Starting phenix.real_space_refine on Tue Mar 12 12:56:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbw_22121/03_2024/6xbw_22121_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbw_22121/03_2024/6xbw_22121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbw_22121/03_2024/6xbw_22121.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbw_22121/03_2024/6xbw_22121.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbw_22121/03_2024/6xbw_22121_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xbw_22121/03_2024/6xbw_22121_updated.pdb" } resolution = 3.37 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= 0.015 sd= 1.129 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: 6 Type Number sf(0) Gaussians P 11 5.49 5 Mg 1 5.21 5 S 357 5.16 5 C 40442 2.51 5 N 10634 2.21 5 O 11645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 193": "OE1" <-> "OE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A GLU 360": "OE1" <-> "OE2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 481": "OE1" <-> "OE2" Residue "A GLU 491": "OE1" <-> "OE2" Residue "A GLU 576": "OE1" <-> "OE2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "B GLU 297": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B ASP 349": "OD1" <-> "OD2" Residue "B GLU 356": "OE1" <-> "OE2" Residue "B GLU 367": "OE1" <-> "OE2" Residue "B TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 485": "OE1" <-> "OE2" Residue "B GLU 491": "OE1" <-> "OE2" Residue "B GLU 503": "OE1" <-> "OE2" Residue "B PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 556": "OE1" <-> "OE2" Residue "B GLU 576": "OE1" <-> "OE2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 286": "OE1" <-> "OE2" Residue "C GLU 293": "OE1" <-> "OE2" Residue "C GLU 297": "OE1" <-> "OE2" Residue "C GLU 367": "OE1" <-> "OE2" Residue "C GLU 387": "OE1" <-> "OE2" Residue "C GLU 481": "OE1" <-> "OE2" Residue "C GLU 485": "OE1" <-> "OE2" Residue "C GLU 572": "OE1" <-> "OE2" Residue "C PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 606": "OE1" <-> "OE2" Residue "D GLU 167": "OE1" <-> "OE2" Residue "D GLU 168": "OE1" <-> "OE2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "D TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 309": "OE1" <-> "OE2" Residue "D GLU 441": "OE1" <-> "OE2" Residue "D GLU 442": "OE1" <-> "OE2" Residue "D ARG 506": "NH1" <-> "NH2" Residue "E TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 239": "OE1" <-> "OE2" Residue "E GLU 250": "OE1" <-> "OE2" Residue "E GLU 309": "OE1" <-> "OE2" Residue "E GLU 315": "OE1" <-> "OE2" Residue "E GLU 453": "OE1" <-> "OE2" Residue "E ARG 485": "NH1" <-> "NH2" Residue "E ARG 506": "NH1" <-> "NH2" Residue "F GLU 225": "OE1" <-> "OE2" Residue "F GLU 250": "OE1" <-> "OE2" Residue "F GLU 270": "OE1" <-> "OE2" Residue "F GLU 290": "OE1" <-> "OE2" Residue "F GLU 315": "OE1" <-> "OE2" Residue "F GLU 441": "OE1" <-> "OE2" Residue "F GLU 469": "OE1" <-> "OE2" Residue "F GLU 490": "OE1" <-> "OE2" Residue "F GLU 502": "OE1" <-> "OE2" Residue "F ARG 506": "NH1" <-> "NH2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G ARG 139": "NH1" <-> "NH2" Residue "G GLU 206": "OE1" <-> "OE2" Residue "G GLU 218": "OE1" <-> "OE2" Residue "G ARG 238": "NH1" <-> "NH2" Residue "G GLU 256": "OE1" <-> "OE2" Residue "G GLU 305": "OE1" <-> "OE2" Residue "G GLU 337": "OE1" <-> "OE2" Residue "G ASP 343": "OD1" <-> "OD2" Residue "H ARG 63": "NH1" <-> "NH2" Residue "H GLU 71": "OE1" <-> "OE2" Residue "H GLU 147": "OE1" <-> "OE2" Residue "H GLU 193": "OE1" <-> "OE2" Residue "H GLU 197": "OE1" <-> "OE2" Residue "H GLU 198": "OE1" <-> "OE2" Residue "I ARG 80": "NH1" <-> "NH2" Residue "I GLU 170": "OE1" <-> "OE2" Residue "I TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 176": "OE1" <-> "OE2" Residue "I GLU 182": "OE1" <-> "OE2" Residue "I GLU 197": "OE1" <-> "OE2" Residue "I GLU 210": "OE1" <-> "OE2" Residue "I ARG 222": "NH1" <-> "NH2" Residue "J GLU 55": "OE1" <-> "OE2" Residue "J GLU 61": "OE1" <-> "OE2" Residue "J GLU 65": "OE1" <-> "OE2" Residue "J ARG 80": "NH1" <-> "NH2" Residue "J GLU 129": "OE1" <-> "OE2" Residue "J ARG 222": "NH1" <-> "NH2" Residue "K ARG 80": "NH1" <-> "NH2" Residue "K GLU 197": "OE1" <-> "OE2" Residue "K GLU 210": "OE1" <-> "OE2" Residue "K ARG 222": "NH1" <-> "NH2" Residue "L GLU 14": "OE1" <-> "OE2" Residue "L GLU 47": "OE1" <-> "OE2" Residue "L GLU 90": "OE1" <-> "OE2" Residue "L TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 74": "OE1" <-> "OE2" Residue "N GLU 93": "OE1" <-> "OE2" Residue "O ARG 92": "NH1" <-> "NH2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "P GLU 154": "OE1" <-> "OE2" Residue "P GLU 195": "OE1" <-> "OE2" Residue "P GLU 261": "OE1" <-> "OE2" Residue "P ARG 265": "NH1" <-> "NH2" Residue "P ARG 272": "NH1" <-> "NH2" Residue "P GLU 286": "OE1" <-> "OE2" Residue "P GLU 301": "OE1" <-> "OE2" Residue "P ARG 364": "NH1" <-> "NH2" Residue "P GLU 367": "OE1" <-> "OE2" Residue "P GLU 381": "OE1" <-> "OE2" Residue "P GLU 398": "OE1" <-> "OE2" Residue "P ARG 408": "NH1" <-> "NH2" Residue "P GLU 411": "OE1" <-> "OE2" Residue "a GLU 8": "OE1" <-> "OE2" Residue "a GLU 20": "OE1" <-> "OE2" Residue "a GLU 31": "OE1" <-> "OE2" Residue "a PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 59": "OE1" <-> "OE2" Residue "a GLU 105": "OE1" <-> "OE2" Residue "a GLU 110": "OE1" <-> "OE2" Residue "a ARG 167": "NH1" <-> "NH2" Residue "a ARG 189": "NH1" <-> "NH2" Residue "a ARG 192": "NH1" <-> "NH2" Residue "a GLU 201": "OE1" <-> "OE2" Residue "a GLU 249": "OE1" <-> "OE2" Residue "a ARG 338": "NH1" <-> "NH2" Residue "a ARG 354": "NH1" <-> "NH2" Residue "a ARG 387": "NH1" <-> "NH2" Residue "a TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 833": "OE1" <-> "OE2" Residue "b ASP 30": "OD1" <-> "OD2" Residue "b PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 129": "NH1" <-> "NH2" Residue "d GLU 40": "OE1" <-> "OE2" Residue "d ARG 120": "NH1" <-> "NH2" Residue "d GLU 149": "OE1" <-> "OE2" Residue "d GLU 175": "OE1" <-> "OE2" Residue "d TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 325": "OE1" <-> "OE2" Residue "d ARG 341": "NH1" <-> "NH2" Residue "e PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 312": "OD1" <-> "OD2" Residue "s TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 341": "OE1" <-> "OE2" Residue "s GLU 344": "OE1" <-> "OE2" Residue "s TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 453": "NH1" <-> "NH2" Residue "c GLU 50": "OE1" <-> "OE2" Residue "k GLU 50": "OE1" <-> "OE2" Residue "l GLU 50": "OE1" <-> "OE2" Residue "m GLU 50": "OE1" <-> "OE2" Residue "o GLU 9": "OE1" <-> "OE2" Residue "o GLU 50": "OE1" <-> "OE2" Residue "p GLU 50": "OE1" <-> "OE2" Residue "p GLU 139": "OE1" <-> "OE2" Residue "q GLU 50": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 63090 Number of models: 1 Model: "" Number of chains: 38 Chain: "A" Number of atoms: 4568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4568 Classifications: {'peptide': 589} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 557} Chain breaks: 1 Chain: "B" Number of atoms: 4582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4582 Classifications: {'peptide': 590} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 559} Chain breaks: 1 Chain: "C" Number of atoms: 4628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4628 Classifications: {'peptide': 597} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 565} Chain: "D" Number of atoms: 3609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3609 Classifications: {'peptide': 461} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 26, 'TRANS': 432} Chain breaks: 1 Chain: "E" Number of atoms: 3585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3585 Classifications: {'peptide': 458} Link IDs: {'CIS': 1, 'PTRANS': 27, 'TRANS': 429} Chain breaks: 1 Chain: "F" Number of atoms: 3594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3594 Classifications: {'peptide': 459} Link IDs: {'CIS': 1, 'PTRANS': 27, 'TRANS': 430} Chain breaks: 1 Chain: "G" Number of atoms: 2823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2823 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 9, 'TRANS': 336} Chain breaks: 3 Chain: "H" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1700 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 3, 'TRANS': 207} Chain: "I" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1614 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 5, 'TRANS': 212} Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 9, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 95 Chain: "J" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1624 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 5, 'TRANS': 212} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 9, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 95 Chain: "K" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1595 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 5, 'TRANS': 214} Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 11, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 120 Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 98} Chain: "M" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 665 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 2, 'TRANS': 105} Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 12, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 142 Chain: "N" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 665 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 2, 'TRANS': 105} Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 12, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 142 Chain: "O" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 665 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 2, 'TRANS': 105} Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 12, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 142 Chain: "P" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2819 Classifications: {'peptide': 368} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 6, 'TRANS': 361} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 211 Unresolved non-hydrogen angles: 272 Unresolved non-hydrogen dihedrals: 177 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 125 Chain: "a" Number of atoms: 6093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 6093 Classifications: {'peptide': 750} Link IDs: {'CIS': 1, 'PTRANS': 30, 'TRANS': 718} Chain breaks: 2 Chain: "b" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1503 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 198} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "d" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2819 Classifications: {'peptide': 348} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 334} Chain: "e" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 590 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 6, 'TRANS': 66} Chain: "s" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1668 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 5, 'TRANS': 199} Chain: "r" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 385 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "c" Number of atoms: 1064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1064 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "g" Number of atoms: 1064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1064 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "k" Number of atoms: 1064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1064 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "l" Number of atoms: 1064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1064 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "m" Number of atoms: 1064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1064 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "n" Number of atoms: 1064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1064 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "o" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1073 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 146} Chain: "p" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1073 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 146} Chain: "q" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1073 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 146} Chain: "f" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 351 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain breaks: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 213 Unusual residues: {'POV': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "s" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 6 Chain: "r" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 114 Unusual residues: {'OLA': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "g" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "p" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Time building chain proxies: 24.32, per 1000 atoms: 0.39 Number of scatterers: 63090 At special positions: 0 Unit cell: (224.91, 204.918, 248.234, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 357 16.00 P 11 15.00 Mg 1 11.99 O 11645 8.00 N 10634 7.00 C 40442 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS s 369 " - pdb=" SG CYS s 416 " distance=2.03 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=2, symmetry=0 Links applied NAG-ASN " NAG s 501 " - " ASN s 271 " " NAG s 502 " - " ASN s 294 " " NAG s 503 " - " ASN s 301 " " NAG s 504 " - " ASN s 348 " " NAG s 505 " - " ASN s 355 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 19.18 Conformation dependent library (CDL) restraints added in 9.8 seconds 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15120 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 279 helices and 44 sheets defined 53.1% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.94 Creating SS restraints... Processing helix chain 'A' and resid 106 through 113 removed outlier: 3.645A pdb=" N SER A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER A 111 " --> pdb=" O SER A 107 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR A 113 " --> pdb=" O ILE A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 236 Processing helix chain 'A' and resid 256 through 265 Processing helix chain 'A' and resid 283 through 293 removed outlier: 3.502A pdb=" N VAL A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) Proline residue: A 292 - end of helix Processing helix chain 'A' and resid 305 through 308 Processing helix chain 'A' and resid 320 through 324 Processing helix chain 'A' and resid 326 through 338 Processing helix chain 'A' and resid 351 through 364 removed outlier: 3.543A pdb=" N ALA A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 388 removed outlier: 4.768A pdb=" N ARG A 388 " --> pdb=" O SER A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 415 No H-bonds generated for 'chain 'A' and resid 413 through 415' Processing helix chain 'A' and resid 422 through 426 Processing helix chain 'A' and resid 437 through 441 Processing helix chain 'A' and resid 458 through 468 removed outlier: 4.197A pdb=" N TYR A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS A 467 " --> pdb=" O GLU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 495 removed outlier: 3.521A pdb=" N GLU A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 491 " --> pdb=" O GLU A 487 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE A 492 " --> pdb=" O ASP A 488 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 493 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLN A 494 " --> pdb=" O ALA A 490 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 518 removed outlier: 3.952A pdb=" N ILE A 507 " --> pdb=" O GLU A 503 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR A 508 " --> pdb=" O THR A 504 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU A 510 " --> pdb=" O LYS A 506 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 511 " --> pdb=" O ILE A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 529 No H-bonds generated for 'chain 'A' and resid 527 through 529' Processing helix chain 'A' and resid 534 through 555 removed outlier: 3.759A pdb=" N LEU A 541 " --> pdb=" O THR A 537 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 546 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 552 " --> pdb=" O TYR A 548 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG A 553 " --> pdb=" O ASP A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 573 removed outlier: 3.584A pdb=" N GLU A 572 " --> pdb=" O SER A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 581 Processing helix chain 'A' and resid 584 through 586 No H-bonds generated for 'chain 'A' and resid 584 through 586' Processing helix chain 'A' and resid 594 through 609 removed outlier: 3.776A pdb=" N GLN A 603 " --> pdb=" O ALA A 599 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 604 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 605 " --> pdb=" O TYR A 601 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU A 606 " --> pdb=" O ALA A 602 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 113 removed outlier: 3.764A pdb=" N SER B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER B 111 " --> pdb=" O SER B 107 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 113 " --> pdb=" O ILE B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 262 through 265 No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 281 through 284 No H-bonds generated for 'chain 'B' and resid 281 through 284' Processing helix chain 'B' and resid 287 through 290 No H-bonds generated for 'chain 'B' and resid 287 through 290' Processing helix chain 'B' and resid 305 through 308 Processing helix chain 'B' and resid 320 through 338 removed outlier: 3.633A pdb=" N SER B 326 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE B 327 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR B 329 " --> pdb=" O SER B 326 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE B 331 " --> pdb=" O TYR B 328 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B 334 " --> pdb=" O ILE B 331 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU B 335 " --> pdb=" O THR B 332 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE B 337 " --> pdb=" O SER B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 364 Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 378 through 388 removed outlier: 4.864A pdb=" N ARG B 388 " --> pdb=" O SER B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 426 removed outlier: 3.597A pdb=" N ALA B 424 " --> pdb=" O PRO B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 441 Processing helix chain 'B' and resid 462 through 465 No H-bonds generated for 'chain 'B' and resid 462 through 465' Processing helix chain 'B' and resid 472 through 493 removed outlier: 3.573A pdb=" N LYS B 478 " --> pdb=" O PRO B 474 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU B 481 " --> pdb=" O THR B 477 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU B 491 " --> pdb=" O GLU B 487 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE B 492 " --> pdb=" O ASP B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 518 removed outlier: 3.530A pdb=" N ILE B 507 " --> pdb=" O GLU B 503 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR B 508 " --> pdb=" O THR B 504 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 511 " --> pdb=" O ILE B 507 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS B 513 " --> pdb=" O LEU B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 557 removed outlier: 3.596A pdb=" N ASN B 543 " --> pdb=" O GLY B 539 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B 555 " --> pdb=" O ALA B 551 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR B 557 " --> pdb=" O ARG B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 573 No H-bonds generated for 'chain 'B' and resid 570 through 573' Processing helix chain 'B' and resid 577 through 582 Processing helix chain 'B' and resid 584 through 586 No H-bonds generated for 'chain 'B' and resid 584 through 586' Processing helix chain 'B' and resid 594 through 609 removed outlier: 3.682A pdb=" N ALA B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET B 608 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN B 609 " --> pdb=" O LEU B 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 111 removed outlier: 3.723A pdb=" N SER C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 236 Processing helix chain 'C' and resid 258 through 266 Processing helix chain 'C' and resid 281 through 290 removed outlier: 3.536A pdb=" N SER C 285 " --> pdb=" O GLY C 281 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG C 289 " --> pdb=" O SER C 285 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP C 290 " --> pdb=" O GLU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 308 removed outlier: 3.519A pdb=" N ARG C 308 " --> pdb=" O ILE C 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 305 through 308' Processing helix chain 'C' and resid 321 through 338 removed outlier: 3.615A pdb=" N ALA C 325 " --> pdb=" O ALA C 321 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 364 removed outlier: 3.578A pdb=" N ARG C 364 " --> pdb=" O GLU C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 373 No H-bonds generated for 'chain 'C' and resid 371 through 373' Processing helix chain 'C' and resid 378 through 388 removed outlier: 4.738A pdb=" N ARG C 388 " --> pdb=" O SER C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 415 No H-bonds generated for 'chain 'C' and resid 413 through 415' Processing helix chain 'C' and resid 422 through 426 Processing helix chain 'C' and resid 438 through 441 No H-bonds generated for 'chain 'C' and resid 438 through 441' Processing helix chain 'C' and resid 462 through 465 No H-bonds generated for 'chain 'C' and resid 462 through 465' Processing helix chain 'C' and resid 473 through 493 removed outlier: 3.659A pdb=" N LYS C 478 " --> pdb=" O PRO C 474 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU C 481 " --> pdb=" O THR C 477 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE C 492 " --> pdb=" O ASP C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 500 No H-bonds generated for 'chain 'C' and resid 498 through 500' Processing helix chain 'C' and resid 503 through 518 removed outlier: 3.841A pdb=" N THR C 508 " --> pdb=" O THR C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 556 removed outlier: 3.585A pdb=" N ASN C 543 " --> pdb=" O GLY C 539 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET C 544 " --> pdb=" O MET C 540 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL C 555 " --> pdb=" O ALA C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 573 removed outlier: 3.881A pdb=" N GLU C 572 " --> pdb=" O SER C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 586 removed outlier: 3.620A pdb=" N MET C 584 " --> pdb=" O LYS C 580 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LYS C 585 " --> pdb=" O LEU C 581 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N PHE C 586 " --> pdb=" O SER C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 593 through 609 removed outlier: 3.676A pdb=" N LEU C 605 " --> pdb=" O TYR C 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 178 No H-bonds generated for 'chain 'D' and resid 175 through 178' Processing helix chain 'D' and resid 203 through 208 Processing helix chain 'D' and resid 238 through 251 removed outlier: 3.754A pdb=" N GLU D 250 " --> pdb=" O SER D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 284 removed outlier: 4.093A pdb=" N ARG D 276 " --> pdb=" O ILE D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 313 removed outlier: 3.842A pdb=" N ALA D 306 " --> pdb=" O SER D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 322 No H-bonds generated for 'chain 'D' and resid 320 through 322' Processing helix chain 'D' and resid 325 through 335 removed outlier: 4.278A pdb=" N TYR D 328 " --> pdb=" O GLY D 325 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU D 331 " --> pdb=" O TYR D 328 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR D 333 " --> pdb=" O ASP D 330 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE D 334 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR D 335 " --> pdb=" O ALA D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 359 No H-bonds generated for 'chain 'D' and resid 357 through 359' Processing helix chain 'D' and resid 364 through 368 Processing helix chain 'D' and resid 381 through 385 Processing helix chain 'D' and resid 402 through 405 No H-bonds generated for 'chain 'D' and resid 402 through 405' Processing helix chain 'D' and resid 413 through 438 removed outlier: 4.235A pdb=" N ALA D 416 " --> pdb=" O LYS D 413 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL D 418 " --> pdb=" O HIS D 415 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER D 419 " --> pdb=" O ALA D 416 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN D 421 " --> pdb=" O VAL D 418 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU D 422 " --> pdb=" O SER D 419 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR D 423 " --> pdb=" O ASN D 420 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N CYS D 425 " --> pdb=" O LEU D 422 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR D 426 " --> pdb=" O TYR D 423 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE D 428 " --> pdb=" O CYS D 425 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY D 429 " --> pdb=" O TYR D 426 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL D 432 " --> pdb=" O GLY D 429 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS D 436 " --> pdb=" O GLN D 433 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL D 438 " --> pdb=" O MET D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 461 removed outlier: 3.567A pdb=" N LYS D 457 " --> pdb=" O GLU D 453 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG D 460 " --> pdb=" O GLN D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 484 Processing helix chain 'D' and resid 497 through 503 removed outlier: 3.504A pdb=" N SER D 501 " --> pdb=" O GLN D 497 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N GLU D 502 " --> pdb=" O SER D 498 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE D 503 " --> pdb=" O THR D 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 497 through 503' Processing helix chain 'E' and resid 175 through 178 No H-bonds generated for 'chain 'E' and resid 175 through 178' Processing helix chain 'E' and resid 199 through 208 Processing helix chain 'E' and resid 238 through 250 Processing helix chain 'E' and resid 253 through 255 No H-bonds generated for 'chain 'E' and resid 253 through 255' Processing helix chain 'E' and resid 268 through 286 removed outlier: 3.749A pdb=" N THR E 274 " --> pdb=" O ARG E 271 " (cutoff:3.500A) Proline residue: E 275 - end of helix removed outlier: 3.821A pdb=" N LEU E 279 " --> pdb=" O ARG E 276 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR E 280 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR E 281 " --> pdb=" O ALA E 278 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLU E 283 " --> pdb=" O THR E 280 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU E 285 " --> pdb=" O ALA E 282 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA E 286 " --> pdb=" O GLU E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 313 removed outlier: 3.511A pdb=" N ALA E 304 " --> pdb=" O MET E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 322 No H-bonds generated for 'chain 'E' and resid 320 through 322' Processing helix chain 'E' and resid 325 through 332 removed outlier: 4.307A pdb=" N TYR E 328 " --> pdb=" O GLY E 325 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP E 330 " --> pdb=" O MET E 327 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU E 331 " --> pdb=" O TYR E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 359 No H-bonds generated for 'chain 'E' and resid 357 through 359' Processing helix chain 'E' and resid 364 through 372 removed outlier: 3.584A pdb=" N GLY E 370 " --> pdb=" O PRO E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 385 Processing helix chain 'E' and resid 413 through 438 removed outlier: 4.185A pdb=" N ALA E 416 " --> pdb=" O LYS E 413 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL E 418 " --> pdb=" O HIS E 415 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N SER E 419 " --> pdb=" O ALA E 416 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU E 422 " --> pdb=" O SER E 419 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR E 423 " --> pdb=" O ASN E 420 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N CYS E 425 " --> pdb=" O LEU E 422 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE E 428 " --> pdb=" O CYS E 425 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY E 429 " --> pdb=" O TYR E 426 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS E 430 " --> pdb=" O ALA E 427 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL E 432 " --> pdb=" O GLY E 429 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN E 433 " --> pdb=" O LYS E 430 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA E 434 " --> pdb=" O ASP E 431 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA E 437 " --> pdb=" O ALA E 434 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL E 438 " --> pdb=" O MET E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 461 removed outlier: 3.886A pdb=" N GLN E 456 " --> pdb=" O LEU E 452 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG E 460 " --> pdb=" O GLN E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 473 through 484 Processing helix chain 'E' and resid 497 through 503 removed outlier: 5.395A pdb=" N GLU E 502 " --> pdb=" O SER E 498 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE E 503 " --> pdb=" O THR E 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 175 through 178 No H-bonds generated for 'chain 'F' and resid 175 through 178' Processing helix chain 'F' and resid 199 through 208 removed outlier: 3.511A pdb=" N CYS F 207 " --> pdb=" O ALA F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 248 Processing helix chain 'F' and resid 253 through 255 No H-bonds generated for 'chain 'F' and resid 253 through 255' Processing helix chain 'F' and resid 269 through 287 removed outlier: 3.613A pdb=" N ILE F 273 " --> pdb=" O GLU F 270 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR F 274 " --> pdb=" O ARG F 271 " (cutoff:3.500A) Proline residue: F 275 - end of helix removed outlier: 3.609A pdb=" N LEU F 279 " --> pdb=" O ARG F 276 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR F 280 " --> pdb=" O LEU F 277 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N THR F 281 " --> pdb=" O ALA F 278 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA F 282 " --> pdb=" O LEU F 279 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU F 283 " --> pdb=" O THR F 280 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU F 285 " --> pdb=" O ALA F 282 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA F 286 " --> pdb=" O GLU F 283 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TYR F 287 " --> pdb=" O PHE F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 313 removed outlier: 3.579A pdb=" N VAL F 310 " --> pdb=" O ALA F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 322 No H-bonds generated for 'chain 'F' and resid 320 through 322' Processing helix chain 'F' and resid 325 through 335 removed outlier: 4.408A pdb=" N TYR F 328 " --> pdb=" O GLY F 325 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU F 331 " --> pdb=" O TYR F 328 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR F 333 " --> pdb=" O ASP F 330 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE F 334 " --> pdb=" O LEU F 331 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR F 335 " --> pdb=" O ALA F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 359 No H-bonds generated for 'chain 'F' and resid 357 through 359' Processing helix chain 'F' and resid 364 through 372 removed outlier: 3.575A pdb=" N LEU F 368 " --> pdb=" O PRO F 364 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE F 372 " --> pdb=" O LEU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 402 No H-bonds generated for 'chain 'F' and resid 400 through 402' Processing helix chain 'F' and resid 413 through 436 removed outlier: 4.272A pdb=" N ALA F 416 " --> pdb=" O LYS F 413 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL F 418 " --> pdb=" O HIS F 415 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N SER F 419 " --> pdb=" O ALA F 416 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN F 420 " --> pdb=" O ASP F 417 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU F 422 " --> pdb=" O SER F 419 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR F 423 " --> pdb=" O ASN F 420 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS F 425 " --> pdb=" O LEU F 422 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE F 428 " --> pdb=" O CYS F 425 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY F 429 " --> pdb=" O TYR F 426 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS F 430 " --> pdb=" O ALA F 427 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL F 432 " --> pdb=" O GLY F 429 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS F 436 " --> pdb=" O GLN F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 461 removed outlier: 4.188A pdb=" N LEU F 450 " --> pdb=" O SER F 446 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR F 451 " --> pdb=" O ASP F 447 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG F 460 " --> pdb=" O GLN F 456 " (cutoff:3.500A) Processing helix chain 'F' and resid 473 through 484 Processing helix chain 'F' and resid 497 through 503 removed outlier: 3.780A pdb=" N SER F 501 " --> pdb=" O GLN F 497 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU F 502 " --> pdb=" O SER F 498 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE F 503 " --> pdb=" O THR F 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 497 through 503' Processing helix chain 'G' and resid 22 through 27 Processing helix chain 'G' and resid 49 through 77 removed outlier: 3.613A pdb=" N SER G 55 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP G 56 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU G 57 " --> pdb=" O GLY G 53 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA G 73 " --> pdb=" O VAL G 69 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ALA G 77 " --> pdb=" O ALA G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 103 removed outlier: 3.601A pdb=" N ILE G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR G 103 " --> pdb=" O VAL G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 156 removed outlier: 3.787A pdb=" N ILE G 124 " --> pdb=" O ASN G 120 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER G 141 " --> pdb=" O LYS G 137 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA G 142 " --> pdb=" O SER G 138 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU G 146 " --> pdb=" O ALA G 142 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU G 154 " --> pdb=" O LEU G 150 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG G 155 " --> pdb=" O GLN G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'G' and resid 194 through 198 Processing helix chain 'G' and resid 231 through 243 removed outlier: 3.980A pdb=" N VAL G 234 " --> pdb=" O ARG G 231 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ASP G 235 " --> pdb=" O LYS G 232 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP G 236 " --> pdb=" O ALA G 233 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE G 237 " --> pdb=" O VAL G 234 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS G 239 " --> pdb=" O ASP G 236 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA G 241 " --> pdb=" O ARG G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 303 removed outlier: 3.584A pdb=" N LYS G 259 " --> pdb=" O GLU G 256 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU G 263 " --> pdb=" O ALA G 260 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU G 268 " --> pdb=" O MET G 265 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASP G 271 " --> pdb=" O LEU G 268 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS G 272 " --> pdb=" O SER G 269 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS G 274 " --> pdb=" O ASP G 271 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN G 275 " --> pdb=" O LYS G 272 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE G 276 " --> pdb=" O LYS G 273 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY G 277 " --> pdb=" O LYS G 274 " (cutoff:3.500A) Proline residue: G 278 - end of helix removed outlier: 3.981A pdb=" N ARG G 281 " --> pdb=" O PRO G 278 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS G 284 " --> pdb=" O ARG G 281 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL G 285 " --> pdb=" O TRP G 282 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N PHE G 287 " --> pdb=" O LYS G 284 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N SER G 288 " --> pdb=" O VAL G 285 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE G 291 " --> pdb=" O SER G 288 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE G 292 " --> pdb=" O GLU G 289 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL G 297 " --> pdb=" O TRP G 294 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU G 300 " --> pdb=" O VAL G 297 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL G 302 " --> pdb=" O ALA G 299 " (cutoff:3.500A) Processing helix chain 'G' and resid 328 through 340 removed outlier: 3.879A pdb=" N LEU G 338 " --> pdb=" O VAL G 334 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 75 removed outlier: 3.843A pdb=" N ASN H 31 " --> pdb=" O GLN H 27 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU H 32 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU H 33 " --> pdb=" O GLY H 29 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS H 36 " --> pdb=" O LEU H 32 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG H 43 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY H 59 " --> pdb=" O LYS H 55 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU H 60 " --> pdb=" O MET H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 85 No H-bonds generated for 'chain 'H' and resid 82 through 85' Processing helix chain 'H' and resid 134 through 175 removed outlier: 3.600A pdb=" N ALA H 141 " --> pdb=" O ASN H 137 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU H 147 " --> pdb=" O GLU H 143 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER H 154 " --> pdb=" O SER H 150 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR H 157 " --> pdb=" O THR H 153 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP H 159 " --> pdb=" O PHE H 155 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU H 160 " --> pdb=" O VAL H 156 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE H 164 " --> pdb=" O GLU H 160 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR H 165 " --> pdb=" O ALA H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 215 removed outlier: 3.516A pdb=" N GLU H 197 " --> pdb=" O GLU H 193 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 25 removed outlier: 3.680A pdb=" N GLN I 11 " --> pdb=" O ASP I 7 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET I 16 " --> pdb=" O ILE I 12 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 107 removed outlier: 4.067A pdb=" N GLU I 35 " --> pdb=" O ASP I 31 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN I 49 " --> pdb=" O LEU I 45 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU I 51 " --> pdb=" O GLN I 47 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS I 52 " --> pdb=" O THR I 48 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N MET I 54 " --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR I 56 " --> pdb=" O LYS I 52 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS I 62 " --> pdb=" O GLU I 58 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE I 64 " --> pdb=" O LYS I 60 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP I 89 " --> pdb=" O ARG I 85 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU I 90 " --> pdb=" O ALA I 86 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU I 94 " --> pdb=" O LEU I 90 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER I 103 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL I 105 " --> pdb=" O ARG I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 127 removed outlier: 4.023A pdb=" N GLY I 118 " --> pdb=" O VAL I 114 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY I 123 " --> pdb=" O LEU I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 158 Proline residue: I 142 - end of helix removed outlier: 3.621A pdb=" N ALA I 146 " --> pdb=" O LEU I 143 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL I 148 " --> pdb=" O LYS I 145 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN I 149 " --> pdb=" O ALA I 146 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS I 150 " --> pdb=" O ALA I 147 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE I 152 " --> pdb=" O GLN I 149 " (cutoff:3.500A) Proline residue: I 153 - end of helix removed outlier: 4.647A pdb=" N LYS I 156 " --> pdb=" O PRO I 153 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA I 158 " --> pdb=" O TYR I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 207 removed outlier: 3.546A pdb=" N ASP I 201 " --> pdb=" O GLU I 197 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU I 202 " --> pdb=" O SER I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 213 No H-bonds generated for 'chain 'I' and resid 210 through 213' Processing helix chain 'J' and resid 7 through 107 removed outlier: 3.652A pdb=" N MET J 15 " --> pdb=" O GLN J 11 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE J 38 " --> pdb=" O ALA J 34 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE J 40 " --> pdb=" O GLU J 36 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY J 43 " --> pdb=" O ASN J 39 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN J 47 " --> pdb=" O GLY J 43 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS J 60 " --> pdb=" O TYR J 56 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN J 63 " --> pdb=" O LYS J 59 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE J 64 " --> pdb=" O LYS J 60 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU J 84 " --> pdb=" O ARG J 80 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE J 91 " --> pdb=" O ARG J 87 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU J 94 " --> pdb=" O LEU J 90 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS J 104 " --> pdb=" O GLN J 100 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL J 105 " --> pdb=" O ARG J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 127 removed outlier: 3.967A pdb=" N VAL J 114 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY J 118 " --> pdb=" O VAL J 114 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU J 121 " --> pdb=" O ASP J 117 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY J 123 " --> pdb=" O LEU J 119 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN J 126 " --> pdb=" O GLN J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 158 Proline residue: J 153 - end of helix removed outlier: 3.790A pdb=" N LYS J 156 " --> pdb=" O ILE J 152 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL J 157 " --> pdb=" O PRO J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 207 removed outlier: 3.598A pdb=" N ILE J 203 " --> pdb=" O ARG J 199 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN J 206 " --> pdb=" O LEU J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 213 No H-bonds generated for 'chain 'J' and resid 210 through 213' Processing helix chain 'K' and resid 5 through 14 removed outlier: 3.855A pdb=" N VAL K 8 " --> pdb=" O ASP K 5 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN K 11 " --> pdb=" O VAL K 8 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N HIS K 14 " --> pdb=" O GLN K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 17 through 32 removed outlier: 3.807A pdb=" N GLU K 25 " --> pdb=" O GLN K 21 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS K 26 " --> pdb=" O GLU K 22 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU K 29 " --> pdb=" O GLU K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 107 removed outlier: 3.650A pdb=" N ARG K 44 " --> pdb=" O ILE K 40 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU K 45 " --> pdb=" O GLU K 41 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN K 47 " --> pdb=" O GLY K 43 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU K 51 " --> pdb=" O GLN K 47 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS K 52 " --> pdb=" O THR K 48 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR K 56 " --> pdb=" O LYS K 52 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS K 59 " --> pdb=" O GLU K 55 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLN K 67 " --> pdb=" O GLN K 63 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS K 68 " --> pdb=" O ILE K 64 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS K 69 " --> pdb=" O GLU K 65 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE K 70 " --> pdb=" O GLN K 66 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN K 71 " --> pdb=" O GLN K 67 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN K 74 " --> pdb=" O ILE K 70 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU K 75 " --> pdb=" O GLN K 71 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU K 90 " --> pdb=" O ALA K 86 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU K 94 " --> pdb=" O LEU K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 127 removed outlier: 3.678A pdb=" N VAL K 114 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY K 118 " --> pdb=" O VAL K 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 141 through 158 removed outlier: 3.574A pdb=" N ALA K 146 " --> pdb=" O PRO K 142 " (cutoff:3.500A) Proline residue: K 153 - end of helix removed outlier: 3.847A pdb=" N LYS K 156 " --> pdb=" O ILE K 152 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL K 157 " --> pdb=" O PRO K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 206 removed outlier: 3.601A pdb=" N GLN K 205 " --> pdb=" O ASP K 201 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN K 206 " --> pdb=" O LEU K 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 213 No H-bonds generated for 'chain 'K' and resid 210 through 213' Processing helix chain 'L' and resid 14 through 23 removed outlier: 3.891A pdb=" N THR L 18 " --> pdb=" O GLU L 14 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY L 19 " --> pdb=" O ASP L 15 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU L 22 " --> pdb=" O THR L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 57 Processing helix chain 'L' and resid 68 through 71 No H-bonds generated for 'chain 'L' and resid 68 through 71' Processing helix chain 'L' and resid 75 through 78 No H-bonds generated for 'chain 'L' and resid 75 through 78' Processing helix chain 'M' and resid 7 through 19 removed outlier: 3.510A pdb=" N GLN M 13 " --> pdb=" O GLN M 9 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG M 17 " --> pdb=" O GLN M 13 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA M 18 " --> pdb=" O ALA M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 21 through 27 Processing helix chain 'M' and resid 31 through 39 removed outlier: 3.682A pdb=" N ALA M 36 " --> pdb=" O ARG M 32 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS M 37 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU M 38 " --> pdb=" O LYS M 34 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU M 39 " --> pdb=" O GLN M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 73 removed outlier: 3.696A pdb=" N ARG M 49 " --> pdb=" O GLN M 46 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU M 50 " --> pdb=" O TYR M 47 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG M 51 " --> pdb=" O ARG M 48 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU M 52 " --> pdb=" O ARG M 49 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN M 60 " --> pdb=" O SER M 57 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA M 61 " --> pdb=" O LYS M 58 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA M 62 " --> pdb=" O GLN M 59 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY M 64 " --> pdb=" O ALA M 61 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER M 65 " --> pdb=" O ALA M 62 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER M 70 " --> pdb=" O GLY M 67 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA M 71 " --> pdb=" O ASN M 68 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL M 73 " --> pdb=" O SER M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 90 removed outlier: 3.635A pdb=" N SER M 87 " --> pdb=" O GLY M 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 92 through 103 removed outlier: 3.513A pdb=" N GLY M 101 " --> pdb=" O ALA M 97 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL M 103 " --> pdb=" O LEU M 99 " (cutoff:3.500A) Processing helix chain 'N' and resid 8 through 39 removed outlier: 3.811A pdb=" N GLN N 13 " --> pdb=" O GLN N 9 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA N 14 " --> pdb=" O GLN N 10 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU N 15 " --> pdb=" O LEU N 11 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU N 20 " --> pdb=" O LYS N 16 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG N 31 " --> pdb=" O LYS N 27 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU N 38 " --> pdb=" O LYS N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 54 removed outlier: 3.549A pdb=" N ARG N 48 " --> pdb=" O VAL N 44 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG N 49 " --> pdb=" O ASP N 45 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU N 54 " --> pdb=" O GLU N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 90 removed outlier: 3.660A pdb=" N GLY N 67 " --> pdb=" O MET N 63 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN N 68 " --> pdb=" O GLY N 64 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU N 69 " --> pdb=" O SER N 65 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN N 80 " --> pdb=" O ALA N 76 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN N 82 " --> pdb=" O ARG N 78 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 101 Processing helix chain 'O' and resid 7 through 28 removed outlier: 4.274A pdb=" N GLN O 13 " --> pdb=" O GLN O 9 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA O 14 " --> pdb=" O GLN O 10 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA O 25 " --> pdb=" O LYS O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 32 through 40 removed outlier: 3.557A pdb=" N LYS O 37 " --> pdb=" O LEU O 33 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 50 removed outlier: 4.458A pdb=" N ARG O 48 " --> pdb=" O VAL O 44 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ARG O 49 " --> pdb=" O ASP O 45 " (cutoff:3.500A) Processing helix chain 'O' and resid 52 through 103 removed outlier: 3.873A pdb=" N ALA O 62 " --> pdb=" O LYS O 58 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET O 63 " --> pdb=" O GLN O 59 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY O 64 " --> pdb=" O GLN O 60 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN O 68 " --> pdb=" O GLY O 64 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER O 70 " --> pdb=" O GLN O 66 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA O 71 " --> pdb=" O GLY O 67 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU O 72 " --> pdb=" O ASN O 68 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU O 74 " --> pdb=" O SER O 70 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN O 75 " --> pdb=" O ALA O 71 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA O 76 " --> pdb=" O GLU O 72 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG O 90 " --> pdb=" O SER O 86 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASN O 91 " --> pdb=" O SER O 87 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLU O 93 " --> pdb=" O GLN O 89 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ARG O 94 " --> pdb=" O ARG O 90 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA O 97 " --> pdb=" O GLU O 93 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN O 98 " --> pdb=" O ARG O 94 " (cutoff:3.500A) Processing helix chain 'P' and resid 74 through 82 removed outlier: 3.612A pdb=" N THR P 82 " --> pdb=" O ILE P 78 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 100 Processing helix chain 'P' and resid 121 through 129 Proline residue: P 128 - end of helix Processing helix chain 'P' and resid 135 through 149 removed outlier: 4.385A pdb=" N HIS P 139 " --> pdb=" O LEU P 135 " (cutoff:3.500A) Processing helix chain 'P' and resid 158 through 172 removed outlier: 3.749A pdb=" N TYR P 163 " --> pdb=" O SER P 159 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASN P 166 " --> pdb=" O ASN P 162 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TRP P 167 " --> pdb=" O TYR P 163 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE P 168 " --> pdb=" O TYR P 164 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N THR P 170 " --> pdb=" O ASN P 166 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLN P 171 " --> pdb=" O TRP P 167 " (cutoff:3.500A) Processing helix chain 'P' and resid 180 through 190 removed outlier: 3.676A pdb=" N ALA P 184 " --> pdb=" O VAL P 180 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU P 189 " --> pdb=" O GLY P 185 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET P 190 " --> pdb=" O CYS P 186 " (cutoff:3.500A) Processing helix chain 'P' and resid 194 through 204 removed outlier: 3.805A pdb=" N PHE P 198 " --> pdb=" O ASN P 194 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA P 199 " --> pdb=" O GLU P 195 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU P 202 " --> pdb=" O PHE P 198 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA P 203 " --> pdb=" O ALA P 199 " (cutoff:3.500A) Processing helix chain 'P' and resid 206 through 213 removed outlier: 3.538A pdb=" N GLY P 211 " --> pdb=" O CYS P 208 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU P 213 " --> pdb=" O MET P 210 " (cutoff:3.500A) Processing helix chain 'P' and resid 221 through 233 removed outlier: 3.553A pdb=" N ALA P 233 " --> pdb=" O VAL P 229 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 242 removed outlier: 3.951A pdb=" N GLU P 240 " --> pdb=" O PRO P 236 " (cutoff:3.500A) Processing helix chain 'P' and resid 247 through 255 Processing helix chain 'P' and resid 263 through 276 removed outlier: 3.615A pdb=" N ALA P 269 " --> pdb=" O ARG P 265 " (cutoff:3.500A) Processing helix chain 'P' and resid 285 through 288 No H-bonds generated for 'chain 'P' and resid 285 through 288' Processing helix chain 'P' and resid 297 through 305 removed outlier: 3.679A pdb=" N GLU P 301 " --> pdb=" O LEU P 297 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASN P 302 " --> pdb=" O LYS P 298 " (cutoff:3.500A) Processing helix chain 'P' and resid 311 through 329 removed outlier: 3.876A pdb=" N LYS P 318 " --> pdb=" O SER P 314 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU P 326 " --> pdb=" O GLU P 322 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER P 327 " --> pdb=" O LYS P 323 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL P 328 " --> pdb=" O LEU P 324 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLN P 329 " --> pdb=" O GLY P 325 " (cutoff:3.500A) Processing helix chain 'P' and resid 335 through 343 removed outlier: 3.522A pdb=" N SER P 343 " --> pdb=" O SER P 339 " (cutoff:3.500A) Processing helix chain 'P' and resid 350 through 353 No H-bonds generated for 'chain 'P' and resid 350 through 353' Processing helix chain 'P' and resid 355 through 360 Processing helix chain 'P' and resid 364 through 367 No H-bonds generated for 'chain 'P' and resid 364 through 367' Processing helix chain 'P' and resid 374 through 382 Processing helix chain 'P' and resid 388 through 402 removed outlier: 3.556A pdb=" N TYR P 399 " --> pdb=" O ASP P 395 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS P 402 " --> pdb=" O GLU P 398 " (cutoff:3.500A) Processing helix chain 'P' and resid 404 through 413 removed outlier: 3.780A pdb=" N ILE P 410 " --> pdb=" O LYS P 407 " (cutoff:3.500A) Processing helix chain 'P' and resid 415 through 424 removed outlier: 4.083A pdb=" N HIS P 424 " --> pdb=" O MET P 420 " (cutoff:3.500A) Processing helix chain 'P' and resid 428 through 440 Processing helix chain 'a' and resid 24 through 32 Processing helix chain 'a' and resid 52 through 75 removed outlier: 3.778A pdb=" N ARG a 56 " --> pdb=" O VAL a 52 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG a 57 " --> pdb=" O ASN a 53 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG a 73 " --> pdb=" O GLU a 69 " (cutoff:3.500A) Processing helix chain 'a' and resid 94 through 114 removed outlier: 3.635A pdb=" N GLU a 98 " --> pdb=" O MET a 94 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA a 99 " --> pdb=" O ILE a 95 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR a 113 " --> pdb=" O LYS a 109 " (cutoff:3.500A) Processing helix chain 'a' and resid 116 through 139 removed outlier: 3.639A pdb=" N LEU a 125 " --> pdb=" O ASN a 121 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU a 127 " --> pdb=" O LEU a 123 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU a 128 " --> pdb=" O GLU a 124 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE a 131 " --> pdb=" O GLU a 127 " (cutoff:3.500A) Processing helix chain 'a' and resid 177 through 190 removed outlier: 3.533A pdb=" N ILE a 180 " --> pdb=" O ARG a 177 " (cutoff:3.500A) Proline residue: a 181 - end of helix removed outlier: 3.768A pdb=" N GLU a 184 " --> pdb=" O PRO a 181 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG a 185 " --> pdb=" O THR a 182 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU a 187 " --> pdb=" O GLU a 184 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL a 190 " --> pdb=" O LEU a 187 " (cutoff:3.500A) Processing helix chain 'a' and resid 231 through 239 removed outlier: 3.838A pdb=" N LYS a 235 " --> pdb=" O ASN a 231 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ILE a 236 " --> pdb=" O ARG a 232 " (cutoff:3.500A) Processing helix chain 'a' and resid 254 through 287 Processing helix chain 'a' and resid 290 through 308 removed outlier: 3.749A pdb=" N ILE a 295 " --> pdb=" O ARG a 291 " (cutoff:3.500A) Processing helix chain 'a' and resid 330 through 340 removed outlier: 3.536A pdb=" N GLN a 334 " --> pdb=" O LEU a 330 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG a 339 " --> pdb=" O PHE a 335 " (cutoff:3.500A) Processing helix chain 'a' and resid 372 through 381 removed outlier: 3.687A pdb=" N VAL a 378 " --> pdb=" O PHE a 374 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TYR a 381 " --> pdb=" O ILE a 377 " (cutoff:3.500A) Processing helix chain 'a' and resid 392 through 406 removed outlier: 4.620A pdb=" N ILE a 397 " --> pdb=" O PRO a 393 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE a 399 " --> pdb=" O THR a 395 " (cutoff:3.500A) Proline residue: a 400 - end of helix removed outlier: 3.891A pdb=" N MET a 406 " --> pdb=" O LEU a 402 " (cutoff:3.500A) Processing helix chain 'a' and resid 410 through 425 Processing helix chain 'a' and resid 427 through 432 Processing helix chain 'a' and resid 438 through 445 removed outlier: 3.637A pdb=" N THR a 442 " --> pdb=" O GLU a 438 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE a 443 " --> pdb=" O MET a 439 " (cutoff:3.500A) Processing helix chain 'a' and resid 449 through 463 Processing helix chain 'a' and resid 482 through 488 Processing helix chain 'a' and resid 493 through 495 No H-bonds generated for 'chain 'a' and resid 493 through 495' Processing helix chain 'a' and resid 529 through 558 removed outlier: 3.651A pdb=" N SER a 535 " --> pdb=" O THR a 531 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET a 538 " --> pdb=" O ASN a 534 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS a 539 " --> pdb=" O SER a 535 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL a 542 " --> pdb=" O MET a 538 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE a 547 " --> pdb=" O ILE a 543 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU a 555 " --> pdb=" O PHE a 551 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER a 556 " --> pdb=" O GLY a 552 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU a 557 " --> pdb=" O VAL a 553 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE a 558 " --> pdb=" O SER a 554 " (cutoff:3.500A) Processing helix chain 'a' and resid 566 through 572 removed outlier: 3.666A pdb=" N TYR a 570 " --> pdb=" O PRO a 566 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE a 571 " --> pdb=" O LEU a 567 " (cutoff:3.500A) Processing helix chain 'a' and resid 574 through 583 Processing helix chain 'a' and resid 585 through 597 removed outlier: 3.685A pdb=" N ILE a 589 " --> pdb=" O GLY a 585 " (cutoff:3.500A) Processing helix chain 'a' and resid 609 through 617 removed outlier: 3.663A pdb=" N MET a 616 " --> pdb=" O HIS a 612 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE a 617 " --> pdb=" O PHE a 613 " (cutoff:3.500A) Processing helix chain 'a' and resid 633 through 655 removed outlier: 3.635A pdb=" N CYS a 638 " --> pdb=" O LYS a 634 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE a 639 " --> pdb=" O GLY a 635 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS a 647 " --> pdb=" O VAL a 643 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL a 648 " --> pdb=" O ALA a 644 " (cutoff:3.500A) Proline residue: a 649 - end of helix removed outlier: 4.059A pdb=" N PHE a 654 " --> pdb=" O TRP a 650 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS a 655 " --> pdb=" O MET a 651 " (cutoff:3.500A) Processing helix chain 'a' and resid 715 through 758 removed outlier: 3.871A pdb=" N VAL a 719 " --> pdb=" O GLY a 715 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN a 721 " --> pdb=" O THR a 717 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE a 723 " --> pdb=" O VAL a 719 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS a 724 " --> pdb=" O HIS a 720 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR a 728 " --> pdb=" O HIS a 724 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY a 731 " --> pdb=" O GLU a 727 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE a 733 " --> pdb=" O CYS a 729 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR a 739 " --> pdb=" O ASN a 735 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU a 740 " --> pdb=" O THR a 736 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ARG a 741 " --> pdb=" O ALA a 737 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LEU a 742 " --> pdb=" O SER a 738 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TRP a 743 " --> pdb=" O TYR a 739 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER a 746 " --> pdb=" O LEU a 742 " (cutoff:3.500A) Processing helix chain 'a' and resid 762 through 765 No H-bonds generated for 'chain 'a' and resid 762 through 765' Processing helix chain 'a' and resid 774 through 789 removed outlier: 4.005A pdb=" N PHE a 778 " --> pdb=" O LEU a 774 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR a 785 " --> pdb=" O ALA a 781 " (cutoff:3.500A) Processing helix chain 'a' and resid 793 through 808 removed outlier: 3.775A pdb=" N LEU a 806 " --> pdb=" O HIS a 802 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N HIS a 807 " --> pdb=" O ALA a 803 " (cutoff:3.500A) Processing helix chain 'b' and resid 4 through 26 removed outlier: 3.673A pdb=" N TYR b 8 " --> pdb=" O LEU b 4 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL b 13 " --> pdb=" O SER b 9 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL b 21 " --> pdb=" O ALA b 17 " (cutoff:3.500A) Processing helix chain 'b' and resid 31 through 34 Processing helix chain 'b' and resid 37 through 43 Processing helix chain 'b' and resid 46 through 79 removed outlier: 3.678A pdb=" N SER b 50 " --> pdb=" O PRO b 46 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE b 58 " --> pdb=" O ILE b 54 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER b 61 " --> pdb=" O ALA b 57 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY b 64 " --> pdb=" O LEU b 60 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR b 70 " --> pdb=" O ALA b 66 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE b 71 " --> pdb=" O TRP b 67 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR b 72 " --> pdb=" O GLY b 68 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER b 75 " --> pdb=" O ILE b 71 " (cutoff:3.500A) Processing helix chain 'b' and resid 84 through 96 removed outlier: 3.760A pdb=" N LYS b 87 " --> pdb=" O PRO b 84 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR b 88 " --> pdb=" O ARG b 85 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASN b 90 " --> pdb=" O LYS b 87 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU b 91 " --> pdb=" O THR b 88 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL b 92 " --> pdb=" O LYS b 89 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER b 93 " --> pdb=" O ASN b 90 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE b 96 " --> pdb=" O SER b 93 " (cutoff:3.500A) Processing helix chain 'b' and resid 99 through 113 removed outlier: 3.567A pdb=" N ASN b 113 " --> pdb=" O ILE b 109 " (cutoff:3.500A) Processing helix chain 'b' and resid 128 through 168 removed outlier: 3.657A pdb=" N ALA b 133 " --> pdb=" O ARG b 129 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET b 137 " --> pdb=" O ALA b 133 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER b 147 " --> pdb=" O THR b 143 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN b 148 " --> pdb=" O VAL b 144 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA b 167 " --> pdb=" O ALA b 163 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN b 168 " --> pdb=" O LEU b 164 " (cutoff:3.500A) Processing helix chain 'b' and resid 170 through 197 removed outlier: 4.075A pdb=" N PHE b 173 " --> pdb=" O PRO b 170 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N VAL b 174 " --> pdb=" O SER b 171 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE b 176 " --> pdb=" O PHE b 173 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU b 177 " --> pdb=" O VAL b 174 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA b 185 " --> pdb=" O PHE b 182 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE b 186 " --> pdb=" O GLY b 183 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE b 192 " --> pdb=" O PHE b 189 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE b 195 " --> pdb=" O ILE b 192 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN b 197 " --> pdb=" O ALA b 194 " (cutoff:3.500A) Processing helix chain 'd' and resid 14 through 22 removed outlier: 3.678A pdb=" N GLY d 18 " --> pdb=" O GLY d 14 " (cutoff:3.500A) Processing helix chain 'd' and resid 30 through 37 removed outlier: 3.571A pdb=" N ASN d 35 " --> pdb=" O ALA d 31 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU d 36 " --> pdb=" O ASP d 32 " (cutoff:3.500A) Processing helix chain 'd' and resid 42 through 51 removed outlier: 3.501A pdb=" N LEU d 47 " --> pdb=" O GLU d 43 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N SER d 51 " --> pdb=" O LEU d 47 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 86 removed outlier: 3.601A pdb=" N ASP d 72 " --> pdb=" O SER d 68 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG d 73 " --> pdb=" O VAL d 69 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET d 78 " --> pdb=" O LEU d 74 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET d 85 " --> pdb=" O GLU d 81 " (cutoff:3.500A) Processing helix chain 'd' and resid 94 through 100 removed outlier: 3.526A pdb=" N ILE d 100 " --> pdb=" O PHE d 96 " (cutoff:3.500A) Processing helix chain 'd' and resid 102 through 117 removed outlier: 3.815A pdb=" N ASP d 107 " --> pdb=" O SER d 103 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLY d 115 " --> pdb=" O LEU d 111 " (cutoff:3.500A) Processing helix chain 'd' and resid 122 through 124 No H-bonds generated for 'chain 'd' and resid 122 through 124' Processing helix chain 'd' and resid 152 through 157 removed outlier: 4.708A pdb=" N ASP d 157 " --> pdb=" O ALA d 153 " (cutoff:3.500A) Processing helix chain 'd' and resid 164 through 166 No H-bonds generated for 'chain 'd' and resid 164 through 166' Processing helix chain 'd' and resid 180 through 199 removed outlier: 3.739A pdb=" N LEU d 185 " --> pdb=" O ILE d 181 " (cutoff:3.500A) Processing helix chain 'd' and resid 202 through 206 removed outlier: 3.603A pdb=" N ASP d 206 " --> pdb=" O THR d 203 " (cutoff:3.500A) Processing helix chain 'd' and resid 209 through 226 removed outlier: 3.636A pdb=" N PHE d 214 " --> pdb=" O PRO d 210 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE d 223 " --> pdb=" O ARG d 219 " (cutoff:3.500A) Processing helix chain 'd' and resid 234 through 239 Processing helix chain 'd' and resid 251 through 257 removed outlier: 3.807A pdb=" N ARG d 257 " --> pdb=" O ALA d 253 " (cutoff:3.500A) Processing helix chain 'd' and resid 261 through 266 Processing helix chain 'd' and resid 290 through 306 removed outlier: 4.131A pdb=" N GLU d 296 " --> pdb=" O ASP d 292 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE d 306 " --> pdb=" O ASN d 302 " (cutoff:3.500A) Processing helix chain 'd' and resid 312 through 337 removed outlier: 3.679A pdb=" N TYR d 316 " --> pdb=" O GLY d 313 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA d 317 " --> pdb=" O VAL d 314 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL d 319 " --> pdb=" O TYR d 316 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU d 323 " --> pdb=" O LYS d 320 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE d 329 " --> pdb=" O CYS d 326 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL d 330 " --> pdb=" O ARG d 327 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU d 334 " --> pdb=" O TRP d 331 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA d 337 " --> pdb=" O GLU d 334 " (cutoff:3.500A) Processing helix chain 'e' and resid 9 through 16 removed outlier: 3.971A pdb=" N THR e 15 " --> pdb=" O VAL e 11 " (cutoff:3.500A) Processing helix chain 'e' and resid 34 through 56 removed outlier: 3.752A pdb=" N LEU e 50 " --> pdb=" O VAL e 46 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA e 55 " --> pdb=" O PHE e 51 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE e 56 " --> pdb=" O TRP e 52 " (cutoff:3.500A) Processing helix chain 'e' and resid 70 through 77 removed outlier: 3.928A pdb=" N TRP e 74 " --> pdb=" O ASN e 70 " (cutoff:3.500A) Processing helix chain 's' and resid 422 through 447 removed outlier: 3.808A pdb=" N LEU s 429 " --> pdb=" O TRP s 425 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE s 433 " --> pdb=" O LEU s 429 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE s 436 " --> pdb=" O LEU s 432 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE s 437 " --> pdb=" O PHE s 433 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER s 447 " --> pdb=" O HIS s 443 " (cutoff:3.500A) Processing helix chain 'r' and resid 304 through 330 removed outlier: 3.649A pdb=" N ASN r 309 " --> pdb=" O PRO r 305 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE r 314 " --> pdb=" O LEU r 310 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR r 321 " --> pdb=" O GLY r 317 " (cutoff:3.500A) Processing helix chain 'c' and resid 9 through 44 removed outlier: 4.046A pdb=" N SER c 12 " --> pdb=" O GLU c 9 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE c 14 " --> pdb=" O ALA c 11 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA c 15 " --> pdb=" O SER c 12 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA c 21 " --> pdb=" O GLY c 18 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA c 22 " --> pdb=" O ALA c 19 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL c 24 " --> pdb=" O ALA c 21 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N PHE c 25 " --> pdb=" O ALA c 22 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER c 26 " --> pdb=" O MET c 23 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY c 29 " --> pdb=" O SER c 26 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA c 31 " --> pdb=" O LEU c 28 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR c 32 " --> pdb=" O GLY c 29 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY c 33 " --> pdb=" O ALA c 30 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA c 35 " --> pdb=" O TYR c 32 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N LYS c 36 " --> pdb=" O GLY c 33 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER c 37 " --> pdb=" O THR c 34 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR c 39 " --> pdb=" O LYS c 36 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA c 42 " --> pdb=" O THR c 39 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA c 43 " --> pdb=" O GLY c 40 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET c 44 " --> pdb=" O ILE c 41 " (cutoff:3.500A) Processing helix chain 'c' and resid 57 through 79 removed outlier: 3.627A pdb=" N ALA c 62 " --> pdb=" O PRO c 58 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE c 65 " --> pdb=" O MET c 61 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA c 66 " --> pdb=" O ALA c 62 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL c 72 " --> pdb=" O TYR c 68 " (cutoff:3.500A) Processing helix chain 'c' and resid 86 through 123 removed outlier: 3.587A pdb=" N LEU c 101 " --> pdb=" O LEU c 97 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER c 102 " --> pdb=" O SER c 98 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA c 105 " --> pdb=" O LEU c 101 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG c 119 " --> pdb=" O ASP c 115 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA c 122 " --> pdb=" O VAL c 118 " (cutoff:3.500A) Processing helix chain 'c' and resid 125 through 153 removed outlier: 3.583A pdb=" N PHE c 128 " --> pdb=" O PRO c 125 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL c 129 " --> pdb=" O ARG c 126 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET c 131 " --> pdb=" O PHE c 128 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE c 132 " --> pdb=" O VAL c 129 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU c 135 " --> pdb=" O ILE c 132 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA c 138 " --> pdb=" O LEU c 135 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL c 140 " --> pdb=" O PHE c 137 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU c 141 " --> pdb=" O ALA c 138 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR c 144 " --> pdb=" O LEU c 141 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE c 147 " --> pdb=" O TYR c 144 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL c 148 " --> pdb=" O GLY c 145 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU c 150 " --> pdb=" O ILE c 147 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE c 151 " --> pdb=" O VAL c 148 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER c 153 " --> pdb=" O LEU c 150 " (cutoff:3.500A) Processing helix chain 'g' and resid 9 through 44 removed outlier: 3.797A pdb=" N SER g 12 " --> pdb=" O GLU g 9 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL g 16 " --> pdb=" O PHE g 13 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER g 20 " --> pdb=" O MET g 17 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA g 21 " --> pdb=" O GLY g 18 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA g 22 " --> pdb=" O ALA g 19 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL g 24 " --> pdb=" O ALA g 21 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE g 25 " --> pdb=" O ALA g 22 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU g 28 " --> pdb=" O PHE g 25 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA g 31 " --> pdb=" O LEU g 28 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA g 35 " --> pdb=" O TYR g 32 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LYS g 36 " --> pdb=" O GLY g 33 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER g 37 " --> pdb=" O THR g 34 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR g 39 " --> pdb=" O LYS g 36 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA g 42 " --> pdb=" O THR g 39 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA g 43 " --> pdb=" O GLY g 40 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET g 44 " --> pdb=" O ILE g 41 " (cutoff:3.500A) Processing helix chain 'g' and resid 55 through 61 Proline residue: g 58 - end of helix removed outlier: 3.706A pdb=" N MET g 61 " --> pdb=" O PRO g 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 55 through 61' Processing helix chain 'g' and resid 63 through 78 removed outlier: 3.672A pdb=" N VAL g 72 " --> pdb=" O TYR g 68 " (cutoff:3.500A) Processing helix chain 'g' and resid 86 through 123 removed outlier: 3.556A pdb=" N LEU g 91 " --> pdb=" O TYR g 87 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN g 92 " --> pdb=" O ARG g 88 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA g 122 " --> pdb=" O VAL g 118 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN g 123 " --> pdb=" O ARG g 119 " (cutoff:3.500A) Processing helix chain 'g' and resid 125 through 153 removed outlier: 3.814A pdb=" N VAL g 129 " --> pdb=" O ARG g 126 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N MET g 131 " --> pdb=" O PHE g 128 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE g 132 " --> pdb=" O VAL g 129 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE g 134 " --> pdb=" O MET g 131 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU g 135 " --> pdb=" O ILE g 132 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE g 136 " --> pdb=" O LEU g 133 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA g 138 " --> pdb=" O LEU g 135 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL g 140 " --> pdb=" O PHE g 137 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU g 141 " --> pdb=" O ALA g 138 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR g 144 " --> pdb=" O LEU g 141 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE g 147 " --> pdb=" O TYR g 144 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL g 148 " --> pdb=" O GLY g 145 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU g 150 " --> pdb=" O ILE g 147 " (cutoff:3.500A) Processing helix chain 'k' and resid 9 through 44 removed outlier: 4.150A pdb=" N SER k 12 " --> pdb=" O GLU k 9 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA k 15 " --> pdb=" O SER k 12 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL k 16 " --> pdb=" O PHE k 13 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER k 20 " --> pdb=" O MET k 17 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA k 21 " --> pdb=" O GLY k 18 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA k 22 " --> pdb=" O ALA k 19 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL k 24 " --> pdb=" O ALA k 21 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N PHE k 25 " --> pdb=" O ALA k 22 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA k 27 " --> pdb=" O VAL k 24 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA k 31 " --> pdb=" O LEU k 28 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY k 33 " --> pdb=" O ALA k 30 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR k 34 " --> pdb=" O ALA k 31 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA k 35 " --> pdb=" O TYR k 32 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS k 36 " --> pdb=" O GLY k 33 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER k 37 " --> pdb=" O THR k 34 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR k 39 " --> pdb=" O LYS k 36 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA k 43 " --> pdb=" O GLY k 40 " (cutoff:3.500A) Processing helix chain 'k' and resid 50 through 55 removed outlier: 4.393A pdb=" N MET k 53 " --> pdb=" O GLU k 50 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LYS k 54 " --> pdb=" O MET k 51 " (cutoff:3.500A) Processing helix chain 'k' and resid 57 through 78 removed outlier: 3.928A pdb=" N ILE k 65 " --> pdb=" O MET k 61 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA k 66 " --> pdb=" O ALA k 62 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL k 72 " --> pdb=" O TYR k 68 " (cutoff:3.500A) Processing helix chain 'k' and resid 86 through 121 removed outlier: 3.602A pdb=" N VAL k 99 " --> pdb=" O ALA k 95 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER k 102 " --> pdb=" O SER k 98 " (cutoff:3.500A) Processing helix chain 'k' and resid 125 through 154 removed outlier: 3.955A pdb=" N VAL k 129 " --> pdb=" O ARG k 126 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET k 131 " --> pdb=" O PHE k 128 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE k 132 " --> pdb=" O VAL k 129 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU k 135 " --> pdb=" O ILE k 132 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL k 140 " --> pdb=" O PHE k 137 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU k 141 " --> pdb=" O ALA k 138 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR k 144 " --> pdb=" O LEU k 141 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE k 147 " --> pdb=" O TYR k 144 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL k 148 " --> pdb=" O GLY k 145 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU k 150 " --> pdb=" O ILE k 147 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE k 151 " --> pdb=" O VAL k 148 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU k 152 " --> pdb=" O ALA k 149 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR k 154 " --> pdb=" O ILE k 151 " (cutoff:3.500A) Processing helix chain 'l' and resid 11 through 44 removed outlier: 3.552A pdb=" N PHE l 14 " --> pdb=" O ALA l 11 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA l 15 " --> pdb=" O SER l 12 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL l 16 " --> pdb=" O PHE l 13 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER l 20 " --> pdb=" O MET l 17 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA l 21 " --> pdb=" O GLY l 18 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA l 22 " --> pdb=" O ALA l 19 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL l 24 " --> pdb=" O ALA l 21 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N PHE l 25 " --> pdb=" O ALA l 22 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA l 27 " --> pdb=" O VAL l 24 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA l 31 " --> pdb=" O LEU l 28 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY l 33 " --> pdb=" O ALA l 30 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA l 35 " --> pdb=" O TYR l 32 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS l 36 " --> pdb=" O GLY l 33 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER l 37 " --> pdb=" O THR l 34 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR l 39 " --> pdb=" O LYS l 36 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA l 42 " --> pdb=" O THR l 39 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA l 43 " --> pdb=" O GLY l 40 " (cutoff:3.500A) Processing helix chain 'l' and resid 53 through 78 removed outlier: 3.663A pdb=" N ILE l 56 " --> pdb=" O MET l 53 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE l 57 " --> pdb=" O LYS l 54 " (cutoff:3.500A) Proline residue: l 58 - end of helix removed outlier: 3.668A pdb=" N MET l 61 " --> pdb=" O PRO l 58 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL l 71 " --> pdb=" O TYR l 68 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL l 72 " --> pdb=" O GLY l 69 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE l 76 " --> pdb=" O ALA l 73 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN l 78 " --> pdb=" O LEU l 75 " (cutoff:3.500A) Processing helix chain 'l' and resid 86 through 120 removed outlier: 3.633A pdb=" N VAL l 99 " --> pdb=" O ALA l 95 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N SER l 102 " --> pdb=" O SER l 98 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL l 113 " --> pdb=" O ALA l 109 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL l 118 " --> pdb=" O GLY l 114 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG l 119 " --> pdb=" O ASP l 115 " (cutoff:3.500A) Processing helix chain 'l' and resid 125 through 153 removed outlier: 3.706A pdb=" N VAL l 129 " --> pdb=" O ARG l 126 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET l 131 " --> pdb=" O PHE l 128 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE l 132 " --> pdb=" O VAL l 129 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU l 135 " --> pdb=" O ILE l 132 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL l 140 " --> pdb=" O PHE l 137 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU l 141 " --> pdb=" O ALA l 138 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR l 144 " --> pdb=" O LEU l 141 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE l 147 " --> pdb=" O TYR l 144 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL l 148 " --> pdb=" O GLY l 145 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU l 150 " --> pdb=" O ILE l 147 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE l 151 " --> pdb=" O VAL l 148 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU l 152 " --> pdb=" O ALA l 149 " (cutoff:3.500A) Processing helix chain 'm' and resid 9 through 45 removed outlier: 4.167A pdb=" N SER m 12 " --> pdb=" O GLU m 9 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE m 14 " --> pdb=" O ALA m 11 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA m 15 " --> pdb=" O SER m 12 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL m 16 " --> pdb=" O PHE m 13 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA m 21 " --> pdb=" O GLY m 18 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA m 22 " --> pdb=" O ALA m 19 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL m 24 " --> pdb=" O ALA m 21 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N PHE m 25 " --> pdb=" O ALA m 22 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER m 26 " --> pdb=" O MET m 23 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA m 31 " --> pdb=" O LEU m 28 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY m 33 " --> pdb=" O ALA m 30 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA m 35 " --> pdb=" O TYR m 32 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS m 36 " --> pdb=" O GLY m 33 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER m 37 " --> pdb=" O THR m 34 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR m 39 " --> pdb=" O LYS m 36 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA m 43 " --> pdb=" O GLY m 40 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER m 45 " --> pdb=" O ALA m 42 " (cutoff:3.500A) Processing helix chain 'm' and resid 55 through 78 Proline residue: m 58 - end of helix removed outlier: 3.632A pdb=" N MET m 61 " --> pdb=" O PRO m 58 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA m 62 " --> pdb=" O VAL m 59 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL m 71 " --> pdb=" O TYR m 68 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL m 72 " --> pdb=" O GLY m 69 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL m 74 " --> pdb=" O VAL m 71 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE m 76 " --> pdb=" O ALA m 73 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN m 78 " --> pdb=" O LEU m 75 " (cutoff:3.500A) Processing helix chain 'm' and resid 86 through 120 removed outlier: 3.532A pdb=" N LEU m 91 " --> pdb=" O TYR m 87 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN m 92 " --> pdb=" O ARG m 88 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N SER m 102 " --> pdb=" O SER m 98 " (cutoff:3.500A) Processing helix chain 'm' and resid 125 through 154 removed outlier: 3.668A pdb=" N VAL m 129 " --> pdb=" O ARG m 126 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N MET m 131 " --> pdb=" O PHE m 128 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE m 132 " --> pdb=" O VAL m 129 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU m 135 " --> pdb=" O ILE m 132 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL m 140 " --> pdb=" O PHE m 137 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU m 141 " --> pdb=" O ALA m 138 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR m 144 " --> pdb=" O LEU m 141 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY m 145 " --> pdb=" O GLY m 142 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE m 147 " --> pdb=" O TYR m 144 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL m 148 " --> pdb=" O GLY m 145 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU m 150 " --> pdb=" O ILE m 147 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE m 151 " --> pdb=" O VAL m 148 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU m 152 " --> pdb=" O ALA m 149 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR m 154 " --> pdb=" O ILE m 151 " (cutoff:3.500A) Processing helix chain 'n' and resid 9 through 44 removed outlier: 4.321A pdb=" N SER n 12 " --> pdb=" O GLU n 9 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE n 13 " --> pdb=" O TYR n 10 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL n 16 " --> pdb=" O PHE n 13 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER n 20 " --> pdb=" O MET n 17 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA n 21 " --> pdb=" O GLY n 18 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA n 22 " --> pdb=" O ALA n 19 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL n 24 " --> pdb=" O ALA n 21 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N PHE n 25 " --> pdb=" O ALA n 22 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER n 26 " --> pdb=" O MET n 23 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA n 27 " --> pdb=" O VAL n 24 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU n 28 " --> pdb=" O PHE n 25 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY n 33 " --> pdb=" O ALA n 30 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA n 35 " --> pdb=" O TYR n 32 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS n 36 " --> pdb=" O GLY n 33 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER n 37 " --> pdb=" O THR n 34 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR n 39 " --> pdb=" O LYS n 36 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA n 42 " --> pdb=" O THR n 39 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA n 43 " --> pdb=" O GLY n 40 " (cutoff:3.500A) Processing helix chain 'n' and resid 57 through 78 removed outlier: 3.590A pdb=" N ILE n 64 " --> pdb=" O VAL n 60 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE n 65 " --> pdb=" O MET n 61 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA n 66 " --> pdb=" O ALA n 62 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL n 72 " --> pdb=" O TYR n 68 " (cutoff:3.500A) Processing helix chain 'n' and resid 86 through 123 removed outlier: 3.595A pdb=" N GLN n 92 " --> pdb=" O ARG n 88 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER n 102 " --> pdb=" O SER n 98 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL n 118 " --> pdb=" O GLY n 114 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG n 119 " --> pdb=" O ASP n 115 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA n 122 " --> pdb=" O VAL n 118 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN n 123 " --> pdb=" O ARG n 119 " (cutoff:3.500A) Processing helix chain 'n' and resid 125 through 153 removed outlier: 3.598A pdb=" N PHE n 128 " --> pdb=" O PRO n 125 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL n 129 " --> pdb=" O ARG n 126 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET n 131 " --> pdb=" O PHE n 128 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE n 132 " --> pdb=" O VAL n 129 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA n 138 " --> pdb=" O LEU n 135 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL n 140 " --> pdb=" O PHE n 137 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU n 141 " --> pdb=" O ALA n 138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR n 144 " --> pdb=" O LEU n 141 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE n 147 " --> pdb=" O TYR n 144 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL n 148 " --> pdb=" O GLY n 145 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU n 150 " --> pdb=" O ILE n 147 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE n 151 " --> pdb=" O VAL n 148 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU n 152 " --> pdb=" O ALA n 149 " (cutoff:3.500A) Processing helix chain 'o' and resid 11 through 44 removed outlier: 3.583A pdb=" N PHE o 14 " --> pdb=" O ALA o 11 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA o 15 " --> pdb=" O SER o 12 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER o 20 " --> pdb=" O MET o 17 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA o 21 " --> pdb=" O GLY o 18 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA o 22 " --> pdb=" O ALA o 19 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL o 24 " --> pdb=" O ALA o 21 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N PHE o 25 " --> pdb=" O ALA o 22 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER o 26 " --> pdb=" O MET o 23 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY o 33 " --> pdb=" O ALA o 30 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA o 35 " --> pdb=" O TYR o 32 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYS o 36 " --> pdb=" O GLY o 33 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER o 37 " --> pdb=" O THR o 34 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR o 39 " --> pdb=" O LYS o 36 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA o 43 " --> pdb=" O GLY o 40 " (cutoff:3.500A) Processing helix chain 'o' and resid 50 through 52 No H-bonds generated for 'chain 'o' and resid 50 through 52' Processing helix chain 'o' and resid 55 through 78 Proline residue: o 58 - end of helix removed outlier: 4.000A pdb=" N MET o 61 " --> pdb=" O PRO o 58 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA o 62 " --> pdb=" O VAL o 59 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE o 64 " --> pdb=" O MET o 61 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL o 71 " --> pdb=" O TYR o 68 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL o 72 " --> pdb=" O GLY o 69 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA o 73 " --> pdb=" O LEU o 70 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE o 76 " --> pdb=" O ALA o 73 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN o 78 " --> pdb=" O LEU o 75 " (cutoff:3.500A) Processing helix chain 'o' and resid 86 through 121 removed outlier: 4.280A pdb=" N SER o 102 " --> pdb=" O SER o 98 " (cutoff:3.500A) Processing helix chain 'o' and resid 125 through 154 removed outlier: 3.835A pdb=" N VAL o 129 " --> pdb=" O ARG o 126 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET o 131 " --> pdb=" O PHE o 128 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE o 132 " --> pdb=" O VAL o 129 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE o 134 " --> pdb=" O MET o 131 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE o 136 " --> pdb=" O LEU o 133 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA o 138 " --> pdb=" O LEU o 135 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL o 140 " --> pdb=" O PHE o 137 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU o 141 " --> pdb=" O ALA o 138 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR o 144 " --> pdb=" O LEU o 141 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE o 147 " --> pdb=" O TYR o 144 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL o 148 " --> pdb=" O GLY o 145 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU o 150 " --> pdb=" O ILE o 147 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE o 151 " --> pdb=" O VAL o 148 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU o 152 " --> pdb=" O ALA o 149 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR o 154 " --> pdb=" O ILE o 151 " (cutoff:3.500A) Processing helix chain 'p' and resid 11 through 45 removed outlier: 3.766A pdb=" N PHE p 14 " --> pdb=" O ALA p 11 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA p 15 " --> pdb=" O SER p 12 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL p 16 " --> pdb=" O PHE p 13 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER p 20 " --> pdb=" O MET p 17 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA p 21 " --> pdb=" O GLY p 18 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA p 22 " --> pdb=" O ALA p 19 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL p 24 " --> pdb=" O ALA p 21 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N PHE p 25 " --> pdb=" O ALA p 22 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER p 26 " --> pdb=" O MET p 23 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU p 28 " --> pdb=" O PHE p 25 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY p 29 " --> pdb=" O SER p 26 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA p 31 " --> pdb=" O LEU p 28 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY p 33 " --> pdb=" O ALA p 30 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA p 35 " --> pdb=" O TYR p 32 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LYS p 36 " --> pdb=" O GLY p 33 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER p 37 " --> pdb=" O THR p 34 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY p 38 " --> pdb=" O ALA p 35 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR p 39 " --> pdb=" O LYS p 36 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA p 42 " --> pdb=" O THR p 39 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA p 43 " --> pdb=" O GLY p 40 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER p 45 " --> pdb=" O ALA p 42 " (cutoff:3.500A) Processing helix chain 'p' and resid 57 through 77 removed outlier: 3.565A pdb=" N ALA p 62 " --> pdb=" O PRO p 58 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY p 63 " --> pdb=" O VAL p 59 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE p 65 " --> pdb=" O MET p 61 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL p 72 " --> pdb=" O TYR p 68 " (cutoff:3.500A) Processing helix chain 'p' and resid 86 through 121 removed outlier: 4.072A pdb=" N SER p 102 " --> pdb=" O SER p 98 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL p 118 " --> pdb=" O GLY p 114 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG p 119 " --> pdb=" O ASP p 115 " (cutoff:3.500A) Processing helix chain 'p' and resid 125 through 154 removed outlier: 3.576A pdb=" N PHE p 128 " --> pdb=" O PRO p 125 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL p 129 " --> pdb=" O ARG p 126 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE p 132 " --> pdb=" O VAL p 129 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU p 135 " --> pdb=" O ILE p 132 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE p 136 " --> pdb=" O LEU p 133 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA p 138 " --> pdb=" O LEU p 135 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL p 140 " --> pdb=" O PHE p 137 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU p 141 " --> pdb=" O ALA p 138 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR p 144 " --> pdb=" O LEU p 141 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE p 147 " --> pdb=" O TYR p 144 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL p 148 " --> pdb=" O GLY p 145 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU p 150 " --> pdb=" O ILE p 147 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE p 151 " --> pdb=" O VAL p 148 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU p 152 " --> pdb=" O ALA p 149 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR p 154 " --> pdb=" O ILE p 151 " (cutoff:3.500A) Processing helix chain 'q' and resid 11 through 44 removed outlier: 3.790A pdb=" N PHE q 14 " --> pdb=" O ALA q 11 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA q 15 " --> pdb=" O SER q 12 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL q 16 " --> pdb=" O PHE q 13 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET q 17 " --> pdb=" O PHE q 14 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA q 21 " --> pdb=" O GLY q 18 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA q 22 " --> pdb=" O ALA q 19 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL q 24 " --> pdb=" O ALA q 21 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N PHE q 25 " --> pdb=" O ALA q 22 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER q 26 " --> pdb=" O MET q 23 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU q 28 " --> pdb=" O PHE q 25 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA q 30 " --> pdb=" O ALA q 27 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA q 31 " --> pdb=" O LEU q 28 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY q 33 " --> pdb=" O ALA q 30 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA q 35 " --> pdb=" O TYR q 32 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS q 36 " --> pdb=" O GLY q 33 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER q 37 " --> pdb=" O THR q 34 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA q 42 " --> pdb=" O THR q 39 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA q 43 " --> pdb=" O GLY q 40 " (cutoff:3.500A) Processing helix chain 'q' and resid 54 through 78 removed outlier: 3.943A pdb=" N ILE q 57 " --> pdb=" O LYS q 54 " (cutoff:3.500A) Proline residue: q 58 - end of helix removed outlier: 3.582A pdb=" N MET q 61 " --> pdb=" O PRO q 58 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA q 62 " --> pdb=" O VAL q 59 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU q 70 " --> pdb=" O ILE q 67 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL q 71 " --> pdb=" O TYR q 68 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL q 72 " --> pdb=" O GLY q 69 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE q 76 " --> pdb=" O ALA q 73 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN q 78 " --> pdb=" O LEU q 75 " (cutoff:3.500A) Processing helix chain 'q' and resid 86 through 121 removed outlier: 3.567A pdb=" N GLN q 92 " --> pdb=" O ARG q 88 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER q 102 " --> pdb=" O SER q 98 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG q 119 " --> pdb=" O ASP q 115 " (cutoff:3.500A) Processing helix chain 'q' and resid 125 through 154 removed outlier: 3.757A pdb=" N VAL q 129 " --> pdb=" O ARG q 126 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N MET q 131 " --> pdb=" O PHE q 128 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ILE q 132 " --> pdb=" O VAL q 129 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU q 135 " --> pdb=" O ILE q 132 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU q 141 " --> pdb=" O ALA q 138 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE q 147 " --> pdb=" O TYR q 144 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL q 148 " --> pdb=" O GLY q 145 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU q 150 " --> pdb=" O ILE q 147 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE q 151 " --> pdb=" O VAL q 148 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU q 152 " --> pdb=" O ALA q 149 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER q 153 " --> pdb=" O LEU q 150 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR q 154 " --> pdb=" O ILE q 151 " (cutoff:3.500A) Processing helix chain 'f' and resid 18 through 35 removed outlier: 4.176A pdb=" N ILE f 24 " --> pdb=" O ALA f 20 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N MET f 25 " --> pdb=" O TRP f 21 " (cutoff:3.500A) Processing helix chain 'f' and resid 65 through 75 Processing helix chain 'f' and resid 81 through 83 No H-bonds generated for 'chain 'f' and resid 81 through 83' Processing sheet with id= A, first strand: chain 'A' and resid 28 through 31 removed outlier: 6.515A pdb=" N GLN A 65 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ILE A 54 " --> pdb=" O GLN A 65 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 87 through 90 Processing sheet with id= C, first strand: chain 'A' and resid 183 through 185 Processing sheet with id= D, first strand: chain 'A' and resid 201 through 203 removed outlier: 3.600A pdb=" N LEU A 192 " --> pdb=" O PHE A 203 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR A 178 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLU A 195 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL A 176 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 431 through 433 removed outlier: 8.272A pdb=" N THR A 246 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE A 406 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ILE A 248 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLY A 408 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL A 271 " --> pdb=" O SER A 345 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N MET A 347 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE A 273 " --> pdb=" O MET A 347 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N ASP A 349 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL A 275 " --> pdb=" O ASP A 349 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 18 through 20 removed outlier: 6.664A pdb=" N THR B 63 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU B 57 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N MET B 61 " --> pdb=" O LEU B 57 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL B 28 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N CYS B 32 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N VAL B 21 " --> pdb=" O CYS B 32 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 87 through 90 Processing sheet with id= H, first strand: chain 'B' and resid 183 through 185 removed outlier: 5.664A pdb=" N ASP B 134 " --> pdb=" O ASN B 157 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASN B 157 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE B 166 " --> pdb=" O TYR B 153 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ILE B 155 " --> pdb=" O HIS B 164 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N HIS B 164 " --> pdb=" O ILE B 155 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 200 through 203 removed outlier: 3.822A pdb=" N TYR B 178 " --> pdb=" O GLU B 193 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLU B 195 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N VAL B 176 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 431 through 433 removed outlier: 8.269A pdb=" N THR B 246 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE B 406 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE B 248 " --> pdb=" O ILE B 406 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLY B 408 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL B 271 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N MET B 347 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE B 273 " --> pdb=" O MET B 347 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ASP B 349 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL B 275 " --> pdb=" O ASP B 349 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 295 through 297 Processing sheet with id= L, first strand: chain 'C' and resid 18 through 20 removed outlier: 6.762A pdb=" N THR C 63 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LEU C 57 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N MET C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL C 28 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N CYS C 32 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N VAL C 21 " --> pdb=" O CYS C 32 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 87 through 90 Processing sheet with id= N, first strand: chain 'C' and resid 183 through 185 removed outlier: 5.831A pdb=" N ASP C 134 " --> pdb=" O ASN C 157 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ASN C 157 " --> pdb=" O ASP C 134 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE C 166 " --> pdb=" O TYR C 153 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ILE C 155 " --> pdb=" O HIS C 164 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N HIS C 164 " --> pdb=" O ILE C 155 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 200 through 203 removed outlier: 3.584A pdb=" N TYR C 178 " --> pdb=" O GLU C 193 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLU C 195 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N VAL C 176 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 245 through 248 removed outlier: 8.307A pdb=" N THR C 246 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE C 406 " --> pdb=" O THR C 246 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ILE C 248 " --> pdb=" O ILE C 406 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N GLY C 408 " --> pdb=" O ILE C 248 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL C 271 " --> pdb=" O SER C 345 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N MET C 347 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ILE C 273 " --> pdb=" O MET C 347 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ASP C 349 " --> pdb=" O ILE C 273 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL C 275 " --> pdb=" O ASP C 349 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 295 through 297 Processing sheet with id= R, first strand: chain 'C' and resid 390 through 393 Processing sheet with id= S, first strand: chain 'D' and resid 45 through 47 removed outlier: 4.137A pdb=" N LEU D 45 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL D 95 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL D 89 " --> pdb=" O LYS D 93 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LYS D 93 " --> pdb=" O VAL D 89 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 120 through 123 removed outlier: 3.673A pdb=" N ASP D 149 " --> pdb=" O VAL D 123 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 376 through 378 Processing sheet with id= V, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.337A pdb=" N PHE D 260 " --> pdb=" O ALA D 233 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N GLY D 235 " --> pdb=" O PHE D 260 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ASN D 262 " --> pdb=" O GLY D 235 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 50 through 54 removed outlier: 6.237A pdb=" N ILE E 59 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL E 53 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU E 57 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLN E 97 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N VAL E 86 " --> pdb=" O GLN E 97 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 120 through 123 removed outlier: 4.032A pdb=" N ASP E 149 " --> pdb=" O VAL E 123 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 130 through 132 removed outlier: 3.799A pdb=" N ARG E 130 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU E 259 " --> pdb=" O ARG E 130 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE E 132 " --> pdb=" O LEU E 259 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE E 229 " --> pdb=" O CYS E 258 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N PHE E 260 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N PHE E 231 " --> pdb=" O PHE E 260 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ASN E 262 " --> pdb=" O PHE E 231 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ALA E 233 " --> pdb=" O ASN E 262 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N SER E 347 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL E 295 " --> pdb=" O SER E 347 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N THR E 349 " --> pdb=" O VAL E 295 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU E 297 " --> pdb=" O THR E 349 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE E 351 " --> pdb=" O LEU E 297 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 376 through 378 Processing sheet with id= AA, first strand: chain 'F' and resid 45 through 47 removed outlier: 4.306A pdb=" N LEU F 45 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL F 95 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL F 89 " --> pdb=" O LYS F 93 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS F 93 " --> pdb=" O VAL F 89 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 120 through 123 Processing sheet with id= AC, first strand: chain 'F' and resid 376 through 378 Processing sheet with id= AD, first strand: chain 'F' and resid 348 through 352 removed outlier: 6.579A pdb=" N VAL F 293 " --> pdb=" O THR F 349 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ILE F 351 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL F 295 " --> pdb=" O ILE F 351 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALA F 228 " --> pdb=" O LEU F 294 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ILE F 296 " --> pdb=" O ALA F 228 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL F 230 " --> pdb=" O ILE F 296 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N THR F 298 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ALA F 232 " --> pdb=" O THR F 298 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N PHE F 260 " --> pdb=" O ALA F 233 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N GLY F 235 " --> pdb=" O PHE F 260 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ASN F 262 " --> pdb=" O GLY F 235 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'G' and resid 247 through 249 removed outlier: 3.691A pdb=" N LEU G 186 " --> pdb=" O ARG G 249 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ASN G 226 " --> pdb=" O VAL G 215 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL G 215 " --> pdb=" O ASN G 226 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 93 through 101 Processing sheet with id= AG, first strand: chain 'I' and resid 132 through 136 removed outlier: 3.661A pdb=" N VAL I 181 " --> pdb=" O ASN I 194 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'J' and resid 134 through 136 Processing sheet with id= AI, first strand: chain 'K' and resid 132 through 135 removed outlier: 3.735A pdb=" N VAL K 181 " --> pdb=" O ASN K 194 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'L' and resid 87 through 91 removed outlier: 7.388A pdb=" N LEU L 7 " --> pdb=" O GLY L 62 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE L 64 " --> pdb=" O LEU L 7 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA L 9 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE L 66 " --> pdb=" O ALA L 9 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'a' and resid 318 through 323 removed outlier: 3.863A pdb=" N ILE a 351 " --> pdb=" O PHE a 16 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'a' and resid 243 through 245 removed outlier: 4.830A pdb=" N ALA a 172 " --> pdb=" O TYR a 245 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY a 173 " --> pdb=" O PHE a 220 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE a 221 " --> pdb=" O ARG a 198 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG a 198 " --> pdb=" O ILE a 221 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 's' and resid 266 through 268 Processing sheet with id= AN, first strand: chain 's' and resid 391 through 395 removed outlier: 3.688A pdb=" N HIS s 279 " --> pdb=" O TYR s 276 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 's' and resid 304 through 310 removed outlier: 3.737A pdb=" N ALA s 305 " --> pdb=" O LEU s 325 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 's' and resid 325 through 330 removed outlier: 3.516A pdb=" N SER s 328 " --> pdb=" O TRP s 337 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG s 335 " --> pdb=" O TYR s 330 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 's' and resid 354 through 356 Processing sheet with id= AR, first strand: chain 's' and resid 366 through 368 removed outlier: 3.708A pdb=" N HIS s 368 " --> pdb=" O SER s 414 " (cutoff:3.500A) 2690 hydrogen bonds defined for protein. 6588 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.96 Time building geometry restraints manager: 21.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.93 - 1.11: 9 1.11 - 1.29: 10466 1.29 - 1.47: 24911 1.47 - 1.65: 28220 1.65 - 1.83: 628 Bond restraints: 64234 Sorted by residual: bond pdb=" C TYR A 535 " pdb=" O TYR A 535 " ideal model delta sigma weight residual 1.236 0.930 0.306 1.26e-02 6.30e+03 5.90e+02 bond pdb=" CA TYR A 535 " pdb=" C TYR A 535 " ideal model delta sigma weight residual 1.523 1.223 0.300 1.35e-02 5.49e+03 4.94e+02 bond pdb=" C ASP B 592 " pdb=" O ASP B 592 " ideal model delta sigma weight residual 1.235 0.981 0.255 1.26e-02 6.30e+03 4.08e+02 bond pdb=" C ALA s 305 " pdb=" N ARG s 306 " ideal model delta sigma weight residual 1.331 1.566 -0.235 1.22e-02 6.72e+03 3.72e+02 bond pdb=" N TYR A 535 " pdb=" CA TYR A 535 " ideal model delta sigma weight residual 1.459 1.216 0.242 1.28e-02 6.10e+03 3.58e+02 ... (remaining 64229 not shown) Histogram of bond angle deviations from ideal: 73.59 - 88.79: 6 88.79 - 103.99: 1066 103.99 - 119.19: 51998 119.19 - 134.39: 33827 134.39 - 149.59: 31 Bond angle restraints: 86928 Sorted by residual: angle pdb=" N LEU D 212 " pdb=" CA LEU D 212 " pdb=" C LEU D 212 " ideal model delta sigma weight residual 109.95 73.59 36.36 1.44e+00 4.82e-01 6.38e+02 angle pdb=" N PHE A 534 " pdb=" CA PHE A 534 " pdb=" C PHE A 534 " ideal model delta sigma weight residual 111.36 132.49 -21.13 1.09e+00 8.42e-01 3.76e+02 angle pdb=" C ILE B 259 " pdb=" CA ILE B 259 " pdb=" CB ILE B 259 " ideal model delta sigma weight residual 111.29 141.56 -30.27 1.64e+00 3.72e-01 3.41e+02 angle pdb=" C ARG I 161 " pdb=" CA ARG I 161 " pdb=" CB ARG I 161 " ideal model delta sigma weight residual 110.42 146.97 -36.55 1.99e+00 2.53e-01 3.37e+02 angle pdb=" C ASP B 588 " pdb=" N PRO B 589 " pdb=" CA PRO B 589 " ideal model delta sigma weight residual 119.84 141.75 -21.91 1.25e+00 6.40e-01 3.07e+02 ... (remaining 86923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.12: 36936 28.12 - 56.25: 1633 56.25 - 84.37: 172 84.37 - 112.50: 25 112.50 - 140.62: 2 Dihedral angle restraints: 38768 sinusoidal: 15210 harmonic: 23558 Sorted by residual: dihedral pdb=" N ASP L 99 " pdb=" C ASP L 99 " pdb=" CA ASP L 99 " pdb=" CB ASP L 99 " ideal model delta harmonic sigma weight residual 122.80 161.56 -38.76 0 2.50e+00 1.60e-01 2.40e+02 dihedral pdb=" C ASP L 99 " pdb=" N ASP L 99 " pdb=" CA ASP L 99 " pdb=" CB ASP L 99 " ideal model delta harmonic sigma weight residual -122.60 -161.04 38.44 0 2.50e+00 1.60e-01 2.36e+02 dihedral pdb=" CA ASN P 369 " pdb=" C ASN P 369 " pdb=" N TYR P 370 " pdb=" CA TYR P 370 " ideal model delta harmonic sigma weight residual -180.00 -104.09 -75.91 0 5.00e+00 4.00e-02 2.30e+02 ... (remaining 38765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.351: 9879 0.351 - 0.703: 67 0.703 - 1.054: 13 1.054 - 1.405: 4 1.405 - 1.757: 3 Chirality restraints: 9966 Sorted by residual: chirality pdb=" CA ASP L 99 " pdb=" N ASP L 99 " pdb=" C ASP L 99 " pdb=" CB ASP L 99 " both_signs ideal model delta sigma weight residual False 2.51 0.75 1.76 2.00e-01 2.50e+01 7.72e+01 chirality pdb=" CA SER B 260 " pdb=" N SER B 260 " pdb=" C SER B 260 " pdb=" CB SER B 260 " both_signs ideal model delta sigma weight residual False 2.51 0.86 1.65 2.00e-01 2.50e+01 6.83e+01 chirality pdb=" CA PHE A 534 " pdb=" N PHE A 534 " pdb=" C PHE A 534 " pdb=" CB PHE A 534 " both_signs ideal model delta sigma weight residual False 2.51 0.97 1.54 2.00e-01 2.50e+01 5.96e+01 ... (remaining 9963 not shown) Planarity restraints: 11114 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA r 403 " 0.289 2.00e-02 2.50e+03 2.21e-01 4.91e+02 pdb=" C11 OLA r 403 " -0.114 2.00e-02 2.50e+03 pdb=" C8 OLA r 403 " 0.118 2.00e-02 2.50e+03 pdb=" C9 OLA r 403 " -0.293 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 535 " -0.183 2.00e-02 2.50e+03 1.12e-01 2.51e+02 pdb=" CG TYR A 535 " 0.119 2.00e-02 2.50e+03 pdb=" CD1 TYR A 535 " 0.190 2.00e-02 2.50e+03 pdb=" CD2 TYR A 535 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR A 535 " -0.097 2.00e-02 2.50e+03 pdb=" CE2 TYR A 535 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 535 " 0.016 2.00e-02 2.50e+03 pdb=" OH TYR A 535 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL N 110 " -0.040 2.00e-02 2.50e+03 9.07e-02 8.22e+01 pdb=" C VAL N 110 " 0.156 2.00e-02 2.50e+03 pdb=" O VAL N 110 " -0.064 2.00e-02 2.50e+03 pdb=" N HIS N 111 " -0.053 2.00e-02 2.50e+03 ... (remaining 11111 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.82: 11 1.82 - 2.59: 686 2.59 - 3.36: 79806 3.36 - 4.13: 151289 4.13 - 4.90: 282971 Nonbonded interactions: 514763 Sorted by model distance: nonbonded pdb=" NZ LYS L 94 " pdb=" OE1 GLN d 338 " model vdw 1.049 2.520 nonbonded pdb=" O SER M 70 " pdb=" OE2 GLU M 74 " model vdw 1.277 3.040 nonbonded pdb=" O SER M 70 " pdb=" CD GLU M 74 " model vdw 1.538 3.270 nonbonded pdb=" ND2 ASN a 465 " pdb=" CB SER a 471 " model vdw 1.633 3.520 nonbonded pdb=" O SER M 70 " pdb=" OE1 GLU M 74 " model vdw 1.669 3.040 ... (remaining 514758 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 'A' and (resid 16 through 250 or resid 258 through 612)) selection = (chain 'B' and (resid 16 through 558 or resid 567 through 612)) selection = (chain 'C' and (resid 16 through 250 or resid 258 through 558 or resid 567 throu \ gh 612)) } ncs_group { reference = (chain 'D' and (resid 38 through 213 or resid 225 through 506)) selection = chain 'E' selection = (chain 'F' and (resid 38 through 213 or resid 225 through 506)) } ncs_group { reference = (chain 'I' and ((resid 6 through 59 and (name N or name CA or name C or name O o \ r name CB )) or resid 60 through 223)) selection = (chain 'J' and ((resid 6 through 59 and (name N or name CA or name C or name O o \ r name CB )) or resid 60 through 223)) selection = (chain 'K' and resid 6 through 223) } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'c' selection = (chain 'g' and resid 6 through 155) selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = (chain 'o' and resid 6 through 155) selection = (chain 'p' and resid 6 through 155) selection = (chain 'q' and resid 6 through 155) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 6.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 28.070 Check model and map are aligned: 0.690 Set scattering table: 0.440 Process input model: 127.980 Find NCS groups from input model: 3.030 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 169.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.434 64234 Z= 0.640 Angle : 1.298 36.550 86928 Z= 0.767 Chirality : 0.086 1.757 9966 Planarity : 0.008 0.221 11109 Dihedral : 15.498 140.621 23645 Min Nonbonded Distance : 1.049 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.27 % Favored : 96.46 % Rotamer: Outliers : 0.61 % Allowed : 7.75 % Favored : 91.64 % Cbeta Deviations : 1.06 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.08 % 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: -5.55 (0.06), residues: 8098 helix: -4.23 (0.03), residues: 4433 sheet: -2.03 (0.17), residues: 707 loop : -2.82 (0.09), residues: 2958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP e 74 HIS 0.027 0.001 HIS N 111 PHE 0.087 0.002 PHE A 534 TYR 0.190 0.002 TYR A 535 ARG 0.012 0.001 ARG P 364 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1547 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1507 time to evaluate : 5.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.7898 (p0) cc_final: 0.7600 (p0) REVERT: A 194 LEU cc_start: 0.8532 (mt) cc_final: 0.8030 (mp) REVERT: A 232 ARG cc_start: 0.8229 (ttm110) cc_final: 0.7812 (mtm-85) REVERT: A 277 CYS cc_start: 0.7183 (t) cc_final: 0.6972 (t) REVERT: A 445 PHE cc_start: 0.7599 (m-80) cc_final: 0.7348 (m-10) REVERT: A 458 MET cc_start: 0.7846 (mtt) cc_final: 0.7494 (mtm) REVERT: A 579 TYR cc_start: 0.7748 (t80) cc_final: 0.7500 (t80) REVERT: B 134 ASP cc_start: 0.7913 (p0) cc_final: 0.7599 (p0) REVERT: B 587 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7406 (mmtp) REVERT: B 605 LEU cc_start: 0.8454 (mp) cc_final: 0.8018 (mt) REVERT: C 109 ILE cc_start: 0.9117 (tt) cc_final: 0.8912 (tt) REVERT: C 605 LEU cc_start: 0.8250 (mp) cc_final: 0.8030 (mp) REVERT: C 610 ASN cc_start: 0.6206 (m110) cc_final: 0.5757 (m-40) REVERT: D 251 ASN cc_start: 0.8495 (OUTLIER) cc_final: 0.7998 (t0) REVERT: D 362 THR cc_start: 0.8710 (m) cc_final: 0.8448 (p) REVERT: D 433 GLN cc_start: 0.8448 (tm-30) cc_final: 0.8181 (tm-30) REVERT: E 408 GLU cc_start: 0.7050 (tp30) cc_final: 0.6824 (tp30) REVERT: F 44 ARG cc_start: 0.8509 (mtt180) cc_final: 0.8157 (mtt-85) REVERT: F 164 ILE cc_start: 0.8995 (tt) cc_final: 0.8642 (pt) REVERT: F 423 TYR cc_start: 0.7509 (t80) cc_final: 0.7288 (t80) REVERT: G 239 HIS cc_start: 0.8414 (m-70) cc_final: 0.8052 (m-70) REVERT: G 262 LYS cc_start: 0.7449 (mmmt) cc_final: 0.7231 (tptp) REVERT: H 160 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7310 (mt-10) REVERT: H 200 TYR cc_start: 0.9169 (t80) cc_final: 0.8944 (t80) REVERT: I 201 ASP cc_start: 0.8049 (t0) cc_final: 0.7804 (t0) REVERT: J 61 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8279 (mm-30) REVERT: J 74 ASN cc_start: 0.8262 (t0) cc_final: 0.8061 (m110) REVERT: K 70 ILE cc_start: 0.8632 (tt) cc_final: 0.8343 (tt) REVERT: K 96 ASN cc_start: 0.8713 (m110) cc_final: 0.8497 (m110) REVERT: K 164 ASP cc_start: 0.7811 (t70) cc_final: 0.7605 (t0) REVERT: L 41 LYS cc_start: 0.8461 (tppt) cc_final: 0.8227 (mmtp) REVERT: L 106 LEU cc_start: 0.8114 (tp) cc_final: 0.7869 (tt) REVERT: N 74 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7452 (tp30) REVERT: N 84 MET cc_start: 0.7949 (ptp) cc_final: 0.7629 (ptt) REVERT: O 75 GLN cc_start: 0.8401 (tp-100) cc_final: 0.7823 (mm-40) REVERT: O 85 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8305 (mm-40) REVERT: O 102 MET cc_start: 0.8623 (mtm) cc_final: 0.8364 (mtp) REVERT: P 223 TYR cc_start: 0.8528 (t80) cc_final: 0.8016 (t80) REVERT: P 366 ASN cc_start: 0.6530 (OUTLIER) cc_final: 0.6319 (m-40) REVERT: a 88 VAL cc_start: 0.8081 (OUTLIER) cc_final: 0.7266 (p) REVERT: a 415 LEU cc_start: 0.9076 (mp) cc_final: 0.8852 (mp) REVERT: a 439 MET cc_start: 0.6134 (tpp) cc_final: 0.5482 (ppp) REVERT: a 610 LEU cc_start: 0.8787 (mm) cc_final: 0.8400 (mt) REVERT: b 19 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8906 (tm) REVERT: b 107 MET cc_start: 0.7891 (tpt) cc_final: 0.7614 (tpp) REVERT: d 171 GLN cc_start: 0.8061 (tt0) cc_final: 0.7535 (tp40) REVERT: e 34 ARG cc_start: 0.7084 (ttt90) cc_final: 0.6072 (tmm160) REVERT: e 48 CYS cc_start: 0.7227 (m) cc_final: 0.6957 (m) REVERT: s 436 PHE cc_start: 0.8101 (t80) cc_final: 0.7878 (t80) REVERT: r 336 TYR cc_start: 0.5518 (p90) cc_final: 0.4645 (p90) REVERT: l 115 ASP cc_start: 0.8035 (t70) cc_final: 0.7794 (t0) REVERT: m 17 MET cc_start: 0.8599 (mmp) cc_final: 0.8203 (mmp) REVERT: m 147 ILE cc_start: 0.8871 (pt) cc_final: 0.8648 (pt) REVERT: n 51 MET cc_start: 0.7985 (mpp) cc_final: 0.7566 (ptp) REVERT: p 68 TYR cc_start: 0.8486 (m-10) cc_final: 0.8227 (m-10) REVERT: p 139 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7647 (tm-30) REVERT: q 50 GLU cc_start: 0.8140 (mp0) cc_final: 0.7753 (mp0) REVERT: f 25 MET cc_start: 0.7904 (ttm) cc_final: 0.7659 (ttm) outliers start: 40 outliers final: 18 residues processed: 1546 average time/residue: 0.6596 time to fit residues: 1663.3075 Evaluate side-chains 1011 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 988 time to evaluate : 5.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain B residue 560 GLN Chi-restraints excluded: chain B residue 587 LYS Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain D residue 250 GLU Chi-restraints excluded: chain D residue 251 ASN Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain I residue 163 VAL Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain O residue 113 ASN Chi-restraints excluded: chain P residue 296 VAL Chi-restraints excluded: chain P residue 366 ASN Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain a residue 482 ARG Chi-restraints excluded: chain b residue 19 LEU Chi-restraints excluded: chain e residue 74 TRP Chi-restraints excluded: chain s residue 270 GLN Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain k residue 59 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 680 optimal weight: 3.9990 chunk 610 optimal weight: 6.9990 chunk 338 optimal weight: 7.9990 chunk 208 optimal weight: 0.9990 chunk 412 optimal weight: 30.0000 chunk 326 optimal weight: 8.9990 chunk 631 optimal weight: 2.9990 chunk 244 optimal weight: 0.7980 chunk 384 optimal weight: 9.9990 chunk 470 optimal weight: 0.6980 chunk 731 optimal weight: 7.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 ASN A 225 HIS ** A 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN B 397 ASN B 523 ASN C 213 GLN C 261 GLN C 522 GLN C 573 HIS C 603 GLN C 609 GLN ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 385 ASN E 482 GLN F 226 ASN ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 GLN F 385 ASN ** F 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 482 GLN G 30 ASN G 149 ASN G 194 HIS G 239 HIS G 275 GLN H 91 GLN ** H 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 78 GLN J 78 GLN J 149 GLN J 206 GLN ** K 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 GLN K 169 GLN L 35 ASN L 57 ASN ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 111 HIS M 113 ASN N 85 GLN N 88 GLN O 80 GLN ** O 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 222 GLN P 241 HIS P 361 ASN P 369 ASN ** P 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 76 ASN a 199 GLN a 376 ASN a 390 ASN a 412 HIS ** a 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 534 ASN a 568 ASN a 626 ASN ** a 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 735 ASN a 751 GLN a 812 GLN ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 132 HIS ** b 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 254 GLN ** d 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 297 HIS d 309 GLN ** e 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 270 GLN s 336 HIS s 358 GLN c 78 ASN g 124 GLN k 6 ASN k 81 ASN l 78 ASN l 92 GLN m 78 ASN n 6 ASN n 123 GLN q 78 ASN ** q 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 64234 Z= 0.270 Angle : 0.672 11.678 86928 Z= 0.352 Chirality : 0.043 0.212 9966 Planarity : 0.006 0.154 11109 Dihedral : 9.069 131.868 9343 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.16 % Favored : 95.67 % Rotamer: Outliers : 2.69 % Allowed : 14.00 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.08 % Twisted Proline : 0.64 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.08), residues: 8098 helix: -2.06 (0.06), residues: 4460 sheet: -1.76 (0.17), residues: 723 loop : -2.26 (0.10), residues: 2915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP e 74 HIS 0.012 0.001 HIS P 139 PHE 0.034 0.002 PHE f 32 TYR 0.029 0.002 TYR L 98 ARG 0.008 0.001 ARG I 131 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1210 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1035 time to evaluate : 5.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.7984 (p0) cc_final: 0.7765 (p0) REVERT: A 232 ARG cc_start: 0.8247 (ttm110) cc_final: 0.7956 (mtm-85) REVERT: A 277 CYS cc_start: 0.6902 (t) cc_final: 0.6690 (t) REVERT: A 445 PHE cc_start: 0.7595 (m-80) cc_final: 0.7342 (m-10) REVERT: B 134 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7631 (p0) REVERT: B 157 ASN cc_start: 0.8206 (p0) cc_final: 0.7792 (p0) REVERT: B 605 LEU cc_start: 0.8247 (mp) cc_final: 0.7934 (mt) REVERT: C 146 HIS cc_start: 0.8048 (OUTLIER) cc_final: 0.7814 (t-90) REVERT: D 251 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.7767 (t0) REVERT: D 326 TYR cc_start: 0.8889 (p90) cc_final: 0.8605 (p90) REVERT: D 433 GLN cc_start: 0.8617 (tm-30) cc_final: 0.8375 (tm-30) REVERT: E 491 MET cc_start: 0.8525 (mtp) cc_final: 0.8173 (mtm) REVERT: F 44 ARG cc_start: 0.8609 (mtt180) cc_final: 0.8301 (mtt-85) REVERT: G 239 HIS cc_start: 0.8380 (m90) cc_final: 0.8144 (m-70) REVERT: H 186 TYR cc_start: 0.8490 (t80) cc_final: 0.8228 (t80) REVERT: J 74 ASN cc_start: 0.8256 (t0) cc_final: 0.8023 (m110) REVERT: J 168 ASP cc_start: 0.7148 (p0) cc_final: 0.6942 (p0) REVERT: K 162 ASP cc_start: 0.7795 (p0) cc_final: 0.7266 (t0) REVERT: K 163 VAL cc_start: 0.9144 (m) cc_final: 0.8812 (m) REVERT: L 41 LYS cc_start: 0.8459 (tppt) cc_final: 0.8204 (mmtp) REVERT: L 47 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7992 (mt-10) REVERT: M 88 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7959 (tm-30) REVERT: M 107 ARG cc_start: 0.8115 (mtm-85) cc_final: 0.7887 (mtm-85) REVERT: N 72 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7787 (tp30) REVERT: N 74 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7513 (tm-30) REVERT: O 79 ARG cc_start: 0.8511 (mtp180) cc_final: 0.8264 (tmt-80) REVERT: O 80 GLN cc_start: 0.7982 (mm-40) cc_final: 0.7702 (mm110) REVERT: P 136 PHE cc_start: 0.7707 (m-80) cc_final: 0.7483 (m-80) REVERT: P 287 TYR cc_start: 0.6275 (m-10) cc_final: 0.5988 (m-10) REVERT: P 366 ASN cc_start: 0.6699 (OUTLIER) cc_final: 0.6357 (m-40) REVERT: a 439 MET cc_start: 0.5811 (tpp) cc_final: 0.5429 (ppp) REVERT: d 171 GLN cc_start: 0.8070 (tt0) cc_final: 0.7513 (tp40) REVERT: e 28 VAL cc_start: 0.7748 (OUTLIER) cc_final: 0.7218 (t) REVERT: e 34 ARG cc_start: 0.6995 (ttt90) cc_final: 0.6077 (tmm160) REVERT: e 48 CYS cc_start: 0.7505 (m) cc_final: 0.7112 (m) REVERT: e 67 GLN cc_start: 0.7314 (tt0) cc_final: 0.7096 (tt0) REVERT: r 336 TYR cc_start: 0.5494 (p90) cc_final: 0.4728 (p90) REVERT: l 121 THR cc_start: 0.8489 (p) cc_final: 0.8270 (m) REVERT: m 17 MET cc_start: 0.8650 (mmp) cc_final: 0.8251 (mmt) REVERT: p 139 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7711 (tm-30) REVERT: q 17 MET cc_start: 0.8161 (tpt) cc_final: 0.7951 (tpt) REVERT: q 50 GLU cc_start: 0.8170 (mp0) cc_final: 0.7759 (mp0) outliers start: 175 outliers final: 95 residues processed: 1142 average time/residue: 0.5963 time to fit residues: 1146.4578 Evaluate side-chains 1023 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 923 time to evaluate : 5.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 600 ASP Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain C residue 18 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 138 CYS Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 481 GLU Chi-restraints excluded: chain C residue 609 GLN Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 251 ASN Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 112 TYR Chi-restraints excluded: chain G residue 175 PHE Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain I residue 73 SER Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 162 ASP Chi-restraints excluded: chain J residue 221 ASN Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain O residue 113 ASN Chi-restraints excluded: chain P residue 187 LEU Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain P residue 279 VAL Chi-restraints excluded: chain P residue 296 VAL Chi-restraints excluded: chain P residue 366 ASN Chi-restraints excluded: chain a residue 328 THR Chi-restraints excluded: chain a residue 330 LEU Chi-restraints excluded: chain a residue 390 ASN Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 755 VAL Chi-restraints excluded: chain a residue 830 HIS Chi-restraints excluded: chain b residue 91 LEU Chi-restraints excluded: chain b residue 128 HIS Chi-restraints excluded: chain d residue 41 THR Chi-restraints excluded: chain d residue 124 GLU Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 27 PHE Chi-restraints excluded: chain e residue 28 VAL Chi-restraints excluded: chain e residue 57 LEU Chi-restraints excluded: chain s residue 265 ILE Chi-restraints excluded: chain s residue 319 VAL Chi-restraints excluded: chain s residue 342 ASN Chi-restraints excluded: chain s residue 343 LEU Chi-restraints excluded: chain s residue 425 TRP Chi-restraints excluded: chain s residue 429 LEU Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain k residue 6 ASN Chi-restraints excluded: chain k residue 56 ILE Chi-restraints excluded: chain l residue 64 ILE Chi-restraints excluded: chain l residue 81 ASN Chi-restraints excluded: chain l residue 82 ASP Chi-restraints excluded: chain l residue 147 ILE Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 67 ILE Chi-restraints excluded: chain m residue 81 ASN Chi-restraints excluded: chain n residue 9 GLU Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain o residue 154 THR Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain q residue 20 SER Chi-restraints excluded: chain q residue 45 SER Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 82 ASP Chi-restraints excluded: chain q residue 91 LEU Chi-restraints excluded: chain q residue 155 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 406 optimal weight: 6.9990 chunk 227 optimal weight: 0.4980 chunk 609 optimal weight: 1.9990 chunk 498 optimal weight: 7.9990 chunk 201 optimal weight: 2.9990 chunk 733 optimal weight: 2.9990 chunk 792 optimal weight: 1.9990 chunk 653 optimal weight: 0.0000 chunk 727 optimal weight: 7.9990 chunk 249 optimal weight: 0.7980 chunk 588 optimal weight: 2.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 GLN B 523 ASN C 430 GLN C 573 HIS C 603 GLN C 609 GLN ** C 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 456 GLN F 262 ASN ** F 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 ASN ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 152 GLN ** K 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 ASN ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 85 GLN O 113 ASN ** P 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 439 GLN ** a 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 90 ASN ** b 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 183 ASN ** d 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 6 ASN l 78 ASN l 92 GLN n 6 ASN n 78 ASN q 124 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 64234 Z= 0.189 Angle : 0.598 11.833 86928 Z= 0.307 Chirality : 0.041 0.188 9966 Planarity : 0.005 0.148 11109 Dihedral : 8.491 129.941 9317 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.32 % Favored : 95.57 % Rotamer: Outliers : 2.94 % Allowed : 16.21 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.08 % Twisted Proline : 0.64 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.09), residues: 8098 helix: -1.08 (0.07), residues: 4467 sheet: -1.50 (0.18), residues: 711 loop : -2.01 (0.11), residues: 2920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP e 74 HIS 0.008 0.001 HIS a 802 PHE 0.019 0.001 PHE f 32 TYR 0.029 0.001 TYR L 98 ARG 0.016 0.000 ARG a 482 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1173 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 982 time to evaluate : 5.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 ARG cc_start: 0.8258 (ttm110) cc_final: 0.7856 (mtm-85) REVERT: A 445 PHE cc_start: 0.7583 (m-80) cc_final: 0.7341 (m-10) REVERT: B 134 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7782 (p0) REVERT: B 157 ASN cc_start: 0.8174 (p0) cc_final: 0.7824 (p0) REVERT: B 605 LEU cc_start: 0.8189 (mp) cc_final: 0.7901 (tt) REVERT: C 146 HIS cc_start: 0.8010 (OUTLIER) cc_final: 0.7777 (t-90) REVERT: C 195 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.7104 (mm-30) REVERT: C 584 MET cc_start: 0.7193 (mtp) cc_final: 0.6689 (tpt) REVERT: C 609 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7727 (mm-40) REVERT: D 161 GLN cc_start: 0.8487 (tp40) cc_final: 0.7990 (tp-100) REVERT: D 249 GLU cc_start: 0.7630 (tt0) cc_final: 0.7336 (mt-10) REVERT: D 251 ASN cc_start: 0.8547 (OUTLIER) cc_final: 0.7785 (t0) REVERT: D 326 TYR cc_start: 0.8909 (p90) cc_final: 0.8588 (p90) REVERT: D 433 GLN cc_start: 0.8644 (tm-30) cc_final: 0.8390 (tm-30) REVERT: E 491 MET cc_start: 0.8617 (mtp) cc_final: 0.8342 (mtm) REVERT: F 44 ARG cc_start: 0.8567 (mtt180) cc_final: 0.8296 (mtt-85) REVERT: F 435 MET cc_start: 0.7332 (tpt) cc_final: 0.6881 (tpt) REVERT: G 239 HIS cc_start: 0.8355 (m90) cc_final: 0.8146 (m-70) REVERT: H 86 ASN cc_start: 0.8762 (m-40) cc_final: 0.8507 (m-40) REVERT: H 152 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8307 (mm-40) REVERT: I 97 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7835 (tm-30) REVERT: J 168 ASP cc_start: 0.7141 (p0) cc_final: 0.6873 (p0) REVERT: K 162 ASP cc_start: 0.7748 (p0) cc_final: 0.7313 (t0) REVERT: K 163 VAL cc_start: 0.9080 (m) cc_final: 0.8789 (m) REVERT: L 47 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8042 (mt-10) REVERT: M 88 GLN cc_start: 0.8274 (tm-30) cc_final: 0.7954 (tm-30) REVERT: M 89 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7644 (mm-40) REVERT: M 107 ARG cc_start: 0.8148 (mtm-85) cc_final: 0.7919 (mtm-85) REVERT: N 72 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7782 (tp30) REVERT: N 74 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7433 (tm-30) REVERT: O 79 ARG cc_start: 0.8504 (mtp180) cc_final: 0.8253 (tmt-80) REVERT: O 80 GLN cc_start: 0.7893 (mm-40) cc_final: 0.7589 (mm110) REVERT: P 287 TYR cc_start: 0.6203 (m-10) cc_final: 0.6000 (m-10) REVERT: P 366 ASN cc_start: 0.6690 (OUTLIER) cc_final: 0.6377 (m-40) REVERT: P 420 MET cc_start: 0.8366 (mmm) cc_final: 0.8120 (mmm) REVERT: a 439 MET cc_start: 0.5695 (tpp) cc_final: 0.5342 (tmm) REVERT: b 166 ASP cc_start: 0.7597 (t0) cc_final: 0.7321 (t0) REVERT: d 325 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7926 (mt-10) REVERT: d 340 HIS cc_start: 0.8345 (t70) cc_final: 0.8125 (t70) REVERT: e 28 VAL cc_start: 0.7674 (t) cc_final: 0.7278 (t) REVERT: e 34 ARG cc_start: 0.6930 (ttt90) cc_final: 0.6577 (ttm-80) REVERT: e 48 CYS cc_start: 0.7496 (m) cc_final: 0.7052 (m) REVERT: e 53 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8864 (tp) REVERT: s 291 GLN cc_start: 0.7892 (tm-30) cc_final: 0.7241 (tm-30) REVERT: r 336 TYR cc_start: 0.5373 (p90) cc_final: 0.4548 (p90) REVERT: g 64 ILE cc_start: 0.8903 (mm) cc_final: 0.8623 (mt) REVERT: g 144 TYR cc_start: 0.8185 (m-10) cc_final: 0.7654 (m-80) REVERT: m 17 MET cc_start: 0.8629 (mmp) cc_final: 0.8219 (mmt) REVERT: n 48 ARG cc_start: 0.7757 (tpp80) cc_final: 0.7237 (ttm-80) REVERT: p 44 MET cc_start: 0.8357 (tmm) cc_final: 0.8044 (tmm) REVERT: p 139 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7694 (tm-30) REVERT: q 131 MET cc_start: 0.8463 (ttp) cc_final: 0.8171 (ttt) outliers start: 191 outliers final: 110 residues processed: 1100 average time/residue: 0.5977 time to fit residues: 1118.1215 Evaluate side-chains 1037 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 919 time to evaluate : 5.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 532 CYS Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 138 CYS Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 609 GLN Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 251 ASN Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 348 ILE Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 112 TYR Chi-restraints excluded: chain G residue 175 PHE Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 152 GLN Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 162 ASP Chi-restraints excluded: chain J residue 221 ASN Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 193 SER Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 35 ASN Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 73 MET Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain P residue 66 LEU Chi-restraints excluded: chain P residue 187 LEU Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain P residue 279 VAL Chi-restraints excluded: chain P residue 296 VAL Chi-restraints excluded: chain P residue 366 ASN Chi-restraints excluded: chain P residue 370 TYR Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 330 LEU Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 520 ASP Chi-restraints excluded: chain a residue 557 LEU Chi-restraints excluded: chain a residue 755 VAL Chi-restraints excluded: chain a residue 830 HIS Chi-restraints excluded: chain b residue 91 LEU Chi-restraints excluded: chain b residue 128 HIS Chi-restraints excluded: chain b residue 201 VAL Chi-restraints excluded: chain d residue 124 GLU Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 53 LEU Chi-restraints excluded: chain e residue 60 LEU Chi-restraints excluded: chain s residue 265 ILE Chi-restraints excluded: chain s residue 342 ASN Chi-restraints excluded: chain s residue 343 LEU Chi-restraints excluded: chain s residue 425 TRP Chi-restraints excluded: chain s residue 429 LEU Chi-restraints excluded: chain s residue 434 MET Chi-restraints excluded: chain s residue 439 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 148 VAL Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain k residue 115 ASP Chi-restraints excluded: chain k residue 147 ILE Chi-restraints excluded: chain l residue 64 ILE Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 81 ASN Chi-restraints excluded: chain l residue 82 ASP Chi-restraints excluded: chain l residue 147 ILE Chi-restraints excluded: chain m residue 6 ASN Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain n residue 6 ASN Chi-restraints excluded: chain n residue 78 ASN Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain q residue 45 SER Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 82 ASP Chi-restraints excluded: chain q residue 84 ILE Chi-restraints excluded: chain q residue 91 LEU Chi-restraints excluded: chain f residue 24 ILE Chi-restraints excluded: chain f residue 82 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 724 optimal weight: 0.3980 chunk 551 optimal weight: 7.9990 chunk 380 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 349 optimal weight: 6.9990 chunk 492 optimal weight: 8.9990 chunk 735 optimal weight: 6.9990 chunk 779 optimal weight: 7.9990 chunk 384 optimal weight: 0.8980 chunk 697 optimal weight: 3.9990 chunk 209 optimal weight: 6.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 523 ASN ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 ASN ** F 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 GLN ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 91 GLN H 152 GLN I 96 ASN J 74 ASN ** K 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 ASN K 169 GLN L 35 ASN ** P 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 278 HIS ** a 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 6 ASN g 6 ASN k 6 ASN ** l 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 6 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 64234 Z= 0.277 Angle : 0.607 11.507 86928 Z= 0.311 Chirality : 0.043 0.211 9966 Planarity : 0.005 0.143 11109 Dihedral : 8.281 130.221 9314 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.94 % Favored : 94.96 % Rotamer: Outliers : 3.26 % Allowed : 17.80 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.08 % Twisted Proline : 0.64 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.09), residues: 8098 helix: -0.60 (0.08), residues: 4518 sheet: -1.40 (0.18), residues: 706 loop : -1.89 (0.11), residues: 2874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP e 74 HIS 0.018 0.001 HIS C 573 PHE 0.022 0.001 PHE E 260 TYR 0.032 0.001 TYR o 144 ARG 0.014 0.000 ARG a 482 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1159 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 947 time to evaluate : 5.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 ARG cc_start: 0.8344 (ttm110) cc_final: 0.7861 (mtm-85) REVERT: A 445 PHE cc_start: 0.7608 (m-80) cc_final: 0.7355 (m-10) REVERT: B 134 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7743 (p0) REVERT: B 157 ASN cc_start: 0.8130 (OUTLIER) cc_final: 0.7792 (p0) REVERT: B 458 MET cc_start: 0.9026 (mmm) cc_final: 0.8757 (mmt) REVERT: B 605 LEU cc_start: 0.8232 (mp) cc_final: 0.8031 (tt) REVERT: C 146 HIS cc_start: 0.8072 (OUTLIER) cc_final: 0.7821 (t-90) REVERT: C 584 MET cc_start: 0.7351 (mtp) cc_final: 0.6725 (tpt) REVERT: C 603 GLN cc_start: 0.7589 (tp-100) cc_final: 0.7260 (tp40) REVERT: D 161 GLN cc_start: 0.8555 (tp40) cc_final: 0.8061 (tp-100) REVERT: D 249 GLU cc_start: 0.7529 (tt0) cc_final: 0.7280 (mt-10) REVERT: D 326 TYR cc_start: 0.8963 (p90) cc_final: 0.8682 (p90) REVERT: D 433 GLN cc_start: 0.8735 (tm-30) cc_final: 0.8397 (tm-30) REVERT: E 371 TYR cc_start: 0.8164 (m-10) cc_final: 0.7932 (m-10) REVERT: F 44 ARG cc_start: 0.8634 (mtt180) cc_final: 0.8344 (mtt-85) REVERT: F 380 ASP cc_start: 0.8062 (t0) cc_final: 0.7667 (m-30) REVERT: F 435 MET cc_start: 0.7307 (tpt) cc_final: 0.6886 (tpt) REVERT: G 224 LEU cc_start: 0.6748 (OUTLIER) cc_final: 0.6343 (mt) REVERT: H 152 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8349 (mm-40) REVERT: I 97 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7998 (tm-30) REVERT: J 168 ASP cc_start: 0.7170 (p0) cc_final: 0.6903 (p0) REVERT: K 72 MET cc_start: 0.8310 (tmm) cc_final: 0.8014 (tmm) REVERT: K 162 ASP cc_start: 0.7792 (p0) cc_final: 0.7395 (t0) REVERT: K 163 VAL cc_start: 0.9105 (OUTLIER) cc_final: 0.8820 (m) REVERT: L 33 HIS cc_start: 0.6687 (m-70) cc_final: 0.6333 (m-70) REVERT: M 89 GLN cc_start: 0.7885 (mm-40) cc_final: 0.7684 (mm-40) REVERT: N 72 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7576 (tp30) REVERT: N 74 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7441 (tm-30) REVERT: O 79 ARG cc_start: 0.8524 (mtp180) cc_final: 0.8250 (tmt-80) REVERT: O 80 GLN cc_start: 0.7822 (mm-40) cc_final: 0.7477 (mm110) REVERT: P 287 TYR cc_start: 0.6334 (m-10) cc_final: 0.6130 (m-10) REVERT: P 366 ASN cc_start: 0.6655 (OUTLIER) cc_final: 0.6403 (m-40) REVERT: a 439 MET cc_start: 0.5596 (tpp) cc_final: 0.5259 (tmm) REVERT: d 309 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7596 (tm130) REVERT: d 325 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7932 (mt-10) REVERT: e 28 VAL cc_start: 0.7756 (t) cc_final: 0.7430 (t) REVERT: e 34 ARG cc_start: 0.6993 (ttt90) cc_final: 0.6732 (ttm-80) REVERT: e 48 CYS cc_start: 0.7574 (m) cc_final: 0.7123 (m) REVERT: e 53 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8937 (tp) REVERT: e 64 PHE cc_start: 0.8073 (OUTLIER) cc_final: 0.7824 (t80) REVERT: r 336 TYR cc_start: 0.5380 (p90) cc_final: 0.4512 (p90) REVERT: c 115 ASP cc_start: 0.7909 (t70) cc_final: 0.7575 (t0) REVERT: g 64 ILE cc_start: 0.8988 (mm) cc_final: 0.8647 (mt) REVERT: g 144 TYR cc_start: 0.8160 (m-10) cc_final: 0.7656 (m-80) REVERT: n 48 ARG cc_start: 0.7851 (tpp80) cc_final: 0.7335 (ttm-80) REVERT: o 44 MET cc_start: 0.8003 (ttp) cc_final: 0.7618 (ttp) REVERT: p 44 MET cc_start: 0.8403 (tmm) cc_final: 0.8156 (tmm) REVERT: p 61 MET cc_start: 0.7983 (mtp) cc_final: 0.7734 (mtp) REVERT: p 139 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7764 (tm-30) REVERT: q 131 MET cc_start: 0.8611 (ttp) cc_final: 0.8337 (ttt) outliers start: 212 outliers final: 150 residues processed: 1084 average time/residue: 0.5865 time to fit residues: 1079.7058 Evaluate side-chains 1051 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 891 time to evaluate : 5.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 532 CYS Chi-restraints excluded: chain A residue 573 HIS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 138 CYS Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 413 LYS Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 348 ILE Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 141 ARG Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 491 MET Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 112 TYR Chi-restraints excluded: chain G residue 175 PHE Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 152 GLN Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 162 ASP Chi-restraints excluded: chain J residue 221 ASN Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 193 SER Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 69 TYR Chi-restraints excluded: chain L residue 73 MET Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain O residue 84 MET Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain O residue 102 MET Chi-restraints excluded: chain P residue 66 LEU Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain P residue 279 VAL Chi-restraints excluded: chain P residue 296 VAL Chi-restraints excluded: chain P residue 366 ASN Chi-restraints excluded: chain P residue 370 TYR Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 102 GLU Chi-restraints excluded: chain a residue 214 TYR Chi-restraints excluded: chain a residue 244 LEU Chi-restraints excluded: chain a residue 290 ILE Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 490 TRP Chi-restraints excluded: chain a residue 520 ASP Chi-restraints excluded: chain a residue 557 LEU Chi-restraints excluded: chain a residue 629 LEU Chi-restraints excluded: chain a residue 755 VAL Chi-restraints excluded: chain a residue 756 LEU Chi-restraints excluded: chain a residue 830 HIS Chi-restraints excluded: chain b residue 26 TYR Chi-restraints excluded: chain b residue 91 LEU Chi-restraints excluded: chain b residue 128 HIS Chi-restraints excluded: chain b residue 201 VAL Chi-restraints excluded: chain d residue 41 THR Chi-restraints excluded: chain d residue 124 GLU Chi-restraints excluded: chain d residue 309 GLN Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 53 LEU Chi-restraints excluded: chain e residue 64 PHE Chi-restraints excluded: chain s residue 265 ILE Chi-restraints excluded: chain s residue 343 LEU Chi-restraints excluded: chain s residue 425 TRP Chi-restraints excluded: chain s residue 429 LEU Chi-restraints excluded: chain s residue 434 MET Chi-restraints excluded: chain s residue 439 THR Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain g residue 6 ASN Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain k residue 44 MET Chi-restraints excluded: chain k residue 59 VAL Chi-restraints excluded: chain k residue 115 ASP Chi-restraints excluded: chain k residue 147 ILE Chi-restraints excluded: chain l residue 64 ILE Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 81 ASN Chi-restraints excluded: chain l residue 82 ASP Chi-restraints excluded: chain l residue 141 LEU Chi-restraints excluded: chain l residue 146 LEU Chi-restraints excluded: chain l residue 147 ILE Chi-restraints excluded: chain m residue 6 ASN Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain n residue 6 ASN Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 154 THR Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain q residue 20 SER Chi-restraints excluded: chain q residue 45 SER Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 82 ASP Chi-restraints excluded: chain q residue 84 ILE Chi-restraints excluded: chain q residue 91 LEU Chi-restraints excluded: chain q residue 155 LYS Chi-restraints excluded: chain f residue 82 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 648 optimal weight: 8.9990 chunk 442 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 580 optimal weight: 9.9990 chunk 321 optimal weight: 9.9990 chunk 664 optimal weight: 2.9990 chunk 538 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 397 optimal weight: 1.9990 chunk 699 optimal weight: 0.6980 chunk 196 optimal weight: 0.0870 overall best weight: 2.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN F 288 GLN ** F 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN H 91 GLN H 152 GLN I 96 ASN I 122 GLN I 194 ASN ** K 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 ASN ** P 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 439 GLN a 53 ASN ** a 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 633 GLN a 720 HIS ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 152 ASN ** d 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 368 HIS g 6 ASN m 124 GLN ** n 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 64234 Z= 0.325 Angle : 0.628 12.573 86928 Z= 0.320 Chirality : 0.044 0.194 9966 Planarity : 0.005 0.139 11109 Dihedral : 8.229 130.843 9311 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.26 % Favored : 94.64 % Rotamer: Outliers : 3.92 % Allowed : 18.44 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.08 % Twisted Proline : 0.64 % 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: -1.47 (0.09), residues: 8098 helix: -0.31 (0.08), residues: 4502 sheet: -1.36 (0.18), residues: 735 loop : -1.79 (0.11), residues: 2861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP r 313 HIS 0.015 0.001 HIS C 573 PHE 0.024 0.001 PHE E 260 TYR 0.030 0.002 TYR o 144 ARG 0.013 0.001 ARG a 482 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1174 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 919 time to evaluate : 5.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 PHE cc_start: 0.7627 (m-80) cc_final: 0.7338 (m-10) REVERT: B 157 ASN cc_start: 0.8067 (OUTLIER) cc_final: 0.7832 (p0) REVERT: B 458 MET cc_start: 0.9050 (mmm) cc_final: 0.8810 (mmt) REVERT: B 494 GLN cc_start: 0.7860 (tm-30) cc_final: 0.7494 (tm-30) REVERT: C 146 HIS cc_start: 0.8071 (OUTLIER) cc_final: 0.7858 (t-90) REVERT: C 609 GLN cc_start: 0.8320 (mm-40) cc_final: 0.8070 (mm-40) REVERT: D 161 GLN cc_start: 0.8586 (tp40) cc_final: 0.8089 (tp-100) REVERT: D 249 GLU cc_start: 0.7621 (tt0) cc_final: 0.7276 (mt-10) REVERT: D 251 ASN cc_start: 0.8641 (OUTLIER) cc_final: 0.7933 (t0) REVERT: D 326 TYR cc_start: 0.8984 (p90) cc_final: 0.8716 (p90) REVERT: D 433 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8535 (tm-30) REVERT: F 44 ARG cc_start: 0.8678 (mtt180) cc_final: 0.8365 (mtt-85) REVERT: F 380 ASP cc_start: 0.8122 (t0) cc_final: 0.7688 (m-30) REVERT: F 435 MET cc_start: 0.7143 (tpt) cc_final: 0.6782 (tpt) REVERT: H 152 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8406 (mm-40) REVERT: I 97 GLU cc_start: 0.8232 (tm-30) cc_final: 0.8015 (tm-30) REVERT: I 206 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.7679 (mp-120) REVERT: J 57 TYR cc_start: 0.6658 (OUTLIER) cc_final: 0.6197 (t80) REVERT: J 168 ASP cc_start: 0.7235 (p0) cc_final: 0.6996 (p0) REVERT: K 162 ASP cc_start: 0.7802 (p0) cc_final: 0.7439 (t0) REVERT: L 33 HIS cc_start: 0.6670 (OUTLIER) cc_final: 0.6463 (m-70) REVERT: M 88 GLN cc_start: 0.8331 (tm-30) cc_final: 0.8114 (tm-30) REVERT: M 89 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7625 (mm-40) REVERT: N 72 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7563 (tp30) REVERT: N 74 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7391 (tm-30) REVERT: O 79 ARG cc_start: 0.8533 (mtp180) cc_final: 0.8254 (tmt-80) REVERT: O 80 GLN cc_start: 0.7785 (mm-40) cc_final: 0.7401 (mm110) REVERT: P 140 MET cc_start: 0.8305 (mpp) cc_final: 0.8058 (mpp) REVERT: P 154 GLU cc_start: 0.5065 (OUTLIER) cc_final: 0.3980 (pm20) REVERT: d 325 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7919 (mt-10) REVERT: e 28 VAL cc_start: 0.7757 (t) cc_final: 0.7553 (t) REVERT: e 48 CYS cc_start: 0.7654 (m) cc_final: 0.7221 (m) REVERT: e 53 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8944 (tp) REVERT: e 64 PHE cc_start: 0.8180 (OUTLIER) cc_final: 0.7900 (t80) REVERT: r 336 TYR cc_start: 0.5533 (p90) cc_final: 0.4562 (p90) REVERT: c 115 ASP cc_start: 0.7914 (t70) cc_final: 0.7524 (t70) REVERT: g 64 ILE cc_start: 0.9024 (mm) cc_final: 0.8562 (mt) REVERT: g 144 TYR cc_start: 0.8155 (m-10) cc_final: 0.7701 (m-80) REVERT: m 68 TYR cc_start: 0.8624 (m-10) cc_final: 0.8368 (m-10) REVERT: m 147 ILE cc_start: 0.8868 (pt) cc_final: 0.8629 (mt) REVERT: o 54 LYS cc_start: 0.8766 (ttpt) cc_final: 0.8518 (ttmt) REVERT: p 61 MET cc_start: 0.8085 (mtp) cc_final: 0.7847 (mtp) REVERT: p 68 TYR cc_start: 0.8418 (m-10) cc_final: 0.8202 (m-10) REVERT: p 119 ARG cc_start: 0.9063 (ttp-110) cc_final: 0.8841 (mtm-85) REVERT: p 139 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7784 (tm-30) REVERT: q 45 SER cc_start: 0.8667 (OUTLIER) cc_final: 0.8465 (t) outliers start: 255 outliers final: 178 residues processed: 1090 average time/residue: 0.6027 time to fit residues: 1121.4007 Evaluate side-chains 1069 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 880 time to evaluate : 5.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 532 CYS Chi-restraints excluded: chain A residue 573 HIS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 138 CYS Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 251 ASN Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 330 ASP Chi-restraints excluded: chain E residue 348 ILE Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 491 MET Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 112 TYR Chi-restraints excluded: chain G residue 175 PHE Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain H residue 152 GLN Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 168 ASP Chi-restraints excluded: chain I residue 206 GLN Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 162 ASP Chi-restraints excluded: chain J residue 221 ASN Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 193 SER Chi-restraints excluded: chain K residue 221 ASN Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 33 HIS Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 69 TYR Chi-restraints excluded: chain L residue 73 MET Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain O residue 84 MET Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain O residue 102 MET Chi-restraints excluded: chain P residue 66 LEU Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain P residue 279 VAL Chi-restraints excluded: chain P residue 296 VAL Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 93 ASP Chi-restraints excluded: chain a residue 102 GLU Chi-restraints excluded: chain a residue 202 ILE Chi-restraints excluded: chain a residue 214 TYR Chi-restraints excluded: chain a residue 244 LEU Chi-restraints excluded: chain a residue 377 ILE Chi-restraints excluded: chain a residue 462 LEU Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 482 ARG Chi-restraints excluded: chain a residue 490 TRP Chi-restraints excluded: chain a residue 520 ASP Chi-restraints excluded: chain a residue 557 LEU Chi-restraints excluded: chain a residue 755 VAL Chi-restraints excluded: chain a residue 756 LEU Chi-restraints excluded: chain a residue 779 ILE Chi-restraints excluded: chain a residue 830 HIS Chi-restraints excluded: chain b residue 26 TYR Chi-restraints excluded: chain b residue 91 LEU Chi-restraints excluded: chain b residue 128 HIS Chi-restraints excluded: chain b residue 201 VAL Chi-restraints excluded: chain d residue 41 THR Chi-restraints excluded: chain d residue 99 PHE Chi-restraints excluded: chain d residue 114 THR Chi-restraints excluded: chain d residue 124 GLU Chi-restraints excluded: chain d residue 143 ILE Chi-restraints excluded: chain d residue 204 THR Chi-restraints excluded: chain d residue 264 VAL Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 50 LEU Chi-restraints excluded: chain e residue 53 LEU Chi-restraints excluded: chain e residue 64 PHE Chi-restraints excluded: chain s residue 253 VAL Chi-restraints excluded: chain s residue 265 ILE Chi-restraints excluded: chain s residue 343 LEU Chi-restraints excluded: chain s residue 360 THR Chi-restraints excluded: chain s residue 394 THR Chi-restraints excluded: chain s residue 425 TRP Chi-restraints excluded: chain s residue 429 LEU Chi-restraints excluded: chain s residue 434 MET Chi-restraints excluded: chain s residue 439 THR Chi-restraints excluded: chain s residue 448 LEU Chi-restraints excluded: chain s residue 452 ASP Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 98 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain k residue 59 VAL Chi-restraints excluded: chain k residue 115 ASP Chi-restraints excluded: chain k residue 147 ILE Chi-restraints excluded: chain l residue 64 ILE Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 81 ASN Chi-restraints excluded: chain l residue 82 ASP Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 141 LEU Chi-restraints excluded: chain l residue 146 LEU Chi-restraints excluded: chain l residue 147 ILE Chi-restraints excluded: chain m residue 6 ASN Chi-restraints excluded: chain m residue 50 GLU Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 61 MET Chi-restraints excluded: chain m residue 121 THR Chi-restraints excluded: chain m residue 124 GLN Chi-restraints excluded: chain n residue 6 ASN Chi-restraints excluded: chain n residue 9 GLU Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 154 THR Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain q residue 17 MET Chi-restraints excluded: chain q residue 20 SER Chi-restraints excluded: chain q residue 45 SER Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 82 ASP Chi-restraints excluded: chain q residue 84 ILE Chi-restraints excluded: chain q residue 91 LEU Chi-restraints excluded: chain f residue 82 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 262 optimal weight: 4.9990 chunk 701 optimal weight: 0.0270 chunk 154 optimal weight: 0.6980 chunk 457 optimal weight: 7.9990 chunk 192 optimal weight: 2.9990 chunk 779 optimal weight: 0.0470 chunk 647 optimal weight: 6.9990 chunk 361 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 257 optimal weight: 7.9990 chunk 409 optimal weight: 30.0000 overall best weight: 1.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 ASN D 387 GLN E 456 GLN ** F 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 91 GLN H 152 GLN I 96 ASN I 122 GLN J 78 GLN ** K 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 ASN ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 390 ASN ** a 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 612 HIS ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 6 ASN m 124 GLN ** q 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 64234 Z= 0.236 Angle : 0.593 11.572 86928 Z= 0.300 Chirality : 0.042 0.220 9966 Planarity : 0.004 0.134 11109 Dihedral : 8.043 129.669 9309 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.10 % Favored : 94.79 % Rotamer: Outliers : 3.57 % Allowed : 19.53 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.08 % Twisted Proline : 0.64 % 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: -1.23 (0.09), residues: 8098 helix: -0.13 (0.08), residues: 4525 sheet: -1.25 (0.18), residues: 730 loop : -1.68 (0.11), residues: 2843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 650 HIS 0.013 0.001 HIS C 573 PHE 0.024 0.001 PHE a 654 TYR 0.044 0.001 TYR c 68 ARG 0.012 0.000 ARG a 482 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1168 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 936 time to evaluate : 5.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 PHE cc_start: 0.7626 (m-80) cc_final: 0.7340 (m-10) REVERT: A 608 MET cc_start: 0.6580 (mmp) cc_final: 0.6281 (mtt) REVERT: B 458 MET cc_start: 0.9055 (mmm) cc_final: 0.8837 (mmt) REVERT: C 146 HIS cc_start: 0.8065 (OUTLIER) cc_final: 0.7864 (t-90) REVERT: C 530 ARG cc_start: 0.8231 (ptt90) cc_final: 0.7938 (ptp90) REVERT: C 584 MET cc_start: 0.7447 (mtp) cc_final: 0.6766 (tpt) REVERT: C 609 GLN cc_start: 0.8326 (mm-40) cc_final: 0.8102 (mm-40) REVERT: D 161 GLN cc_start: 0.8550 (tp40) cc_final: 0.8063 (tp-100) REVERT: D 249 GLU cc_start: 0.7588 (tt0) cc_final: 0.7271 (mt-10) REVERT: D 251 ASN cc_start: 0.8606 (OUTLIER) cc_final: 0.7967 (t0) REVERT: D 326 TYR cc_start: 0.8963 (p90) cc_final: 0.8706 (p90) REVERT: D 433 GLN cc_start: 0.8849 (tm-30) cc_final: 0.8475 (tm-30) REVERT: D 453 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7746 (tm-30) REVERT: E 456 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7125 (mm110) REVERT: F 44 ARG cc_start: 0.8644 (mtt180) cc_final: 0.8361 (mtt-85) REVERT: F 380 ASP cc_start: 0.8107 (t0) cc_final: 0.7679 (m-30) REVERT: F 435 MET cc_start: 0.6875 (tpt) cc_final: 0.6605 (tpt) REVERT: F 444 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6896 (mt) REVERT: G 224 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6516 (mt) REVERT: I 55 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8068 (tm-30) REVERT: I 97 GLU cc_start: 0.8235 (tm-30) cc_final: 0.8010 (tm-30) REVERT: I 206 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.7635 (mp-120) REVERT: J 57 TYR cc_start: 0.6656 (OUTLIER) cc_final: 0.6149 (t80) REVERT: J 72 MET cc_start: 0.7684 (tmm) cc_final: 0.7466 (ttm) REVERT: J 168 ASP cc_start: 0.7222 (p0) cc_final: 0.6986 (p0) REVERT: K 162 ASP cc_start: 0.7801 (p0) cc_final: 0.7484 (t0) REVERT: L 33 HIS cc_start: 0.6652 (OUTLIER) cc_final: 0.6316 (m-70) REVERT: M 88 GLN cc_start: 0.8388 (tm-30) cc_final: 0.8078 (tm-30) REVERT: M 89 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7621 (tp40) REVERT: M 107 ARG cc_start: 0.8232 (mtm-85) cc_final: 0.7604 (mtm-85) REVERT: N 72 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7567 (tp30) REVERT: N 74 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7410 (tm-30) REVERT: O 79 ARG cc_start: 0.8514 (mtp180) cc_final: 0.8261 (tmt-80) REVERT: O 80 GLN cc_start: 0.7768 (mm-40) cc_final: 0.7365 (mm110) REVERT: P 154 GLU cc_start: 0.5052 (OUTLIER) cc_final: 0.3921 (pm20) REVERT: a 439 MET cc_start: 0.6200 (tmm) cc_final: 0.5876 (tmm) REVERT: d 309 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7802 (tm130) REVERT: d 325 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7906 (mt-10) REVERT: e 28 VAL cc_start: 0.7944 (t) cc_final: 0.7539 (t) REVERT: e 34 ARG cc_start: 0.6549 (ttm-80) cc_final: 0.5957 (ttm-80) REVERT: e 48 CYS cc_start: 0.7648 (m) cc_final: 0.7190 (m) REVERT: e 53 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8924 (tp) REVERT: e 64 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7841 (t80) REVERT: r 336 TYR cc_start: 0.5544 (p90) cc_final: 0.4567 (p90) REVERT: g 64 ILE cc_start: 0.8991 (mm) cc_final: 0.8509 (mt) REVERT: g 144 TYR cc_start: 0.8112 (m-10) cc_final: 0.7685 (m-80) REVERT: k 17 MET cc_start: 0.8483 (mmp) cc_final: 0.8140 (mmp) REVERT: m 68 TYR cc_start: 0.8610 (m-10) cc_final: 0.8290 (m-10) REVERT: m 123 GLN cc_start: 0.8369 (mt0) cc_final: 0.8127 (mt0) REVERT: m 147 ILE cc_start: 0.8831 (pt) cc_final: 0.8604 (mt) REVERT: o 44 MET cc_start: 0.7976 (ttp) cc_final: 0.7564 (ttp) REVERT: o 51 MET cc_start: 0.7767 (mmm) cc_final: 0.7409 (mmm) REVERT: p 139 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7842 (tm-30) REVERT: q 131 MET cc_start: 0.8693 (ttp) cc_final: 0.8454 (ttt) outliers start: 232 outliers final: 168 residues processed: 1090 average time/residue: 0.5818 time to fit residues: 1079.7860 Evaluate side-chains 1076 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 896 time to evaluate : 5.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 532 CYS Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 573 HIS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 153 TYR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 138 CYS Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 146 HIS Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 251 ASN Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 413 LYS Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 348 ILE Chi-restraints excluded: chain E residue 456 GLN Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 317 VAL Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 491 MET Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 112 TYR Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 206 GLN Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 162 ASP Chi-restraints excluded: chain J residue 183 ILE Chi-restraints excluded: chain J residue 221 ASN Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 193 SER Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 33 HIS Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 69 TYR Chi-restraints excluded: chain L residue 73 MET Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain M residue 110 VAL Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain O residue 102 MET Chi-restraints excluded: chain P residue 66 LEU Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain P residue 279 VAL Chi-restraints excluded: chain P residue 296 VAL Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 93 ASP Chi-restraints excluded: chain a residue 202 ILE Chi-restraints excluded: chain a residue 204 ASN Chi-restraints excluded: chain a residue 214 TYR Chi-restraints excluded: chain a residue 244 LEU Chi-restraints excluded: chain a residue 333 ILE Chi-restraints excluded: chain a residue 360 THR Chi-restraints excluded: chain a residue 390 ASN Chi-restraints excluded: chain a residue 395 THR Chi-restraints excluded: chain a residue 462 LEU Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 482 ARG Chi-restraints excluded: chain a residue 490 TRP Chi-restraints excluded: chain a residue 520 ASP Chi-restraints excluded: chain a residue 527 THR Chi-restraints excluded: chain a residue 557 LEU Chi-restraints excluded: chain a residue 755 VAL Chi-restraints excluded: chain a residue 756 LEU Chi-restraints excluded: chain a residue 779 ILE Chi-restraints excluded: chain a residue 791 LEU Chi-restraints excluded: chain a residue 830 HIS Chi-restraints excluded: chain b residue 26 TYR Chi-restraints excluded: chain b residue 91 LEU Chi-restraints excluded: chain b residue 128 HIS Chi-restraints excluded: chain b residue 142 LEU Chi-restraints excluded: chain b residue 201 VAL Chi-restraints excluded: chain d residue 69 VAL Chi-restraints excluded: chain d residue 99 PHE Chi-restraints excluded: chain d residue 124 GLU Chi-restraints excluded: chain d residue 143 ILE Chi-restraints excluded: chain d residue 309 GLN Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 53 LEU Chi-restraints excluded: chain e residue 64 PHE Chi-restraints excluded: chain s residue 265 ILE Chi-restraints excluded: chain s residue 343 LEU Chi-restraints excluded: chain s residue 360 THR Chi-restraints excluded: chain s residue 394 THR Chi-restraints excluded: chain s residue 424 ILE Chi-restraints excluded: chain s residue 425 TRP Chi-restraints excluded: chain s residue 429 LEU Chi-restraints excluded: chain s residue 448 LEU Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain g residue 6 ASN Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 81 ASN Chi-restraints excluded: chain k residue 115 ASP Chi-restraints excluded: chain k residue 147 ILE Chi-restraints excluded: chain l residue 64 ILE Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 81 ASN Chi-restraints excluded: chain l residue 82 ASP Chi-restraints excluded: chain l residue 141 LEU Chi-restraints excluded: chain l residue 146 LEU Chi-restraints excluded: chain l residue 147 ILE Chi-restraints excluded: chain m residue 6 ASN Chi-restraints excluded: chain m residue 50 GLU Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 124 GLN Chi-restraints excluded: chain m residue 129 VAL Chi-restraints excluded: chain n residue 9 GLU Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain q residue 17 MET Chi-restraints excluded: chain q residue 20 SER Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 82 ASP Chi-restraints excluded: chain q residue 84 ILE Chi-restraints excluded: chain q residue 91 LEU Chi-restraints excluded: chain f residue 82 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 751 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 444 optimal weight: 30.0000 chunk 569 optimal weight: 2.9990 chunk 441 optimal weight: 20.0000 chunk 656 optimal weight: 0.9980 chunk 435 optimal weight: 3.9990 chunk 776 optimal weight: 0.7980 chunk 486 optimal weight: 10.0000 chunk 473 optimal weight: 30.0000 chunk 358 optimal weight: 5.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 HIS ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 456 GLN ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 91 GLN I 96 ASN ** K 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 122 GLN ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 524 ASN ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 124 GLN ** q 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 64234 Z= 0.348 Angle : 0.640 12.245 86928 Z= 0.324 Chirality : 0.044 0.213 9966 Planarity : 0.005 0.133 11109 Dihedral : 8.099 129.513 9309 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.45 % Favored : 94.46 % Rotamer: Outliers : 3.81 % Allowed : 19.90 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.08 % Twisted Proline : 0.64 % 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: -1.15 (0.09), residues: 8098 helix: -0.05 (0.08), residues: 4525 sheet: -1.23 (0.18), residues: 718 loop : -1.67 (0.11), residues: 2855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP a 650 HIS 0.008 0.001 HIS a 802 PHE 0.036 0.001 PHE G 246 TYR 0.050 0.002 TYR c 68 ARG 0.013 0.001 ARG a 482 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1156 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 908 time to evaluate : 5.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 PHE cc_start: 0.7673 (m-80) cc_final: 0.7372 (m-10) REVERT: A 608 MET cc_start: 0.6624 (mmp) cc_final: 0.6361 (mtt) REVERT: B 458 MET cc_start: 0.9049 (mmm) cc_final: 0.8826 (mmt) REVERT: C 530 ARG cc_start: 0.8237 (ptt90) cc_final: 0.7967 (ptp90) REVERT: D 161 GLN cc_start: 0.8582 (tp40) cc_final: 0.8076 (tp-100) REVERT: D 249 GLU cc_start: 0.7596 (tt0) cc_final: 0.7271 (mt-10) REVERT: D 251 ASN cc_start: 0.8690 (OUTLIER) cc_final: 0.8038 (t0) REVERT: D 326 TYR cc_start: 0.9015 (p90) cc_final: 0.8744 (p90) REVERT: F 44 ARG cc_start: 0.8687 (mtt180) cc_final: 0.8379 (mtt-85) REVERT: F 413 LYS cc_start: 0.7987 (tttm) cc_final: 0.7768 (ttmt) REVERT: F 441 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6975 (tm-30) REVERT: F 444 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.7045 (mt) REVERT: F 456 GLN cc_start: 0.7626 (mp-120) cc_final: 0.7111 (pp30) REVERT: G 224 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6630 (mt) REVERT: G 265 MET cc_start: 0.7564 (mtt) cc_final: 0.7238 (mtt) REVERT: H 160 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7217 (mt-10) REVERT: I 206 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.7648 (mp-120) REVERT: J 57 TYR cc_start: 0.6585 (OUTLIER) cc_final: 0.6068 (t80) REVERT: J 168 ASP cc_start: 0.7237 (p0) cc_final: 0.7021 (p0) REVERT: K 162 ASP cc_start: 0.7760 (p0) cc_final: 0.7459 (t0) REVERT: L 33 HIS cc_start: 0.6727 (OUTLIER) cc_final: 0.6455 (m-70) REVERT: M 88 GLN cc_start: 0.8389 (tm-30) cc_final: 0.8086 (tm-30) REVERT: M 89 GLN cc_start: 0.7823 (mm-40) cc_final: 0.7523 (mm-40) REVERT: M 105 ASP cc_start: 0.8546 (m-30) cc_final: 0.8342 (m-30) REVERT: N 72 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7552 (tp30) REVERT: N 74 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7403 (tm-30) REVERT: N 105 ASP cc_start: 0.8427 (t70) cc_final: 0.7815 (t70) REVERT: O 79 ARG cc_start: 0.8552 (mtp180) cc_final: 0.8254 (tmt-80) REVERT: O 80 GLN cc_start: 0.7716 (mm-40) cc_final: 0.7324 (mm110) REVERT: P 154 GLU cc_start: 0.5123 (OUTLIER) cc_final: 0.4040 (pm20) REVERT: a 94 MET cc_start: 0.8947 (tmm) cc_final: 0.8710 (tmm) REVERT: a 118 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8697 (mp) REVERT: d 309 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7860 (tm130) REVERT: d 325 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7941 (mt-10) REVERT: e 28 VAL cc_start: 0.8005 (OUTLIER) cc_final: 0.7493 (t) REVERT: e 34 ARG cc_start: 0.6659 (ttm-80) cc_final: 0.5806 (mtp85) REVERT: e 48 CYS cc_start: 0.7671 (m) cc_final: 0.7202 (m) REVERT: e 53 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8969 (tp) REVERT: e 64 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.7955 (t80) REVERT: r 336 TYR cc_start: 0.5601 (p90) cc_final: 0.4564 (p90) REVERT: g 64 ILE cc_start: 0.9038 (mm) cc_final: 0.8546 (mt) REVERT: g 144 TYR cc_start: 0.8142 (m-10) cc_final: 0.7707 (m-80) REVERT: m 68 TYR cc_start: 0.8705 (m-10) cc_final: 0.8309 (m-10) REVERT: o 44 MET cc_start: 0.8018 (ttp) cc_final: 0.7635 (ttp) REVERT: p 68 TYR cc_start: 0.8414 (m-10) cc_final: 0.8154 (m-10) REVERT: p 139 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7776 (tm-30) outliers start: 248 outliers final: 199 residues processed: 1082 average time/residue: 0.6630 time to fit residues: 1236.0826 Evaluate side-chains 1079 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 868 time to evaluate : 5.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 532 CYS Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 573 HIS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 153 TYR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 138 CYS Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 251 ASN Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 413 LYS Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 348 ILE Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 491 MET Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 112 TYR Chi-restraints excluded: chain G residue 175 PHE Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 263 GLU Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 56 TYR Chi-restraints excluded: chain I residue 57 TYR Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 168 ASP Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 206 GLN Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 162 ASP Chi-restraints excluded: chain J residue 221 ASN Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 157 VAL Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 193 SER Chi-restraints excluded: chain K residue 221 ASN Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 33 HIS Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 69 TYR Chi-restraints excluded: chain L residue 73 MET Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 106 VAL Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain O residue 102 MET Chi-restraints excluded: chain P residue 66 LEU Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain P residue 279 VAL Chi-restraints excluded: chain P residue 296 VAL Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 93 ASP Chi-restraints excluded: chain a residue 118 LEU Chi-restraints excluded: chain a residue 202 ILE Chi-restraints excluded: chain a residue 204 ASN Chi-restraints excluded: chain a residue 214 TYR Chi-restraints excluded: chain a residue 244 LEU Chi-restraints excluded: chain a residue 333 ILE Chi-restraints excluded: chain a residue 360 THR Chi-restraints excluded: chain a residue 377 ILE Chi-restraints excluded: chain a residue 395 THR Chi-restraints excluded: chain a residue 462 LEU Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 482 ARG Chi-restraints excluded: chain a residue 504 ASN Chi-restraints excluded: chain a residue 520 ASP Chi-restraints excluded: chain a residue 527 THR Chi-restraints excluded: chain a residue 557 LEU Chi-restraints excluded: chain a residue 755 VAL Chi-restraints excluded: chain a residue 756 LEU Chi-restraints excluded: chain a residue 761 ILE Chi-restraints excluded: chain a residue 779 ILE Chi-restraints excluded: chain a residue 791 LEU Chi-restraints excluded: chain a residue 830 HIS Chi-restraints excluded: chain b residue 26 TYR Chi-restraints excluded: chain b residue 91 LEU Chi-restraints excluded: chain b residue 128 HIS Chi-restraints excluded: chain b residue 142 LEU Chi-restraints excluded: chain b residue 201 VAL Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 69 VAL Chi-restraints excluded: chain d residue 99 PHE Chi-restraints excluded: chain d residue 114 THR Chi-restraints excluded: chain d residue 124 GLU Chi-restraints excluded: chain d residue 143 ILE Chi-restraints excluded: chain d residue 203 THR Chi-restraints excluded: chain d residue 204 THR Chi-restraints excluded: chain d residue 264 VAL Chi-restraints excluded: chain d residue 309 GLN Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 28 VAL Chi-restraints excluded: chain e residue 50 LEU Chi-restraints excluded: chain e residue 53 LEU Chi-restraints excluded: chain e residue 64 PHE Chi-restraints excluded: chain s residue 253 VAL Chi-restraints excluded: chain s residue 265 ILE Chi-restraints excluded: chain s residue 300 TRP Chi-restraints excluded: chain s residue 338 PHE Chi-restraints excluded: chain s residue 343 LEU Chi-restraints excluded: chain s residue 360 THR Chi-restraints excluded: chain s residue 394 THR Chi-restraints excluded: chain s residue 424 ILE Chi-restraints excluded: chain s residue 425 TRP Chi-restraints excluded: chain s residue 429 LEU Chi-restraints excluded: chain s residue 434 MET Chi-restraints excluded: chain s residue 439 THR Chi-restraints excluded: chain s residue 448 LEU Chi-restraints excluded: chain s residue 452 ASP Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain c residue 67 ILE Chi-restraints excluded: chain c residue 98 SER Chi-restraints excluded: chain g residue 56 ILE Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 81 ASN Chi-restraints excluded: chain k residue 44 MET Chi-restraints excluded: chain k residue 59 VAL Chi-restraints excluded: chain k residue 115 ASP Chi-restraints excluded: chain k residue 147 ILE Chi-restraints excluded: chain l residue 50 GLU Chi-restraints excluded: chain l residue 64 ILE Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 81 ASN Chi-restraints excluded: chain l residue 82 ASP Chi-restraints excluded: chain l residue 121 THR Chi-restraints excluded: chain l residue 141 LEU Chi-restraints excluded: chain l residue 146 LEU Chi-restraints excluded: chain l residue 147 ILE Chi-restraints excluded: chain m residue 6 ASN Chi-restraints excluded: chain m residue 50 GLU Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 129 VAL Chi-restraints excluded: chain n residue 9 GLU Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain o residue 154 THR Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain p residue 75 LEU Chi-restraints excluded: chain q residue 17 MET Chi-restraints excluded: chain q residue 20 SER Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 82 ASP Chi-restraints excluded: chain q residue 84 ILE Chi-restraints excluded: chain q residue 91 LEU Chi-restraints excluded: chain f residue 82 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 480 optimal weight: 7.9990 chunk 310 optimal weight: 0.7980 chunk 463 optimal weight: 50.0000 chunk 234 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 493 optimal weight: 6.9990 chunk 529 optimal weight: 0.9980 chunk 384 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 610 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 ASN B 494 GLN ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 ASN ** F 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 91 GLN H 152 GLN I 96 ASN K 67 GLN K 96 ASN ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 439 GLN a 36 GLN a 390 ASN ** a 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 548 HIS b 90 ASN ** b 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 124 GLN o 81 ASN ** q 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 64234 Z= 0.169 Angle : 0.575 13.414 86928 Z= 0.290 Chirality : 0.041 0.216 9966 Planarity : 0.004 0.128 11109 Dihedral : 7.683 126.202 9309 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.91 % Favored : 95.00 % Rotamer: Outliers : 2.84 % Allowed : 21.28 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.08 % Twisted Proline : 0.64 % 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: -0.88 (0.09), residues: 8098 helix: 0.19 (0.08), residues: 4525 sheet: -1.15 (0.18), residues: 717 loop : -1.59 (0.11), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP a 650 HIS 0.007 0.001 HIS P 139 PHE 0.033 0.001 PHE G 246 TYR 0.053 0.001 TYR c 68 ARG 0.010 0.000 ARG a 482 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1137 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 952 time to evaluate : 5.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 PHE cc_start: 0.7667 (m-80) cc_final: 0.7366 (m-10) REVERT: A 492 ILE cc_start: 0.7397 (OUTLIER) cc_final: 0.6742 (pt) REVERT: B 458 MET cc_start: 0.9046 (mmm) cc_final: 0.8843 (mmt) REVERT: B 486 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7782 (tm-30) REVERT: B 494 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7657 (tm130) REVERT: C 584 MET cc_start: 0.7402 (mtp) cc_final: 0.6755 (tpt) REVERT: D 161 GLN cc_start: 0.8506 (tp40) cc_final: 0.8031 (tp-100) REVERT: D 249 GLU cc_start: 0.7490 (tt0) cc_final: 0.7196 (mt-10) REVERT: D 326 TYR cc_start: 0.8976 (p90) cc_final: 0.8694 (p90) REVERT: F 44 ARG cc_start: 0.8602 (mtt180) cc_final: 0.8343 (mtt-85) REVERT: F 277 LEU cc_start: 0.8971 (mp) cc_final: 0.8701 (mp) REVERT: F 380 ASP cc_start: 0.8079 (t0) cc_final: 0.7706 (m-30) REVERT: F 413 LYS cc_start: 0.7983 (tttm) cc_final: 0.7734 (ttmt) REVERT: F 441 GLU cc_start: 0.7227 (mm-30) cc_final: 0.6996 (tm-30) REVERT: F 444 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6989 (mt) REVERT: F 456 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7082 (pp30) REVERT: G 265 MET cc_start: 0.7515 (mtt) cc_final: 0.7187 (mtt) REVERT: I 97 GLU cc_start: 0.8252 (tm-30) cc_final: 0.8016 (tm-30) REVERT: J 162 ASP cc_start: 0.7394 (OUTLIER) cc_final: 0.7080 (m-30) REVERT: J 168 ASP cc_start: 0.7218 (p0) cc_final: 0.7005 (p0) REVERT: K 162 ASP cc_start: 0.7683 (p0) cc_final: 0.7473 (t0) REVERT: L 33 HIS cc_start: 0.6782 (OUTLIER) cc_final: 0.6353 (m-70) REVERT: M 88 GLN cc_start: 0.8391 (tm-30) cc_final: 0.8092 (tm-30) REVERT: M 89 GLN cc_start: 0.7900 (mm-40) cc_final: 0.7686 (tp40) REVERT: N 72 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7530 (tp30) REVERT: N 74 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7378 (tm-30) REVERT: O 79 ARG cc_start: 0.8525 (mtp180) cc_final: 0.8259 (tmt-80) REVERT: O 80 GLN cc_start: 0.7676 (mm-40) cc_final: 0.7286 (mm110) REVERT: O 89 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7932 (mm-40) REVERT: P 140 MET cc_start: 0.8539 (mpp) cc_final: 0.8016 (mpp) REVERT: P 154 GLU cc_start: 0.4948 (OUTLIER) cc_final: 0.3850 (pm20) REVERT: a 830 HIS cc_start: 0.8463 (OUTLIER) cc_final: 0.8072 (t-90) REVERT: d 340 HIS cc_start: 0.8351 (t70) cc_final: 0.8138 (t70) REVERT: e 28 VAL cc_start: 0.8007 (t) cc_final: 0.7776 (t) REVERT: e 34 ARG cc_start: 0.6739 (ttm-80) cc_final: 0.5810 (mtp-110) REVERT: e 48 CYS cc_start: 0.7621 (m) cc_final: 0.7146 (m) REVERT: e 64 PHE cc_start: 0.8008 (OUTLIER) cc_final: 0.7713 (t80) REVERT: r 336 TYR cc_start: 0.5442 (p90) cc_final: 0.4445 (p90) REVERT: g 64 ILE cc_start: 0.8952 (mm) cc_final: 0.8447 (mt) REVERT: g 144 TYR cc_start: 0.7990 (m-10) cc_final: 0.7704 (m-80) REVERT: k 17 MET cc_start: 0.8481 (mmp) cc_final: 0.8211 (mmt) REVERT: l 147 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8885 (mt) REVERT: m 68 TYR cc_start: 0.8602 (m-10) cc_final: 0.8244 (m-10) REVERT: o 44 MET cc_start: 0.7887 (ttp) cc_final: 0.7547 (ttp) REVERT: o 51 MET cc_start: 0.7708 (mmm) cc_final: 0.7490 (mmt) REVERT: p 139 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7883 (tm-30) REVERT: f 25 MET cc_start: 0.8469 (ttp) cc_final: 0.8234 (ttm) REVERT: f 32 PHE cc_start: 0.8129 (m-80) cc_final: 0.7841 (m-80) outliers start: 185 outliers final: 141 residues processed: 1072 average time/residue: 0.5902 time to fit residues: 1078.6176 Evaluate side-chains 1040 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 889 time to evaluate : 5.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 532 CYS Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 573 HIS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 140 ASN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 138 CYS Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 413 LYS Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 348 ILE Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 456 GLN Chi-restraints excluded: chain F residue 491 MET Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 112 TYR Chi-restraints excluded: chain G residue 133 ASP Chi-restraints excluded: chain G residue 181 TYR Chi-restraints excluded: chain G residue 263 GLU Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 56 TYR Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 162 ASP Chi-restraints excluded: chain J residue 221 ASN Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 193 SER Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 15 ASP Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 33 HIS Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 69 TYR Chi-restraints excluded: chain L residue 73 MET Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain O residue 102 MET Chi-restraints excluded: chain P residue 66 LEU Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain P residue 279 VAL Chi-restraints excluded: chain P residue 296 VAL Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 93 ASP Chi-restraints excluded: chain a residue 202 ILE Chi-restraints excluded: chain a residue 214 TYR Chi-restraints excluded: chain a residue 333 ILE Chi-restraints excluded: chain a residue 360 THR Chi-restraints excluded: chain a residue 462 LEU Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 482 ARG Chi-restraints excluded: chain a residue 504 ASN Chi-restraints excluded: chain a residue 520 ASP Chi-restraints excluded: chain a residue 527 THR Chi-restraints excluded: chain a residue 557 LEU Chi-restraints excluded: chain a residue 755 VAL Chi-restraints excluded: chain a residue 756 LEU Chi-restraints excluded: chain a residue 791 LEU Chi-restraints excluded: chain a residue 830 HIS Chi-restraints excluded: chain b residue 26 TYR Chi-restraints excluded: chain b residue 91 LEU Chi-restraints excluded: chain b residue 128 HIS Chi-restraints excluded: chain b residue 142 LEU Chi-restraints excluded: chain b residue 201 VAL Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 69 VAL Chi-restraints excluded: chain d residue 99 PHE Chi-restraints excluded: chain d residue 264 VAL Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 64 PHE Chi-restraints excluded: chain s residue 253 VAL Chi-restraints excluded: chain s residue 265 ILE Chi-restraints excluded: chain s residue 279 HIS Chi-restraints excluded: chain s residue 300 TRP Chi-restraints excluded: chain s residue 338 PHE Chi-restraints excluded: chain s residue 343 LEU Chi-restraints excluded: chain s residue 424 ILE Chi-restraints excluded: chain s residue 425 TRP Chi-restraints excluded: chain s residue 429 LEU Chi-restraints excluded: chain s residue 452 ASP Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 81 ASN Chi-restraints excluded: chain k residue 115 ASP Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 81 ASN Chi-restraints excluded: chain l residue 82 ASP Chi-restraints excluded: chain l residue 141 LEU Chi-restraints excluded: chain l residue 146 LEU Chi-restraints excluded: chain l residue 147 ILE Chi-restraints excluded: chain m residue 6 ASN Chi-restraints excluded: chain m residue 50 GLU Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 124 GLN Chi-restraints excluded: chain m residue 129 VAL Chi-restraints excluded: chain m residue 143 LEU Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 91 LEU Chi-restraints excluded: chain f residue 68 ASN Chi-restraints excluded: chain f residue 82 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 706 optimal weight: 8.9990 chunk 744 optimal weight: 4.9990 chunk 679 optimal weight: 0.5980 chunk 723 optimal weight: 4.9990 chunk 435 optimal weight: 5.9990 chunk 315 optimal weight: 7.9990 chunk 568 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 654 optimal weight: 0.9990 chunk 684 optimal weight: 4.9990 chunk 721 optimal weight: 7.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 96 ASN K 96 ASN ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 36 GLN ** a 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 10 ASN ** d 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 64234 Z= 0.325 Angle : 0.632 12.305 86928 Z= 0.320 Chirality : 0.044 0.242 9966 Planarity : 0.004 0.129 11109 Dihedral : 7.757 125.543 9309 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.40 % Favored : 94.53 % Rotamer: Outliers : 3.14 % Allowed : 21.16 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.08 % Twisted Proline : 0.64 % 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: -0.89 (0.09), residues: 8098 helix: 0.20 (0.08), residues: 4546 sheet: -1.16 (0.18), residues: 722 loop : -1.61 (0.11), residues: 2830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP a 650 HIS 0.008 0.001 HIS a 802 PHE 0.030 0.001 PHE G 246 TYR 0.054 0.002 TYR L 98 ARG 0.012 0.000 ARG a 482 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1096 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 892 time to evaluate : 5.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 PHE cc_start: 0.7677 (m-80) cc_final: 0.7374 (m-10) REVERT: A 492 ILE cc_start: 0.7492 (OUTLIER) cc_final: 0.6829 (pt) REVERT: B 458 MET cc_start: 0.9088 (mmm) cc_final: 0.8880 (mmt) REVERT: B 486 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7860 (tm-30) REVERT: C 360 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7150 (tm-30) REVERT: D 161 GLN cc_start: 0.8567 (tp40) cc_final: 0.8064 (tp-100) REVERT: D 249 GLU cc_start: 0.7607 (tt0) cc_final: 0.7283 (mt-10) REVERT: D 251 ASN cc_start: 0.8678 (OUTLIER) cc_final: 0.8083 (t0) REVERT: D 326 TYR cc_start: 0.9027 (p90) cc_final: 0.8742 (p90) REVERT: F 44 ARG cc_start: 0.8676 (mtt180) cc_final: 0.8371 (mtt-85) REVERT: F 380 ASP cc_start: 0.8113 (t0) cc_final: 0.7749 (m-30) REVERT: F 444 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7082 (mt) REVERT: F 456 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7098 (pp30) REVERT: G 265 MET cc_start: 0.7542 (mtt) cc_final: 0.7206 (mtt) REVERT: J 57 TYR cc_start: 0.6712 (OUTLIER) cc_final: 0.6177 (t80) REVERT: J 96 ASN cc_start: 0.8539 (m-40) cc_final: 0.8197 (t0) REVERT: K 117 ASP cc_start: 0.8294 (p0) cc_final: 0.8083 (p0) REVERT: K 162 ASP cc_start: 0.7695 (p0) cc_final: 0.7465 (t0) REVERT: M 105 ASP cc_start: 0.8493 (m-30) cc_final: 0.8268 (m-30) REVERT: N 72 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7563 (tp30) REVERT: N 74 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7374 (tm-30) REVERT: N 105 ASP cc_start: 0.8464 (t70) cc_final: 0.8013 (t70) REVERT: O 79 ARG cc_start: 0.8549 (mtp180) cc_final: 0.8268 (tmt-80) REVERT: O 80 GLN cc_start: 0.7709 (mm-40) cc_final: 0.7299 (mm110) REVERT: P 140 MET cc_start: 0.8597 (mpp) cc_final: 0.8074 (mpp) REVERT: P 154 GLU cc_start: 0.5016 (OUTLIER) cc_final: 0.3971 (pm20) REVERT: a 118 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8684 (mp) REVERT: a 830 HIS cc_start: 0.8500 (OUTLIER) cc_final: 0.8106 (t-90) REVERT: e 28 VAL cc_start: 0.8059 (t) cc_final: 0.7784 (t) REVERT: e 34 ARG cc_start: 0.6787 (ttm-80) cc_final: 0.5873 (mtp-110) REVERT: e 48 CYS cc_start: 0.7692 (m) cc_final: 0.7207 (m) REVERT: e 64 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7846 (t80) REVERT: r 336 TYR cc_start: 0.5519 (p90) cc_final: 0.4460 (p90) REVERT: g 64 ILE cc_start: 0.9030 (mm) cc_final: 0.8523 (mt) REVERT: g 144 TYR cc_start: 0.8055 (m-10) cc_final: 0.7674 (m-80) REVERT: k 17 MET cc_start: 0.8495 (mmp) cc_final: 0.8143 (mmp) REVERT: m 68 TYR cc_start: 0.8700 (m-10) cc_final: 0.8273 (m-10) REVERT: m 139 GLU cc_start: 0.8845 (tp30) cc_final: 0.8612 (tp30) REVERT: o 44 MET cc_start: 0.7973 (ttp) cc_final: 0.7580 (ttp) REVERT: p 139 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7935 (tm-30) REVERT: f 25 MET cc_start: 0.8539 (ttp) cc_final: 0.7880 (ttm) REVERT: f 32 PHE cc_start: 0.8213 (m-80) cc_final: 0.7945 (m-80) outliers start: 204 outliers final: 170 residues processed: 1032 average time/residue: 0.5744 time to fit residues: 1010.9415 Evaluate side-chains 1052 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 873 time to evaluate : 5.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 532 CYS Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 573 HIS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 153 TYR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 349 ASP Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 138 CYS Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 251 ASN Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 413 LYS Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 348 ILE Chi-restraints excluded: chain E residue 449 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 456 GLN Chi-restraints excluded: chain F residue 491 MET Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 112 TYR Chi-restraints excluded: chain G residue 133 ASP Chi-restraints excluded: chain G residue 175 PHE Chi-restraints excluded: chain G residue 181 TYR Chi-restraints excluded: chain G residue 263 GLU Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 56 TYR Chi-restraints excluded: chain I residue 115 LEU Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 168 ASP Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 162 ASP Chi-restraints excluded: chain J residue 221 ASN Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 193 SER Chi-restraints excluded: chain K residue 221 ASN Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 69 TYR Chi-restraints excluded: chain L residue 73 MET Chi-restraints excluded: chain M residue 95 VAL Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain O residue 84 MET Chi-restraints excluded: chain O residue 96 LEU Chi-restraints excluded: chain O residue 102 MET Chi-restraints excluded: chain P residue 66 LEU Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain P residue 279 VAL Chi-restraints excluded: chain P residue 296 VAL Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 93 ASP Chi-restraints excluded: chain a residue 118 LEU Chi-restraints excluded: chain a residue 202 ILE Chi-restraints excluded: chain a residue 204 ASN Chi-restraints excluded: chain a residue 244 LEU Chi-restraints excluded: chain a residue 333 ILE Chi-restraints excluded: chain a residue 360 THR Chi-restraints excluded: chain a residue 462 LEU Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 482 ARG Chi-restraints excluded: chain a residue 504 ASN Chi-restraints excluded: chain a residue 520 ASP Chi-restraints excluded: chain a residue 527 THR Chi-restraints excluded: chain a residue 557 LEU Chi-restraints excluded: chain a residue 629 LEU Chi-restraints excluded: chain a residue 755 VAL Chi-restraints excluded: chain a residue 756 LEU Chi-restraints excluded: chain a residue 779 ILE Chi-restraints excluded: chain a residue 791 LEU Chi-restraints excluded: chain a residue 830 HIS Chi-restraints excluded: chain b residue 26 TYR Chi-restraints excluded: chain b residue 91 LEU Chi-restraints excluded: chain b residue 128 HIS Chi-restraints excluded: chain b residue 142 LEU Chi-restraints excluded: chain b residue 201 VAL Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 69 VAL Chi-restraints excluded: chain d residue 99 PHE Chi-restraints excluded: chain d residue 124 GLU Chi-restraints excluded: chain d residue 203 THR Chi-restraints excluded: chain d residue 204 THR Chi-restraints excluded: chain d residue 264 VAL Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 64 PHE Chi-restraints excluded: chain s residue 253 VAL Chi-restraints excluded: chain s residue 265 ILE Chi-restraints excluded: chain s residue 300 TRP Chi-restraints excluded: chain s residue 338 PHE Chi-restraints excluded: chain s residue 343 LEU Chi-restraints excluded: chain s residue 348 ASN Chi-restraints excluded: chain s residue 371 HIS Chi-restraints excluded: chain s residue 394 THR Chi-restraints excluded: chain s residue 425 TRP Chi-restraints excluded: chain s residue 429 LEU Chi-restraints excluded: chain s residue 448 LEU Chi-restraints excluded: chain s residue 452 ASP Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain k residue 115 ASP Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 81 ASN Chi-restraints excluded: chain l residue 82 ASP Chi-restraints excluded: chain l residue 141 LEU Chi-restraints excluded: chain l residue 146 LEU Chi-restraints excluded: chain l residue 147 ILE Chi-restraints excluded: chain m residue 50 GLU Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 129 VAL Chi-restraints excluded: chain n residue 9 GLU Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain q residue 17 MET Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 82 ASP Chi-restraints excluded: chain q residue 84 ILE Chi-restraints excluded: chain q residue 91 LEU Chi-restraints excluded: chain f residue 82 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 475 optimal weight: 6.9990 chunk 765 optimal weight: 2.9990 chunk 467 optimal weight: 20.0000 chunk 363 optimal weight: 0.8980 chunk 532 optimal weight: 0.0050 chunk 802 optimal weight: 0.9990 chunk 739 optimal weight: 1.9990 chunk 639 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 493 optimal weight: 7.9990 chunk 392 optimal weight: 10.0000 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 494 GLN ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 456 GLN ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 GLN ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 91 GLN I 96 ASN ** I 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 ASN K 122 GLN ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 36 GLN ** a 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 90 ASN d 10 ASN ** d 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 64234 Z= 0.209 Angle : 0.596 13.488 86928 Z= 0.300 Chirality : 0.042 0.202 9966 Planarity : 0.004 0.127 11109 Dihedral : 7.617 124.200 9309 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.14 % Favored : 94.80 % Rotamer: Outliers : 2.81 % Allowed : 21.67 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.08 % Twisted Proline : 0.64 % 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: -0.74 (0.09), residues: 8098 helix: 0.32 (0.08), residues: 4518 sheet: -1.11 (0.18), residues: 727 loop : -1.51 (0.12), residues: 2853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP a 650 HIS 0.007 0.001 HIS a 802 PHE 0.019 0.001 PHE E 260 TYR 0.042 0.001 TYR c 68 ARG 0.011 0.000 ARG a 482 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16196 Ramachandran restraints generated. 8098 Oldfield, 0 Emsley, 8098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1083 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 900 time to evaluate : 5.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 PHE cc_start: 0.7661 (m-80) cc_final: 0.7358 (m-10) REVERT: A 492 ILE cc_start: 0.7511 (OUTLIER) cc_final: 0.6865 (pt) REVERT: B 486 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7832 (tm-30) REVERT: D 161 GLN cc_start: 0.8524 (tp40) cc_final: 0.8041 (tp-100) REVERT: D 249 GLU cc_start: 0.7533 (tt0) cc_final: 0.7198 (mt-10) REVERT: D 251 ASN cc_start: 0.8614 (OUTLIER) cc_final: 0.8040 (t0) REVERT: D 326 TYR cc_start: 0.9004 (p90) cc_final: 0.8713 (p90) REVERT: E 456 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7184 (mm110) REVERT: F 44 ARG cc_start: 0.8631 (mtt180) cc_final: 0.8361 (mtt-85) REVERT: F 277 LEU cc_start: 0.9038 (mp) cc_final: 0.8648 (mp) REVERT: F 380 ASP cc_start: 0.8117 (t0) cc_final: 0.7735 (m-30) REVERT: F 444 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6989 (mt) REVERT: F 456 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7084 (pp30) REVERT: G 224 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.5844 (tp) REVERT: I 97 GLU cc_start: 0.8315 (tm-30) cc_final: 0.8069 (tm-30) REVERT: J 57 TYR cc_start: 0.6709 (OUTLIER) cc_final: 0.6223 (t80) REVERT: J 96 ASN cc_start: 0.8506 (m-40) cc_final: 0.8190 (t0) REVERT: K 117 ASP cc_start: 0.8278 (p0) cc_final: 0.8072 (p0) REVERT: L 33 HIS cc_start: 0.7077 (OUTLIER) cc_final: 0.6726 (m-70) REVERT: M 88 GLN cc_start: 0.8354 (tm-30) cc_final: 0.8078 (tm-30) REVERT: M 105 ASP cc_start: 0.8470 (m-30) cc_final: 0.7599 (m-30) REVERT: M 107 ARG cc_start: 0.8350 (mtm-85) cc_final: 0.7670 (mtm-85) REVERT: N 72 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7570 (tp30) REVERT: N 74 GLU cc_start: 0.7562 (tm-30) cc_final: 0.7283 (tm-30) REVERT: N 105 ASP cc_start: 0.8471 (t70) cc_final: 0.8003 (t70) REVERT: O 79 ARG cc_start: 0.8534 (mtp180) cc_final: 0.8272 (tmt-80) REVERT: O 80 GLN cc_start: 0.7687 (mm-40) cc_final: 0.7294 (mm110) REVERT: O 89 GLN cc_start: 0.8081 (mm-40) cc_final: 0.7744 (mm-40) REVERT: P 66 LEU cc_start: 0.6503 (OUTLIER) cc_final: 0.6296 (mt) REVERT: P 140 MET cc_start: 0.8571 (mpp) cc_final: 0.8124 (mpp) REVERT: P 154 GLU cc_start: 0.4895 (OUTLIER) cc_final: 0.4332 (pt0) REVERT: a 118 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8672 (mp) REVERT: a 628 MET cc_start: 0.8485 (mmp) cc_final: 0.8269 (mmp) REVERT: a 830 HIS cc_start: 0.8468 (OUTLIER) cc_final: 0.8084 (t-90) REVERT: d 105 MET cc_start: 0.8365 (ttm) cc_final: 0.8165 (ttm) REVERT: d 340 HIS cc_start: 0.8389 (t70) cc_final: 0.8181 (t70) REVERT: e 28 VAL cc_start: 0.8068 (t) cc_final: 0.7850 (t) REVERT: e 34 ARG cc_start: 0.6805 (ttm-80) cc_final: 0.5858 (mtp-110) REVERT: e 48 CYS cc_start: 0.7669 (m) cc_final: 0.7181 (m) REVERT: e 64 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7820 (t80) REVERT: r 336 TYR cc_start: 0.5530 (p90) cc_final: 0.4458 (p90) REVERT: g 64 ILE cc_start: 0.8993 (mm) cc_final: 0.8473 (mt) REVERT: g 123 GLN cc_start: 0.8994 (mm-40) cc_final: 0.8260 (mm-40) REVERT: g 144 TYR cc_start: 0.7977 (m-10) cc_final: 0.7626 (m-80) REVERT: k 17 MET cc_start: 0.8466 (mmp) cc_final: 0.8152 (mmp) REVERT: l 147 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8888 (mt) REVERT: m 68 TYR cc_start: 0.8642 (m-10) cc_final: 0.8233 (m-10) REVERT: o 44 MET cc_start: 0.7950 (ttp) cc_final: 0.7603 (ttp) REVERT: p 139 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7924 (tm-30) REVERT: f 25 MET cc_start: 0.8510 (ttp) cc_final: 0.7945 (ttm) REVERT: f 32 PHE cc_start: 0.8188 (m-80) cc_final: 0.7894 (m-80) outliers start: 183 outliers final: 158 residues processed: 1024 average time/residue: 0.5884 time to fit residues: 1030.4538 Evaluate side-chains 1052 residues out of total 6850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 880 time to evaluate : 5.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 466 ASP Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 532 CYS Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 573 HIS Chi-restraints excluded: chain B residue 18 PHE Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 488 ASP Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 138 CYS Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 612 PHE Chi-restraints excluded: chain D residue 237 ASN Chi-restraints excluded: chain D residue 251 ASN Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 265 ASN Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 348 ILE Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 413 LYS Chi-restraints excluded: chain D residue 438 VAL Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 348 ILE Chi-restraints excluded: chain E residue 456 GLN Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain F residue 53 VAL Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 456 GLN Chi-restraints excluded: chain F residue 491 MET Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 112 TYR Chi-restraints excluded: chain G residue 133 ASP Chi-restraints excluded: chain G residue 181 TYR Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 263 GLU Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 101 VAL Chi-restraints excluded: chain I residue 56 TYR Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 221 ASN Chi-restraints excluded: chain J residue 57 TYR Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 221 ASN Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 193 SER Chi-restraints excluded: chain K residue 221 ASN Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 30 LYS Chi-restraints excluded: chain L residue 33 HIS Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 39 VAL Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 69 TYR Chi-restraints excluded: chain L residue 73 MET Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain N residue 99 LEU Chi-restraints excluded: chain O residue 84 MET Chi-restraints excluded: chain O residue 102 MET Chi-restraints excluded: chain P residue 66 LEU Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 242 LEU Chi-restraints excluded: chain P residue 279 VAL Chi-restraints excluded: chain P residue 296 VAL Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 93 ASP Chi-restraints excluded: chain a residue 118 LEU Chi-restraints excluded: chain a residue 202 ILE Chi-restraints excluded: chain a residue 244 LEU Chi-restraints excluded: chain a residue 333 ILE Chi-restraints excluded: chain a residue 360 THR Chi-restraints excluded: chain a residue 462 LEU Chi-restraints excluded: chain a residue 472 LEU Chi-restraints excluded: chain a residue 482 ARG Chi-restraints excluded: chain a residue 504 ASN Chi-restraints excluded: chain a residue 520 ASP Chi-restraints excluded: chain a residue 527 THR Chi-restraints excluded: chain a residue 557 LEU Chi-restraints excluded: chain a residue 629 LEU Chi-restraints excluded: chain a residue 755 VAL Chi-restraints excluded: chain a residue 756 LEU Chi-restraints excluded: chain a residue 761 ILE Chi-restraints excluded: chain a residue 791 LEU Chi-restraints excluded: chain a residue 830 HIS Chi-restraints excluded: chain b residue 26 TYR Chi-restraints excluded: chain b residue 91 LEU Chi-restraints excluded: chain b residue 128 HIS Chi-restraints excluded: chain b residue 142 LEU Chi-restraints excluded: chain b residue 201 VAL Chi-restraints excluded: chain d residue 7 LEU Chi-restraints excluded: chain d residue 69 VAL Chi-restraints excluded: chain d residue 99 PHE Chi-restraints excluded: chain d residue 124 GLU Chi-restraints excluded: chain d residue 203 THR Chi-restraints excluded: chain d residue 264 VAL Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 37 ILE Chi-restraints excluded: chain e residue 64 PHE Chi-restraints excluded: chain s residue 253 VAL Chi-restraints excluded: chain s residue 265 ILE Chi-restraints excluded: chain s residue 279 HIS Chi-restraints excluded: chain s residue 300 TRP Chi-restraints excluded: chain s residue 338 PHE Chi-restraints excluded: chain s residue 343 LEU Chi-restraints excluded: chain s residue 348 ASN Chi-restraints excluded: chain s residue 371 HIS Chi-restraints excluded: chain s residue 394 THR Chi-restraints excluded: chain s residue 425 TRP Chi-restraints excluded: chain s residue 429 LEU Chi-restraints excluded: chain s residue 448 LEU Chi-restraints excluded: chain s residue 452 ASP Chi-restraints excluded: chain c residue 59 VAL Chi-restraints excluded: chain c residue 60 VAL Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 81 ASN Chi-restraints excluded: chain k residue 115 ASP Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 81 ASN Chi-restraints excluded: chain l residue 82 ASP Chi-restraints excluded: chain l residue 141 LEU Chi-restraints excluded: chain l residue 146 LEU Chi-restraints excluded: chain l residue 147 ILE Chi-restraints excluded: chain m residue 50 GLU Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 129 VAL Chi-restraints excluded: chain n residue 9 GLU Chi-restraints excluded: chain o residue 59 VAL Chi-restraints excluded: chain p residue 59 VAL Chi-restraints excluded: chain q residue 17 MET Chi-restraints excluded: chain q residue 59 VAL Chi-restraints excluded: chain q residue 84 ILE Chi-restraints excluded: chain q residue 91 LEU Chi-restraints excluded: chain f residue 82 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 507 optimal weight: 9.9990 chunk 681 optimal weight: 4.9990 chunk 195 optimal weight: 5.9990 chunk 589 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 chunk 640 optimal weight: 4.9990 chunk 268 optimal weight: 2.9990 chunk 657 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 ASN ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 ASN F 42 GLN ** F 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 91 GLN I 96 ASN I 122 GLN ** L 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 10 ASN ** d 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.109885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.082665 restraints weight = 131333.370| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.04 r_work: 0.2898 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 64234 Z= 0.373 Angle : 0.665 12.290 86928 Z= 0.336 Chirality : 0.045 0.203 9966 Planarity : 0.005 0.127 11109 Dihedral : 7.828 126.232 9309 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.89 % Favored : 94.05 % Rotamer: Outliers : 3.04 % Allowed : 21.56 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.08 % Twisted Proline : 0.64 % 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: -0.86 (0.09), residues: 8098 helix: 0.23 (0.08), residues: 4524 sheet: -1.19 (0.18), residues: 747 loop : -1.59 (0.12), residues: 2827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP r 313 HIS 0.008 0.001 HIS a 802 PHE 0.026 0.002 PHE E 260 TYR 0.043 0.002 TYR c 68 ARG 0.012 0.001 ARG a 482 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18207.73 seconds wall clock time: 318 minutes 19.13 seconds (19099.13 seconds total)