chains 643 residues out of total 7109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 549 time to evaluate : 5.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 347 VAL Chi-restraints excluded: chain 2 residue 352 CYS Chi-restraints excluded: chain 2 residue 428 THR Chi-restraints excluded: chain 2 residue 481 ILE Chi-restraints excluded: chain 2 residue 524 ASP Chi-restraints excluded: chain 2 residue 565 VAL Chi-restraints excluded: chain 2 residue 620 LEU Chi-restraints excluded: chain 2 residue 621 GLN Chi-restraints excluded: chain 2 residue 752 LYS Chi-restraints excluded: chain 2 residue 767 ILE Chi-restraints excluded: chain 2 residue 820 ARG Chi-restraints excluded: chain 2 residue 833 LEU Chi-restraints excluded: chain 2 residue 839 LEU Chi-restraints excluded: chain 2 residue 860 VAL Chi-restraints excluded: chain 2 residue 888 MET Chi-restraints excluded: chain 3 residue 33 GLN Chi-restraints excluded: chain 3 residue 386 GLN Chi-restraints excluded: chain 3 residue 473 ASP Chi-restraints excluded: chain 3 residue 555 THR Chi-restraints excluded: chain 3 residue 639 LEU Chi-restraints excluded: chain 4 residue 157 VAL Chi-restraints excluded: chain 4 residue 187 ASP Chi-restraints excluded: chain 4 residue 327 VAL Chi-restraints excluded: chain 4 residue 399 ILE Chi-restraints excluded: chain 4 residue 401 VAL Chi-restraints excluded: chain 4 residue 552 GLU Chi-restraints excluded: chain 4 residue 754 GLU Chi-restraints excluded: chain 5 residue 27 ARG Chi-restraints excluded: chain 5 residue 44 VAL Chi-restraints excluded: chain 5 residue 109 GLU Chi-restraints excluded: chain 5 residue 128 LEU Chi-restraints excluded: chain 5 residue 430 GLU Chi-restraints excluded: chain 5 residue 504 ILE Chi-restraints excluded: chain 5 residue 670 GLU Chi-restraints excluded: chain 5 residue 721 ILE Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain 6 residue 168 VAL Chi-restraints excluded: chain 6 residue 206 VAL Chi-restraints excluded: chain 6 residue 226 VAL Chi-restraints excluded: chain 6 residue 233 VAL Chi-restraints excluded: chain 6 residue 278 THR Chi-restraints excluded: chain 6 residue 390 ILE Chi-restraints excluded: chain 6 residue 469 ASP Chi-restraints excluded: chain 6 residue 479 GLN Chi-restraints excluded: chain 6 residue 489 VAL Chi-restraints excluded: chain 6 residue 661 THR Chi-restraints excluded: chain 6 residue 771 ARG Chi-restraints excluded: chain 7 residue 125 GLN Chi-restraints excluded: chain 7 residue 220 LEU Chi-restraints excluded: chain 7 residue 242 ASP Chi-restraints excluded: chain 7 residue 405 THR Chi-restraints excluded: chain 7 residue 531 LEU Chi-restraints excluded: chain 7 residue 590 ARG Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 360 CYS Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 499 LYS Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 638 HIS Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 631 MET Chi-restraints excluded: chain E residue 731 LEU Chi-restraints excluded: chain E residue 782 HIS Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain F residue 458 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 818 random chunks: chunk 487 optimal weight: 0.5980 chunk 314 optimal weight: 4.9990 chunk 470 optimal weight: 20.0000 chunk 237 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 501 optimal weight: 0.4980 chunk 537 optimal weight: 2.9990 chunk 389 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 619 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 671 GLN 2 829 ASN 2 855 GLN ** 3 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 785 HIS ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 ASN ** D 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 GLN E 440 HIS F 18 GLN F 87 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 70199 Z= 0.212 Angle : 0.590 14.370 95681 Z= 0.306 Chirality : 0.042 0.211 10823 Planarity : 0.004 0.047 11700 Dihedral : 17.687 179.718 11593 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.83 % Favored : 95.16 % Rotamer: Outliers : 2.04 % Allowed : 15.63 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.09), residues: 8066 helix: 1.21 (0.09), residues: 3186 sheet: -0.50 (0.13), residues: 1515 loop : -0.82 (0.11), residues: 3365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 614 HIS 0.019 0.001 HIS 5 540 PHE 0.033 0.001 PHE D 51 TYR 0.015 0.001 TYR 3 32 ARG 0.012 0.000 ARG 2 887 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16132 Ramachandran restraints generated. 8066 Oldfield, 0 Emsley, 8066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16132 Ramachandran restraints generated. 8066 Oldfield, 0 Emsley, 8066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 7109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 578 time to evaluate : 5.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 188 MET cc_start: 0.6611 (mtt) cc_final: 0.6109 (ptp) REVERT: 2 481 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8156 (pt) REVERT: 2 588 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7958 (mm-30) REVERT: 2 620 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8317 (pp) REVERT: 2 752 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.6541 (mmpt) REVERT: 2 820 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.7268 (ppt-90) REVERT: 2 843 GLN cc_start: 0.7480 (tm-30) cc_final: 0.7072 (tm-30) REVERT: 2 871 GLN cc_start: 0.7558 (mt0) cc_final: 0.7302 (mt0) REVERT: 2 882 ASP cc_start: 0.7717 (m-30) cc_final: 0.7259 (p0) REVERT: 3 33 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.7780 (tm130) REVERT: 3 257 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7333 (mtp-110) REVERT: 5 27 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7550 (mtp85) REVERT: 5 128 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8494 (mt) REVERT: 5 504 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8028 (pp) REVERT: 5 671 MET cc_start: 0.4448 (mpt) cc_final: 0.3372 (ppp) REVERT: 6 736 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7472 (pp20) REVERT: 6 771 ARG cc_start: 0.5796 (OUTLIER) cc_final: 0.4582 (tmt90) REVERT: 7 125 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7832 (pm20) REVERT: 7 210 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7834 (tt0) REVERT: 7 220 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8024 (pp) REVERT: A 224 LYS cc_start: 0.8662 (mtpm) cc_final: 0.8319 (mttp) REVERT: A 838 GLN cc_start: 0.8815 (tm-30) cc_final: 0.8492 (tm-30) REVERT: B 38 GLU cc_start: 0.7483 (tp30) cc_final: 0.7182 (tp30) REVERT: C 591 MET cc_start: 0.9059 (mtp) cc_final: 0.8534 (mtm) REVERT: D 215 MET cc_start: 0.8901 (mtp) cc_final: 0.8617 (mtp) REVERT: D 449 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8091 (mtpt) REVERT: D 715 MET cc_start: 0.6850 (tpp) cc_final: 0.6230 (pp-130) REVERT: E 73 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7745 (tm-30) REVERT: F 118 MET cc_start: 0.7112 (ttp) cc_final: 0.6752 (ttt) REVERT: F 375 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8520 (mt) REVERT: F 460 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8192 (tt0) REVERT: F 528 ASP cc_start: 0.7833 (OUTLIER) cc_final: 0.7556 (m-30) REVERT: F 565 MET cc_start: 0.8497 (ptp) cc_final: 0.8217 (ptm) outliers start: 144 outliers final: 82 residues processed: 680 average time/residue: 1.6080 time to fit residues: 1424.4482 Evaluate side-chains 652 residues out of total 7109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 551 time to evaluate : 5.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 291 VAL Chi-restraints excluded: chain 2 residue 347 VAL Chi-restraints excluded: chain 2 residue 352 CYS Chi-restraints excluded: chain 2 residue 428 THR Chi-restraints excluded: chain 2 residue 481 ILE Chi-restraints excluded: chain 2 residue 524 ASP Chi-restraints excluded: chain 2 residue 565 VAL Chi-restraints excluded: chain 2 residue 620 LEU Chi-restraints excluded: chain 2 residue 752 LYS Chi-restraints excluded: chain 2 residue 757 THR Chi-restraints excluded: chain 2 residue 820 ARG Chi-restraints excluded: chain 2 residue 833 LEU Chi-restraints excluded: chain 2 residue 839 LEU Chi-restraints excluded: chain 2 residue 860 VAL Chi-restraints excluded: chain 3 residue 33 GLN Chi-restraints excluded: chain 3 residue 257 ARG Chi-restraints excluded: chain 3 residue 473 ASP Chi-restraints excluded: chain 3 residue 555 THR Chi-restraints excluded: chain 3 residue 562 MET Chi-restraints excluded: chain 3 residue 639 LEU Chi-restraints excluded: chain 4 residue 157 VAL Chi-restraints excluded: chain 4 residue 187 ASP Chi-restraints excluded: chain 4 residue 327 VAL Chi-restraints excluded: chain 4 residue 399 ILE Chi-restraints excluded: chain 4 residue 401 VAL Chi-restraints excluded: chain 5 residue 27 ARG Chi-restraints excluded: chain 5 residue 44 VAL Chi-restraints excluded: chain 5 residue 128 LEU Chi-restraints excluded: chain 5 residue 199 THR Chi-restraints excluded: chain 5 residue 430 GLU Chi-restraints excluded: chain 5 residue 504 ILE Chi-restraints excluded: chain 5 residue 510 ILE Chi-restraints excluded: chain 5 residue 721 ILE Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain 6 residue 168 VAL Chi-restraints excluded: chain 6 residue 206 VAL Chi-restraints excluded: chain 6 residue 226 VAL Chi-restraints excluded: chain 6 residue 233 VAL Chi-restraints excluded: chain 6 residue 278 THR Chi-restraints excluded: chain 6 residue 390 ILE Chi-restraints excluded: chain 6 residue 489 VAL Chi-restraints excluded: chain 6 residue 661 THR Chi-restraints excluded: chain 6 residue 736 GLU Chi-restraints excluded: chain 6 residue 771 ARG Chi-restraints excluded: chain 7 residue 125 GLN Chi-restraints excluded: chain 7 residue 210 GLU Chi-restraints excluded: chain 7 residue 220 LEU Chi-restraints excluded: chain 7 residue 242 ASP Chi-restraints excluded: chain 7 residue 405 THR Chi-restraints excluded: chain 7 residue 590 ARG Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 888 MET Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 360 CYS Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 638 HIS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 449 LYS Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 631 MET Chi-restraints excluded: chain E residue 782 HIS Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain F residue 460 GLU Chi-restraints excluded: chain F residue 528 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 818 random chunks: chunk 717 optimal weight: 7.9990 chunk 755 optimal weight: 8.9990 chunk 689 optimal weight: 1.9990 chunk 734 optimal weight: 5.9990 chunk 442 optimal weight: 6.9990 chunk 320 optimal weight: 7.9990 chunk 576 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 663 optimal weight: 2.9990 chunk 694 optimal weight: 0.5980 chunk 732 optimal weight: 0.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 829 ASN ** 3 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 785 HIS ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 ASN ** D 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 HIS ** F 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 70199 Z= 0.264 Angle : 0.614 14.959 95681 Z= 0.318 Chirality : 0.043 0.216 10823 Planarity : 0.004 0.056 11700 Dihedral : 17.688 179.960 11593 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.93 % Favored : 95.06 % Rotamer: Outliers : 1.89 % Allowed : 16.10 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.09), residues: 8066 helix: 1.16 (0.09), residues: 3190 sheet: -0.49 (0.13), residues: 1496 loop : -0.84 (0.10), residues: 3380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 614 HIS 0.020 0.001 HIS 5 540 PHE 0.027 0.001 PHE D 393 TYR 0.016 0.001 TYR 3 32 ARG 0.013 0.000 ARG 2 887 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16132 Ramachandran restraints generated. 8066 Oldfield, 0 Emsley, 8066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16132 Ramachandran restraints generated. 8066 Oldfield, 0 Emsley, 8066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 7109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 561 time to evaluate : 5.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 188 MET cc_start: 0.6623 (mtt) cc_final: 0.6130 (ptp) REVERT: 2 481 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8190 (pt) REVERT: 2 588 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7999 (mm-30) REVERT: 2 620 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8357 (pp) REVERT: 2 752 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.6599 (mmpt) REVERT: 2 820 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7284 (ppt-90) REVERT: 2 843 GLN cc_start: 0.7436 (tm-30) cc_final: 0.7014 (tm-30) REVERT: 2 871 GLN cc_start: 0.7558 (mt0) cc_final: 0.7303 (mt0) REVERT: 2 882 ASP cc_start: 0.7725 (m-30) cc_final: 0.7262 (p0) REVERT: 3 33 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.7790 (tm130) REVERT: 3 257 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7334 (mtp-110) REVERT: 3 531 ASP cc_start: 0.7869 (t70) cc_final: 0.7565 (t0) REVERT: 5 27 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7563 (mtp85) REVERT: 5 73 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7897 (mt-10) REVERT: 5 128 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8527 (mt) REVERT: 5 504 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8006 (pp) REVERT: 6 736 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7472 (pp20) REVERT: 6 771 ARG cc_start: 0.5796 (OUTLIER) cc_final: 0.4621 (tmt90) REVERT: 7 125 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7826 (pm20) REVERT: 7 220 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8030 (pp) REVERT: 7 371 ILE cc_start: 0.8429 (OUTLIER) cc_final: 0.8219 (pt) REVERT: A 224 LYS cc_start: 0.8679 (mtpm) cc_final: 0.8244 (mttp) REVERT: A 838 GLN cc_start: 0.8827 (tm-30) cc_final: 0.8505 (tm-30) REVERT: B 38 GLU cc_start: 0.7493 (tp30) cc_final: 0.7192 (tp30) REVERT: C 591 MET cc_start: 0.9008 (mtp) cc_final: 0.8574 (mtm) REVERT: C 600 LYS cc_start: 0.6342 (ptpt) cc_final: 0.4989 (mptm) REVERT: D 215 MET cc_start: 0.8929 (mtp) cc_final: 0.8665 (mtp) REVERT: D 641 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8986 (mm) REVERT: D 715 MET cc_start: 0.6878 (tpp) cc_final: 0.6259 (pp-130) REVERT: E 73 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7767 (tm-30) REVERT: E 442 PHE cc_start: 0.7765 (m-80) cc_final: 0.7509 (m-80) REVERT: F 375 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8506 (mt) REVERT: F 460 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8196 (tt0) REVERT: F 528 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7561 (m-30) REVERT: F 565 MET cc_start: 0.8510 (ptp) cc_final: 0.8229 (ptm) outliers start: 133 outliers final: 91 residues processed: 655 average time/residue: 1.5717 time to fit residues: 1341.8954 Evaluate side-chains 653 residues out of total 7109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 542 time to evaluate : 5.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 291 VAL Chi-restraints excluded: chain 2 residue 347 VAL Chi-restraints excluded: chain 2 residue 352 CYS Chi-restraints excluded: chain 2 residue 428 THR Chi-restraints excluded: chain 2 residue 481 ILE Chi-restraints excluded: chain 2 residue 524 ASP Chi-restraints excluded: chain 2 residue 565 VAL Chi-restraints excluded: chain 2 residue 620 LEU Chi-restraints excluded: chain 2 residue 752 LYS Chi-restraints excluded: chain 2 residue 757 THR Chi-restraints excluded: chain 2 residue 820 ARG Chi-restraints excluded: chain 2 residue 833 LEU Chi-restraints excluded: chain 2 residue 839 LEU Chi-restraints excluded: chain 2 residue 860 VAL Chi-restraints excluded: chain 3 residue 11 GLU Chi-restraints excluded: chain 3 residue 33 GLN Chi-restraints excluded: chain 3 residue 257 ARG Chi-restraints excluded: chain 3 residue 473 ASP Chi-restraints excluded: chain 3 residue 555 THR Chi-restraints excluded: chain 3 residue 562 MET Chi-restraints excluded: chain 3 residue 639 LEU Chi-restraints excluded: chain 4 residue 157 VAL Chi-restraints excluded: chain 4 residue 187 ASP Chi-restraints excluded: chain 4 residue 295 LEU Chi-restraints excluded: chain 4 residue 399 ILE Chi-restraints excluded: chain 4 residue 401 VAL Chi-restraints excluded: chain 4 residue 608 ASN Chi-restraints excluded: chain 5 residue 27 ARG Chi-restraints excluded: chain 5 residue 44 VAL Chi-restraints excluded: chain 5 residue 73 GLU Chi-restraints excluded: chain 5 residue 128 LEU Chi-restraints excluded: chain 5 residue 199 THR Chi-restraints excluded: chain 5 residue 224 PHE Chi-restraints excluded: chain 5 residue 430 GLU Chi-restraints excluded: chain 5 residue 504 ILE Chi-restraints excluded: chain 5 residue 510 ILE Chi-restraints excluded: chain 5 residue 670 GLU Chi-restraints excluded: chain 5 residue 721 ILE Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain 6 residue 168 VAL Chi-restraints excluded: chain 6 residue 206 VAL Chi-restraints excluded: chain 6 residue 226 VAL Chi-restraints excluded: chain 6 residue 233 VAL Chi-restraints excluded: chain 6 residue 278 THR Chi-restraints excluded: chain 6 residue 354 LEU Chi-restraints excluded: chain 6 residue 390 ILE Chi-restraints excluded: chain 6 residue 489 VAL Chi-restraints excluded: chain 6 residue 661 THR Chi-restraints excluded: chain 6 residue 736 GLU Chi-restraints excluded: chain 6 residue 771 ARG Chi-restraints excluded: chain 6 residue 780 LEU Chi-restraints excluded: chain 7 residue 125 GLN Chi-restraints excluded: chain 7 residue 220 LEU Chi-restraints excluded: chain 7 residue 242 ASP Chi-restraints excluded: chain 7 residue 371 ILE Chi-restraints excluded: chain 7 residue 405 THR Chi-restraints excluded: chain 7 residue 590 ARG Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain B residue 360 CYS Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 638 HIS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 631 MET Chi-restraints excluded: chain E residue 782 HIS Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain F residue 460 GLU Chi-restraints excluded: chain F residue 528 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 818 random chunks: chunk 482 optimal weight: 0.6980 chunk 776 optimal weight: 9.9990 chunk 474 optimal weight: 7.9990 chunk 368 optimal weight: 5.9990 chunk 540 optimal weight: 0.8980 chunk 814 optimal weight: 10.0000 chunk 750 optimal weight: 0.5980 chunk 648 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 501 optimal weight: 4.9990 chunk 397 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 829 ASN ** 3 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 785 HIS 7 223 GLN ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 ASN ** D 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 HIS ** F 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 70199 Z= 0.257 Angle : 0.614 14.866 95681 Z= 0.318 Chirality : 0.043 0.220 10823 Planarity : 0.004 0.081 11700 Dihedral : 17.656 179.987 11593 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.95 % Favored : 95.04 % Rotamer: Outliers : 1.84 % Allowed : 16.27 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.09), residues: 8066 helix: 1.17 (0.09), residues: 3188 sheet: -0.50 (0.13), residues: 1498 loop : -0.84 (0.10), residues: 3380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 614 HIS 0.023 0.001 HIS 5 540 PHE 0.027 0.001 PHE D 393 TYR 0.016 0.001 TYR 3 32 ARG 0.021 0.000 ARG E 468 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16132 Ramachandran restraints generated. 8066 Oldfield, 0 Emsley, 8066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16132 Ramachandran restraints generated. 8066 Oldfield, 0 Emsley, 8066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 7109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 561 time to evaluate : 5.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 188 MET cc_start: 0.6614 (mtt) cc_final: 0.6125 (ptp) REVERT: 2 481 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8199 (pt) REVERT: 2 588 GLU cc_start: 0.8265 (mm-30) cc_final: 0.8016 (mm-30) REVERT: 2 620 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8344 (pp) REVERT: 2 752 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.6604 (mmpt) REVERT: 2 820 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.7290 (ppt-90) REVERT: 2 843 GLN cc_start: 0.7502 (tm-30) cc_final: 0.7070 (tm-30) REVERT: 2 871 GLN cc_start: 0.7549 (mt0) cc_final: 0.7304 (mt0) REVERT: 2 882 ASP cc_start: 0.7654 (m-30) cc_final: 0.7228 (p0) REVERT: 2 899 MET cc_start: 0.6062 (OUTLIER) cc_final: 0.4967 (tpt) REVERT: 3 33 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7794 (tm130) REVERT: 3 531 ASP cc_start: 0.7902 (t70) cc_final: 0.7619 (t0) REVERT: 5 27 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7560 (mtp85) REVERT: 5 128 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8464 (mt) REVERT: 6 736 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7461 (pp20) REVERT: 6 771 ARG cc_start: 0.5795 (OUTLIER) cc_final: 0.4674 (tmt90) REVERT: 7 125 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7838 (pm20) REVERT: 7 220 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8039 (pp) REVERT: A 224 LYS cc_start: 0.8675 (mtpm) cc_final: 0.8344 (mttp) REVERT: A 838 GLN cc_start: 0.8824 (tm-30) cc_final: 0.8499 (tm-30) REVERT: B 38 GLU cc_start: 0.7500 (tp30) cc_final: 0.7195 (tp30) REVERT: C 288 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8628 (ttm) REVERT: C 591 MET cc_start: 0.9016 (mtp) cc_final: 0.8579 (mtm) REVERT: C 600 LYS cc_start: 0.6344 (ptpt) cc_final: 0.4989 (mptm) REVERT: D 215 MET cc_start: 0.8923 (mtp) cc_final: 0.8645 (mtp) REVERT: D 449 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8089 (mtpt) REVERT: D 641 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8931 (mm) REVERT: D 715 MET cc_start: 0.6881 (tpp) cc_final: 0.6261 (pp-130) REVERT: E 73 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7772 (tm-30) REVERT: E 442 PHE cc_start: 0.7739 (m-80) cc_final: 0.7478 (m-80) REVERT: F 375 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8491 (mt) REVERT: F 460 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8204 (tt0) REVERT: F 528 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7558 (m-30) REVERT: F 565 MET cc_start: 0.8508 (ptp) cc_final: 0.8227 (ptm) outliers start: 130 outliers final: 93 residues processed: 653 average time/residue: 1.5863 time to fit residues: 1350.1089 Evaluate side-chains 659 residues out of total 7109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 547 time to evaluate : 5.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 291 VAL Chi-restraints excluded: chain 2 residue 347 VAL Chi-restraints excluded: chain 2 residue 352 CYS Chi-restraints excluded: chain 2 residue 428 THR Chi-restraints excluded: chain 2 residue 481 ILE Chi-restraints excluded: chain 2 residue 524 ASP Chi-restraints excluded: chain 2 residue 565 VAL Chi-restraints excluded: chain 2 residue 620 LEU Chi-restraints excluded: chain 2 residue 621 GLN Chi-restraints excluded: chain 2 residue 752 LYS Chi-restraints excluded: chain 2 residue 757 THR Chi-restraints excluded: chain 2 residue 820 ARG Chi-restraints excluded: chain 2 residue 833 LEU Chi-restraints excluded: chain 2 residue 839 LEU Chi-restraints excluded: chain 2 residue 860 VAL Chi-restraints excluded: chain 2 residue 899 MET Chi-restraints excluded: chain 3 residue 33 GLN Chi-restraints excluded: chain 3 residue 339 ILE Chi-restraints excluded: chain 3 residue 473 ASP Chi-restraints excluded: chain 3 residue 555 THR Chi-restraints excluded: chain 3 residue 562 MET Chi-restraints excluded: chain 3 residue 639 LEU Chi-restraints excluded: chain 4 residue 157 VAL Chi-restraints excluded: chain 4 residue 187 ASP Chi-restraints excluded: chain 4 residue 295 LEU Chi-restraints excluded: chain 4 residue 399 ILE Chi-restraints excluded: chain 4 residue 401 VAL Chi-restraints excluded: chain 4 residue 608 ASN Chi-restraints excluded: chain 5 residue 27 ARG Chi-restraints excluded: chain 5 residue 44 VAL Chi-restraints excluded: chain 5 residue 128 LEU Chi-restraints excluded: chain 5 residue 199 THR Chi-restraints excluded: chain 5 residue 224 PHE Chi-restraints excluded: chain 5 residue 430 GLU Chi-restraints excluded: chain 5 residue 510 ILE Chi-restraints excluded: chain 5 residue 670 GLU Chi-restraints excluded: chain 6 residue 63 VAL Chi-restraints excluded: chain 6 residue 168 VAL Chi-restraints excluded: chain 6 residue 206 VAL Chi-restraints excluded: chain 6 residue 226 VAL Chi-restraints excluded: chain 6 residue 233 VAL Chi-restraints excluded: chain 6 residue 278 THR Chi-restraints excluded: chain 6 residue 354 LEU Chi-restraints excluded: chain 6 residue 390 ILE Chi-restraints excluded: chain 6 residue 489 VAL Chi-restraints excluded: chain 6 residue 661 THR Chi-restraints excluded: chain 6 residue 736 GLU Chi-restraints excluded: chain 6 residue 771 ARG Chi-restraints excluded: chain 6 residue 780 LEU Chi-restraints excluded: chain 7 residue 125 GLN Chi-restraints excluded: chain 7 residue 220 LEU Chi-restraints excluded: chain 7 residue 242 ASP Chi-restraints excluded: chain 7 residue 405 THR Chi-restraints excluded: chain 7 residue 590 ARG Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain B residue 360 CYS Chi-restraints excluded: chain B residue 414 MET Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 499 LYS Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 604 ILE Chi-restraints excluded: chain C residue 638 HIS Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain D residue 224 PHE Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 449 LYS Chi-restraints excluded: chain D residue 641 LEU Chi-restraints excluded: chain D residue 649 LEU Chi-restraints excluded: chain D residue 650 ASP Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 73 GLN Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 631 MET Chi-restraints excluded: chain E residue 782 HIS Chi-restraints excluded: chain F residue 108 MET Chi-restraints excluded: chain F residue 220 LEU Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain F residue 375 ILE Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain F residue 460 GLU Chi-restraints excluded: chain F residue 528 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 818 random chunks: chunk 515 optimal weight: 2.9990 chunk 691 optimal weight: 0.7980 chunk 198 optimal weight: 0.6980 chunk 598 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 chunk 649 optimal weight: 2.9990 chunk 272 optimal weight: 0.5980 chunk 667 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 829 ASN ** 3 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 785 HIS ** 7 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 ASN ** D 596 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 GLN E 440 HIS F 18 GLN F 87 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.124198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.087119 restraints weight = 353700.063| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.80 r_work: 0.2892 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 64 | |-----------------------------------------------------------------------------| r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 70199 Z= 0.202 Angle : 0.591 14.349 95681 Z= 0.307 Chirality : 0.042 0.222 10823 Planarity : 0.004 0.082 11700 Dihedral : 17.576 179.663 11593 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.75 % Favored : 95.24 % Rotamer: Outliers : 1.67 % Allowed : 16.51 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.09), residues: 8066 helix: 1.20 (0.09), residues: 3198 sheet: -0.49 (0.13), residues: 1495 loop : -0.80 (0.10), residues: 3373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 614 HIS 0.022 0.001 HIS 5 540 PHE 0.025 0.001 PHE D 393 TYR 0.015 0.001 TYR 3 32 ARG 0.020 0.000 ARG E 468 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21744.87 seconds wall clock time: 379 minutes 55.31 seconds (22795.31 seconds total)