Starting phenix.real_space_refine on Mon Apr 15 16:15:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pks_13479/04_2024/7pks_13479.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pks_13479/04_2024/7pks_13479.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pks_13479/04_2024/7pks_13479.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pks_13479/04_2024/7pks_13479.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pks_13479/04_2024/7pks_13479.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pks_13479/04_2024/7pks_13479.pdb" } resolution = 3.6 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= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Mn 2 7.51 5 Zn 10 6.06 5 P 74 5.49 5 Mg 1 5.21 5 S 584 5.16 5 C 63842 2.51 5 N 17659 2.21 5 O 18975 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 500": "OE1" <-> "OE2" Residue "A ASP 540": "OD1" <-> "OD2" Residue "A ASP 849": "OD1" <-> "OD2" Residue "A GLU 902": "OE1" <-> "OE2" Residue "A TYR 1383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 281": "OD1" <-> "OD2" Residue "B TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 671": "OE1" <-> "OE2" Residue "B PHE 1086": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C ASP 104": "OD1" <-> "OD2" Residue "D TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 88": "OD1" <-> "OD2" Residue "F GLU 96": "OE1" <-> "OE2" Residue "F ASP 121": "OD1" <-> "OD2" Residue "G PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H GLU 100": "OE1" <-> "OE2" Residue "I GLU 19": "OE1" <-> "OE2" Residue "I GLU 82": "OE1" <-> "OE2" Residue "J TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 57": "OE1" <-> "OE2" Residue "K PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 24": "OD1" <-> "OD2" Residue "K GLU 38": "OE1" <-> "OE2" Residue "K PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 102": "OE1" <-> "OE2" Residue "M TYR 1622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 1264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 2050": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 726": "OD1" <-> "OD2" Residue "b ASP 1135": "OD1" <-> "OD2" Residue "b GLU 1195": "OE1" <-> "OE2" Residue "d ASP 414": "OD1" <-> "OD2" Residue "e ASP 429": "OD1" <-> "OD2" Residue "e ASP 823": "OD1" <-> "OD2" Residue "f GLU 76": "OE1" <-> "OE2" Residue "f PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 395": "OD1" <-> "OD2" Residue "f TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 171": "OD1" <-> "OD2" Residue "g TYR 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 687": "OD1" <-> "OD2" Residue "h PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 790": "OD1" <-> "OD2" Residue "i PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 106": "OD1" <-> "OD2" Residue "p TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 280": "OD1" <-> "OD2" Residue "q ASP 290": "OD1" <-> "OD2" Time to flip residues: 0.24s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 101147 Number of models: 1 Model: "" Number of chains: 41 Chain: "A" Number of atoms: 11012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1392, 11012 Classifications: {'peptide': 1392} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 66, 'TRANS': 1323} Chain breaks: 6 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 8901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1112, 8901 Classifications: {'peptide': 1112} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 53, 'TRANS': 1058} Chain breaks: 7 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2096 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 15, 'TRANS': 245} Chain breaks: 1 Chain: "D" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 975 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 122} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "E" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1721 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 627 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "G" Number of atoms: 1316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1316 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 944 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 111} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 383 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 95 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 4, 'TRANS': 8} Chain: "N" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 489 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain breaks: 1 Chain: "P" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 361 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 7, 'rna3p_pyr': 5} Link IDs: {'rna2p': 5, 'rna3p': 11} Chain: "T" Number of atoms: 682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 682 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "U" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1398 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 171} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "V" Number of atoms: 2040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 2040 Classifications: {'peptide': 451} Incomplete info: {'backbone_only': 347, 'truncation_to_alanine': 33} Link IDs: {'PTRANS': 17, 'TRANS': 433} Chain breaks: 9 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1628 Unresolved non-hydrogen angles: 2332 Unresolved non-hydrogen dihedrals: 1041 Unresolved non-hydrogen chiralities: 462 Planarities with less than four sites: {'GLN:plan1': 17, 'HIS:plan': 8, 'ASN:plan1': 8, 'TYR:plan': 8, 'UNK:plan-1': 33, 'TRP:plan': 3, 'ASP:plan': 21, 'PHE:plan': 23, 'GLU:plan': 28, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 748 Chain: "W" Number of atoms: 3854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3854 Classifications: {'peptide': 508} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 486} Chain breaks: 5 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'UNK:plan-1': 24, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 93 Chain: "X" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 110 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'UNK:plan-1': 22} Unresolved non-hydrogen planarities: 22 Chain: "Z" Number of atoms: 2174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2174 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 7, 'TRANS': 265} Chain breaks: 3 Chain: "a" Number of atoms: 8337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1227, 8337 Classifications: {'peptide': 1227} Incomplete info: {'truncation_to_alanine': 398} Link IDs: {'PTRANS': 55, 'TRANS': 1171} Chain breaks: 24 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1465 Unresolved non-hydrogen angles: 1877 Unresolved non-hydrogen dihedrals: 1216 Unresolved non-hydrogen chiralities: 142 Planarities with less than four sites: {'GLN:plan1': 23, 'HIS:plan': 15, 'TYR:plan': 9, 'ASN:plan1': 21, 'TRP:plan': 9, 'ASP:plan': 22, 'PHE:plan': 14, 'GLU:plan': 34, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 785 Chain: "b" Number of atoms: 7926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1047, 7926 Classifications: {'peptide': 1047} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 52, 'TRANS': 994} Chain breaks: 9 Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 381 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 16, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 209 Chain: "d" Number of atoms: 6410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 820, 6410 Classifications: {'peptide': 820} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 41, 'TRANS': 778} Chain breaks: 4 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "e" Number of atoms: 4671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 649, 4671 Classifications: {'peptide': 649} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 44, 'TRANS': 604} Chain breaks: 7 Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 391 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 5, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 185 Chain: "f" Number of atoms: 4075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4075 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 45, 'TRANS': 490} Chain breaks: 5 Unresolved non-hydrogen bonds: 184 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 99 Chain: "g" Number of atoms: 6710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 886, 6710 Classifications: {'peptide': 886} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 29, 'TRANS': 856} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 259 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 128 Chain: "h" Number of atoms: 6749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 887, 6749 Classifications: {'peptide': 887} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PTRANS': 32, 'TRANS': 854} Chain breaks: 10 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 393 Unresolved non-hydrogen angles: 481 Unresolved non-hydrogen dihedrals: 319 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 8, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 23, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 231 Chain: "i" Number of atoms: 4249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4249 Classifications: {'peptide': 550} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 45, 'TRANS': 504} Chain breaks: 2 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 56 Chain: "k" Number of atoms: 3336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3336 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 21, 'TRANS': 436} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 380 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 4, 'PHE:plan': 4, 'GLU:plan': 15, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 200 Chain: "p" Number of atoms: 4388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4388 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 26, 'TRANS': 548} Chain breaks: 1 Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 12, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 71 Chain: "q" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2322 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 278} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "u" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 144 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'UNK:plan-1': 26} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 768 SG CYS A 111 157.396 71.049 189.608 1.00150.16 S ATOM 796 SG CYS A 114 160.223 68.680 188.321 1.00148.77 S ATOM 1109 SG CYS A 154 156.394 67.637 188.955 1.00166.49 S ATOM 1123 SG CYS A 184 159.050 68.097 191.611 1.00166.17 S ATOM 464 SG CYS A 71 153.539 108.627 161.562 1.00 96.35 S ATOM 486 SG CYS A 74 152.235 106.246 158.725 1.00 95.56 S ATOM 533 SG CYS A 81 149.669 108.046 161.042 1.00 85.79 S ATOM 19482 SG CYS B1119 153.599 90.534 157.178 1.00 88.52 S ATOM 19504 SG CYS B1122 152.645 90.723 160.905 1.00 91.36 S ATOM 19619 SG CYS B1137 155.080 93.212 159.368 1.00102.94 S ATOM 19640 SG CYS B1140 155.924 89.509 160.172 1.00107.79 S ATOM 20607 SG CYS C 88 101.954 148.748 138.600 1.00 47.42 S ATOM 20620 SG CYS C 90 104.728 149.409 140.703 1.00 52.75 S ATOM 20655 SG CYS C 94 101.968 151.882 140.629 1.00 43.54 S ATOM 20677 SG CYS C 97 101.476 148.570 142.545 1.00 41.18 S ATOM 27903 SG CYS I 17 115.866 81.337 241.344 1.00 95.78 S ATOM 27927 SG CYS I 20 118.485 83.274 239.143 1.00100.29 S ATOM 28088 SG CYS I 39 117.623 79.764 238.156 1.00108.49 S ATOM 28113 SG CYS I 42 119.381 80.694 241.511 1.00107.13 S ATOM 28465 SG CYS I 86 76.033 93.676 226.354 1.00 74.93 S ATOM 28489 SG CYS I 89 74.657 96.632 228.329 1.00 77.85 S ATOM 28687 SG CYS I 114 76.791 97.231 225.240 1.00 67.43 S ATOM 28722 SG CYS I 119 78.378 96.066 228.366 1.00 77.26 S ATOM 28833 SG CYS J 7 85.282 134.067 164.849 1.00 27.00 S ATOM 28857 SG CYS J 10 83.127 134.981 161.721 1.00 29.17 S ATOM 29121 SG CYS J 44 81.972 132.300 164.353 1.00 31.89 S ATOM 29127 SG CYS J 45 81.896 136.038 164.763 1.00 32.18 S ATOM 30289 SG CYS L 19 120.745 151.875 183.363 1.00 58.62 S ATOM 30308 SG CYS L 22 119.814 155.467 183.740 1.00 64.99 S ATOM 30425 SG CYS L 36 123.508 154.528 183.285 1.00 71.51 S ATOM 30451 SG CYS L 39 121.717 153.892 186.502 1.00 71.03 S Time building chain proxies: 39.82, per 1000 atoms: 0.39 Number of scatterers: 101147 At special positions: 0 Unit cell: (210, 253.05, 255.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 10 29.99 Mn 2 24.99 S 584 16.00 P 74 15.00 Mg 1 11.99 O 18975 8.00 N 17659 7.00 C 63842 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS g 638 " - pdb=" SG CYS g 778 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 31.82 Conformation dependent library (CDL) restraints added in 13.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2003 " - pdb=" SG CYS A 71 " pdb=" ZN B2000 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1122 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1140 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1137 " pdb="ZN ZN B2000 " - pdb=" SG CYS B1119 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 97 " pdb=" ZN I 200 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 42 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 200 " - pdb=" SG CYS I 39 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 86 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb=" ZN k1001 " pdb="ZN ZN k1001 " - pdb=" NE2 HIS k 414 " pdb="ZN ZN k1001 " - pdb=" NE2 HIS k 73 " pdb=" ZN k1002 " pdb="ZN ZN k1002 " - pdb=" NE2 HIS k 68 " pdb="ZN ZN k1002 " - pdb=" ND1 HIS k 70 " pdb="ZN ZN k1002 " - pdb=" NE2 HIS k 157 " Number of angles added : 45 25772 Ramachandran restraints generated. 12886 Oldfield, 0 Emsley, 12886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 24532 Finding SS restraints... Secondary structure from input PDB file: 649 helices and 78 sheets defined 59.5% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.90 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 137 through 149 Processing helix chain 'A' and resid 217 through 227 removed outlier: 3.836A pdb=" N ARG A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 236 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 274 through 296 Processing helix chain 'A' and resid 301 through 319 Processing helix chain 'A' and resid 349 through 354 Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.508A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 521 through 525 Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 556 through 564 Processing helix chain 'A' and resid 565 through 567 No H-bonds generated for 'chain 'A' and resid 565 through 567' Processing helix chain 'A' and resid 588 through 596 Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 661 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.626A pdb=" N THR A 665 " --> pdb=" O GLY A 661 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 695 through 722 Processing helix chain 'A' and resid 732 through 759 removed outlier: 3.501A pdb=" N SER A 759 " --> pdb=" O SER A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 772 Processing helix chain 'A' and resid 777 through 786 Processing helix chain 'A' and resid 832 through 868 removed outlier: 4.504A pdb=" N TYR A 859 " --> pdb=" O ALA A 855 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET A 868 " --> pdb=" O LEU A 864 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 Processing helix chain 'A' and resid 926 through 934 Processing helix chain 'A' and resid 935 through 945 Processing helix chain 'A' and resid 945 through 970 Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1020 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1078 Processing helix chain 'A' and resid 1086 through 1097 Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1144 through 1149 removed outlier: 3.559A pdb=" N SER A1147 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1162 Processing helix chain 'A' and resid 1165 through 1168 Processing helix chain 'A' and resid 1189 through 1195 removed outlier: 3.616A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1224 removed outlier: 3.691A pdb=" N ARG A1224 " --> pdb=" O HIS A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1281 through 1295 Processing helix chain 'A' and resid 1342 through 1348 removed outlier: 3.502A pdb=" N VAL A1346 " --> pdb=" O SER A1342 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER A1348 " --> pdb=" O MET A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1370 removed outlier: 3.505A pdb=" N ILE A1365 " --> pdb=" O ASP A1361 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1388 Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 3.847A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1433 removed outlier: 3.680A pdb=" N PHE A1432 " --> pdb=" O MET A1428 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A1433 " --> pdb=" O LYS A1429 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1446 Processing helix chain 'A' and resid 1453 through 1460 removed outlier: 3.719A pdb=" N ASN A1457 " --> pdb=" O GLY A1453 " (cutoff:3.500A) Processing helix chain 'A' and resid 1466 through 1469 Processing helix chain 'A' and resid 1478 through 1483 removed outlier: 3.753A pdb=" N TYR A1482 " --> pdb=" O LYS A1479 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A1483 " --> pdb=" O CYS A1480 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 281 through 289 Processing helix chain 'B' and resid 294 through 308 removed outlier: 4.084A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 357 through 378 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 424 removed outlier: 3.580A pdb=" N ASP B 424 " --> pdb=" O GLN B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 436 through 451 removed outlier: 4.244A pdb=" N ILE B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 495 through 500 removed outlier: 4.290A pdb=" N ARG B 499 " --> pdb=" O LEU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 538 through 548 Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 557 through 561 removed outlier: 3.528A pdb=" N ILE B 561 " --> pdb=" O PRO B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 593 Processing helix chain 'B' and resid 636 through 645 removed outlier: 3.566A pdb=" N ILE B 640 " --> pdb=" O LYS B 636 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B 645 " --> pdb=" O ASP B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 667 through 671 Processing helix chain 'B' and resid 678 through 682 Processing helix chain 'B' and resid 699 through 704 removed outlier: 3.657A pdb=" N ILE B 703 " --> pdb=" O PRO B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 711 Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 761 through 766 removed outlier: 3.570A pdb=" N GLU B 765 " --> pdb=" O ARG B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 844 through 848 removed outlier: 3.654A pdb=" N LYS B 847 " --> pdb=" O ILE B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 972 Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.880A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 Processing helix chain 'B' and resid 1054 through 1058 Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1152 through 1165 Processing helix chain 'C' and resid 27 through 41 Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 129 through 133 Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 removed outlier: 3.518A pdb=" N GLU C 202 " --> pdb=" O LYS C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 271 Processing helix chain 'D' and resid 33 through 51 Processing helix chain 'D' and resid 59 through 71 Processing helix chain 'D' and resid 76 through 88 removed outlier: 3.643A pdb=" N ILE D 80 " --> pdb=" O ASN D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 removed outlier: 4.165A pdb=" N CYS D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 removed outlier: 4.223A pdb=" N ILE D 115 " --> pdb=" O SER D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'E' and resid 3 through 24 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 83 through 96 removed outlier: 3.508A pdb=" N ILE E 87 " --> pdb=" O GLY E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 121 Processing helix chain 'E' and resid 133 through 136 Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 163 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 99 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 4.040A pdb=" N GLU G 35 " --> pdb=" O PHE G 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 88 Processing helix chain 'I' and resid 63 through 68 removed outlier: 3.621A pdb=" N GLN I 67 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.741A pdb=" N VAL I 72 " --> pdb=" O ILE I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 105 removed outlier: 3.989A pdb=" N GLU I 105 " --> pdb=" O ALA I 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.754A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.871A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 52 removed outlier: 4.122A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 114 Processing helix chain 'U' and resid 8 through 18 Processing helix chain 'U' and resid 28 through 33 Processing helix chain 'U' and resid 34 through 42 Processing helix chain 'U' and resid 49 through 60 Processing helix chain 'U' and resid 64 through 71 removed outlier: 3.695A pdb=" N MET U 71 " --> pdb=" O THR U 67 " (cutoff:3.500A) Processing helix chain 'U' and resid 71 through 83 removed outlier: 3.587A pdb=" N LEU U 75 " --> pdb=" O MET U 71 " (cutoff:3.500A) Processing helix chain 'U' and resid 87 through 98 Processing helix chain 'U' and resid 99 through 104 removed outlier: 4.037A pdb=" N THR U 103 " --> pdb=" O SER U 99 " (cutoff:3.500A) Processing helix chain 'U' and resid 114 through 131 removed outlier: 4.080A pdb=" N LYS U 127 " --> pdb=" O GLU U 123 " (cutoff:3.500A) Processing helix chain 'U' and resid 138 through 143 removed outlier: 3.589A pdb=" N GLN U 142 " --> pdb=" O LEU U 139 " (cutoff:3.500A) Processing helix chain 'U' and resid 145 through 153 Processing helix chain 'U' and resid 169 through 187 removed outlier: 3.891A pdb=" N THR U 173 " --> pdb=" O PRO U 169 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN U 187 " --> pdb=" O THR U 183 " (cutoff:3.500A) Processing helix chain 'V' and resid 6 through 20 Processing helix chain 'V' and resid 25 through 36 removed outlier: 3.647A pdb=" N UNK V 29 " --> pdb=" O UNK V 25 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N UNK V 30 " --> pdb=" O UNK V 26 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 53 Proline residue: V 49 - end of helix removed outlier: 3.606A pdb=" N LEU V 53 " --> pdb=" O PRO V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 57 through 72 removed outlier: 4.032A pdb=" N PHE V 61 " --> pdb=" O PRO V 57 " (cutoff:3.500A) Processing helix chain 'V' and resid 73 through 82 Processing helix chain 'V' and resid 87 through 101 Processing helix chain 'V' and resid 102 through 104 No H-bonds generated for 'chain 'V' and resid 102 through 104' Processing helix chain 'V' and resid 108 through 118 removed outlier: 3.588A pdb=" N CYS V 115 " --> pdb=" O PRO V 111 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS V 118 " --> pdb=" O MET V 114 " (cutoff:3.500A) Processing helix chain 'V' and resid 123 through 138 removed outlier: 4.645A pdb=" N LYS V 129 " --> pdb=" O GLU V 125 " (cutoff:3.500A) Processing helix chain 'V' and resid 142 through 153 Processing helix chain 'V' and resid 154 through 177 Proline residue: V 163 - end of helix Processing helix chain 'V' and resid 200 through 207 Processing helix chain 'V' and resid 211 through 229 removed outlier: 3.515A pdb=" N THR V 229 " --> pdb=" O LEU V 225 " (cutoff:3.500A) Processing helix chain 'V' and resid 235 through 248 removed outlier: 4.077A pdb=" N ALA V 239 " --> pdb=" O CYS V 235 " (cutoff:3.500A) Processing helix chain 'V' and resid 250 through 257 removed outlier: 3.706A pdb=" N ASP V 257 " --> pdb=" O ILE V 253 " (cutoff:3.500A) Processing helix chain 'V' and resid 259 through 273 Processing helix chain 'V' and resid 276 through 289 Processing helix chain 'V' and resid 297 through 307 removed outlier: 3.564A pdb=" N ASP V 307 " --> pdb=" O MET V 303 " (cutoff:3.500A) Processing helix chain 'V' and resid 307 through 329 Processing helix chain 'V' and resid 339 through 350 Processing helix chain 'V' and resid 366 through 388 Proline residue: V 375 - end of helix Processing helix chain 'V' and resid 409 through 417 Processing helix chain 'V' and resid 419 through 432 removed outlier: 3.694A pdb=" N GLY V 425 " --> pdb=" O ALA V 421 " (cutoff:3.500A) Processing helix chain 'V' and resid 439 through 453 Proline residue: V 446 - end of helix Processing helix chain 'V' and resid 459 through 471 removed outlier: 3.669A pdb=" N HIS V 463 " --> pdb=" O ASP V 459 " (cutoff:3.500A) Processing helix chain 'V' and resid 479 through 488 Processing helix chain 'V' and resid 497 through 506 Processing helix chain 'W' and resid 58 through 64 Processing helix chain 'W' and resid 75 through 87 Processing helix chain 'W' and resid 92 through 105 Processing helix chain 'W' and resid 109 through 126 removed outlier: 4.454A pdb=" N HIS W 126 " --> pdb=" O LEU W 122 " (cutoff:3.500A) Processing helix chain 'W' and resid 130 through 136 Processing helix chain 'W' and resid 154 through 166 Processing helix chain 'W' and resid 169 through 182 Processing helix chain 'W' and resid 197 through 216 removed outlier: 3.992A pdb=" N GLY W 216 " --> pdb=" O ILE W 212 " (cutoff:3.500A) Processing helix chain 'W' and resid 216 through 232 Proline residue: W 225 - end of helix Processing helix chain 'W' and resid 234 through 249 Processing helix chain 'W' and resid 254 through 272 removed outlier: 3.646A pdb=" N VAL W 258 " --> pdb=" O GLY W 254 " (cutoff:3.500A) Processing helix chain 'W' and resid 276 through 283 Processing helix chain 'W' and resid 289 through 303 Processing helix chain 'W' and resid 306 through 318 Processing helix chain 'W' and resid 330 through 342 Processing helix chain 'W' and resid 349 through 364 removed outlier: 4.188A pdb=" N HIS W 354 " --> pdb=" O GLN W 350 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYS W 355 " --> pdb=" O ASP W 351 " (cutoff:3.500A) Processing helix chain 'W' and resid 380 through 400 removed outlier: 4.051A pdb=" N LYS W 384 " --> pdb=" O LYS W 380 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER W 385 " --> pdb=" O ASP W 381 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU W 400 " --> pdb=" O LEU W 396 " (cutoff:3.500A) Processing helix chain 'W' and resid 407 through 409 No H-bonds generated for 'chain 'W' and resid 407 through 409' Processing helix chain 'W' and resid 410 through 419 removed outlier: 3.593A pdb=" N LEU W 414 " --> pdb=" O GLU W 410 " (cutoff:3.500A) Processing helix chain 'W' and resid 420 through 436 Processing helix chain 'W' and resid 440 through 444 Processing helix chain 'W' and resid 449 through 462 removed outlier: 3.521A pdb=" N ALA W 453 " --> pdb=" O PRO W 449 " (cutoff:3.500A) Processing helix chain 'W' and resid 465 through 479 Processing helix chain 'W' and resid 485 through 506 Processing helix chain 'W' and resid 509 through 522 removed outlier: 3.662A pdb=" N GLU W 521 " --> pdb=" O ARG W 517 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS W 522 " --> pdb=" O LYS W 518 " (cutoff:3.500A) Processing helix chain 'W' and resid 526 through 539 Processing helix chain 'W' and resid 546 through 554 Processing helix chain 'W' and resid 555 through 558 Processing helix chain 'W' and resid 575 through 586 Processing helix chain 'X' and resid 4 through 24 Processing helix chain 'Z' and resid 514 through 516 No H-bonds generated for 'chain 'Z' and resid 514 through 516' Processing helix chain 'Z' and resid 630 through 633 removed outlier: 4.194A pdb=" N GLY Z 633 " --> pdb=" O VAL Z 630 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 630 through 633' Processing helix chain 'a' and resid 366 through 375 removed outlier: 3.531A pdb=" N LYS a 370 " --> pdb=" O LEU a 366 " (cutoff:3.500A) Processing helix chain 'a' and resid 381 through 398 removed outlier: 3.522A pdb=" N ASP a 386 " --> pdb=" O ARG a 382 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR a 397 " --> pdb=" O MET a 393 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N HIS a 398 " --> pdb=" O ASN a 394 " (cutoff:3.500A) Processing helix chain 'a' and resid 420 through 431 removed outlier: 3.590A pdb=" N ARG a 428 " --> pdb=" O MET a 424 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU a 429 " --> pdb=" O LEU a 425 " (cutoff:3.500A) Processing helix chain 'a' and resid 432 through 434 No H-bonds generated for 'chain 'a' and resid 432 through 434' Processing helix chain 'a' and resid 435 through 448 removed outlier: 3.995A pdb=" N THR a 441 " --> pdb=" O ASN a 437 " (cutoff:3.500A) Processing helix chain 'a' and resid 449 through 452 removed outlier: 3.822A pdb=" N SER a 452 " --> pdb=" O GLU a 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 449 through 452' Processing helix chain 'a' and resid 459 through 468 removed outlier: 3.647A pdb=" N ALA a 465 " --> pdb=" O VAL a 461 " (cutoff:3.500A) Processing helix chain 'a' and resid 472 through 487 Processing helix chain 'a' and resid 491 through 507 Processing helix chain 'a' and resid 511 through 521 Processing helix chain 'a' and resid 533 through 551 Processing helix chain 'a' and resid 554 through 567 Processing helix chain 'a' and resid 571 through 597 Processing helix chain 'a' and resid 604 through 616 Processing helix chain 'a' and resid 635 through 644 removed outlier: 3.849A pdb=" N PHE a 639 " --> pdb=" O ASP a 635 " (cutoff:3.500A) Processing helix chain 'a' and resid 650 through 662 Processing helix chain 'a' and resid 668 through 686 Processing helix chain 'a' and resid 697 through 710 Processing helix chain 'a' and resid 730 through 744 removed outlier: 3.604A pdb=" N TRP a 735 " --> pdb=" O SER a 731 " (cutoff:3.500A) Proline residue: a 739 - end of helix Processing helix chain 'a' and resid 761 through 773 removed outlier: 3.750A pdb=" N ASN a 773 " --> pdb=" O MET a 769 " (cutoff:3.500A) Processing helix chain 'a' and resid 784 through 804 Processing helix chain 'a' and resid 850 through 861 Processing helix chain 'a' and resid 950 through 965 removed outlier: 4.455A pdb=" N GLY a 960 " --> pdb=" O ASP a 956 " (cutoff:3.500A) Proline residue: a 961 - end of helix Processing helix chain 'a' and resid 968 through 978 removed outlier: 3.590A pdb=" N LEU a 972 " --> pdb=" O THR a 968 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG a 978 " --> pdb=" O TYR a 974 " (cutoff:3.500A) Processing helix chain 'a' and resid 979 through 981 No H-bonds generated for 'chain 'a' and resid 979 through 981' Processing helix chain 'a' and resid 983 through 998 removed outlier: 3.884A pdb=" N ARG a 987 " --> pdb=" O GLN a 983 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU a 996 " --> pdb=" O LYS a 992 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL a 997 " --> pdb=" O GLY a 993 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU a 998 " --> pdb=" O LEU a 994 " (cutoff:3.500A) Processing helix chain 'a' and resid 1021 through 1030 removed outlier: 3.681A pdb=" N LEU a1030 " --> pdb=" O TYR a1026 " (cutoff:3.500A) Processing helix chain 'a' and resid 1038 through 1042 removed outlier: 3.619A pdb=" N VAL a1042 " --> pdb=" O PHE a1039 " (cutoff:3.500A) Processing helix chain 'a' and resid 1043 through 1054 removed outlier: 3.854A pdb=" N ALA a1049 " --> pdb=" O THR a1045 " (cutoff:3.500A) Processing helix chain 'a' and resid 1059 through 1073 Processing helix chain 'a' and resid 1080 through 1095 Processing helix chain 'a' and resid 1097 through 1104 Processing helix chain 'a' and resid 1110 through 1132 Processing helix chain 'a' and resid 1164 through 1175 removed outlier: 3.601A pdb=" N HIS a1168 " --> pdb=" O ILE a1164 " (cutoff:3.500A) Processing helix chain 'a' and resid 1184 through 1193 removed outlier: 4.285A pdb=" N TRP a1193 " --> pdb=" O LEU a1189 " (cutoff:3.500A) Processing helix chain 'a' and resid 1218 through 1223 removed outlier: 4.544A pdb=" N ARG a1222 " --> pdb=" O TRP a1218 " (cutoff:3.500A) Processing helix chain 'a' and resid 1228 through 1237 removed outlier: 3.516A pdb=" N VAL a1232 " --> pdb=" O VAL a1228 " (cutoff:3.500A) Processing helix chain 'a' and resid 1240 through 1248 removed outlier: 3.729A pdb=" N LEU a1244 " --> pdb=" O GLU a1240 " (cutoff:3.500A) Processing helix chain 'a' and resid 1254 through 1272 Processing helix chain 'a' and resid 1272 through 1280 removed outlier: 4.490A pdb=" N LEU a1276 " --> pdb=" O ASP a1272 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE a1280 " --> pdb=" O LEU a1276 " (cutoff:3.500A) Processing helix chain 'a' and resid 1283 through 1295 Processing helix chain 'a' and resid 1301 through 1312 removed outlier: 3.623A pdb=" N SER a1306 " --> pdb=" O GLN a1302 " (cutoff:3.500A) Processing helix chain 'a' and resid 1361 through 1369 Processing helix chain 'a' and resid 1374 through 1393 Processing helix chain 'a' and resid 1402 through 1415 removed outlier: 3.810A pdb=" N SER a1415 " --> pdb=" O THR a1411 " (cutoff:3.500A) Processing helix chain 'a' and resid 1421 through 1428 Processing helix chain 'a' and resid 1428 through 1446 Proline residue: a1434 - end of helix Processing helix chain 'a' and resid 1451 through 1468 Processing helix chain 'a' and resid 1475 through 1489 Processing helix chain 'a' and resid 1490 through 1492 No H-bonds generated for 'chain 'a' and resid 1490 through 1492' Processing helix chain 'a' and resid 1496 through 1510 Processing helix chain 'a' and resid 1513 through 1531 Processing helix chain 'a' and resid 1537 through 1552 Processing helix chain 'a' and resid 1555 through 1566 removed outlier: 3.731A pdb=" N ALA a1566 " --> pdb=" O ALA a1562 " (cutoff:3.500A) Processing helix chain 'a' and resid 1579 through 1589 removed outlier: 3.660A pdb=" N GLN a1589 " --> pdb=" O SER a1585 " (cutoff:3.500A) Processing helix chain 'a' and resid 1611 through 1613 No H-bonds generated for 'chain 'a' and resid 1611 through 1613' Processing helix chain 'a' and resid 1614 through 1626 removed outlier: 3.550A pdb=" N LEU a1618 " --> pdb=" O SER a1614 " (cutoff:3.500A) Processing helix chain 'a' and resid 1633 through 1642 removed outlier: 3.725A pdb=" N GLN a1637 " --> pdb=" O CYS a1633 " (cutoff:3.500A) Processing helix chain 'a' and resid 1656 through 1668 removed outlier: 3.544A pdb=" N HIS a1666 " --> pdb=" O THR a1662 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER a1668 " --> pdb=" O PHE a1664 " (cutoff:3.500A) Processing helix chain 'a' and resid 1669 through 1682 Processing helix chain 'a' and resid 1690 through 1703 Processing helix chain 'a' and resid 1728 through 1748 Processing helix chain 'a' and resid 1755 through 1769 Proline residue: a1763 - end of helix Processing helix chain 'a' and resid 2047 through 2056 Processing helix chain 'a' and resid 2059 through 2077 removed outlier: 3.805A pdb=" N MET a2073 " --> pdb=" O ASP a2069 " (cutoff:3.500A) Processing helix chain 'a' and resid 2078 through 2083 removed outlier: 3.600A pdb=" N LEU a2081 " --> pdb=" O PRO a2078 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER a2082 " --> pdb=" O GLU a2079 " (cutoff:3.500A) Processing helix chain 'a' and resid 2084 through 2092 Processing helix chain 'a' and resid 2096 through 2114 removed outlier: 3.750A pdb=" N ARG a2100 " --> pdb=" O GLU a2096 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN a2113 " --> pdb=" O ARG a2109 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER a2114 " --> pdb=" O SER a2110 " (cutoff:3.500A) Processing helix chain 'a' and resid 2115 through 2120 removed outlier: 3.875A pdb=" N ALA a2119 " --> pdb=" O SER a2116 " (cutoff:3.500A) Processing helix chain 'a' and resid 2121 through 2130 Processing helix chain 'a' and resid 2133 through 2143 removed outlier: 3.548A pdb=" N ASN a2143 " --> pdb=" O THR a2139 " (cutoff:3.500A) Processing helix chain 'a' and resid 2143 through 2152 Processing helix chain 'a' and resid 2155 through 2169 Processing helix chain 'a' and resid 2173 through 2189 Processing helix chain 'b' and resid 19 through 28 Processing helix chain 'b' and resid 30 through 35 Processing helix chain 'b' and resid 38 through 55 Proline residue: b 47 - end of helix Processing helix chain 'b' and resid 61 through 78 removed outlier: 3.730A pdb=" N ARG b 73 " --> pdb=" O LYS b 69 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU b 74 " --> pdb=" O LEU b 70 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU b 75 " --> pdb=" O ILE b 71 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY b 77 " --> pdb=" O ARG b 73 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL b 78 " --> pdb=" O LEU b 74 " (cutoff:3.500A) Processing helix chain 'b' and resid 80 through 89 removed outlier: 3.869A pdb=" N ILE b 84 " --> pdb=" O ALA b 80 " (cutoff:3.500A) Processing helix chain 'b' and resid 91 through 107 removed outlier: 4.036A pdb=" N LEU b 95 " --> pdb=" O ASP b 91 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN b 97 " --> pdb=" O HIS b 93 " (cutoff:3.500A) Processing helix chain 'b' and resid 126 through 133 Processing helix chain 'b' and resid 134 through 156 Processing helix chain 'b' and resid 174 through 188 Processing helix chain 'b' and resid 193 through 201 Processing helix chain 'b' and resid 206 through 218 removed outlier: 3.779A pdb=" N PHE b 210 " --> pdb=" O ASN b 206 " (cutoff:3.500A) Processing helix chain 'b' and resid 221 through 231 Processing helix chain 'b' and resid 240 through 257 removed outlier: 3.540A pdb=" N ARG b 245 " --> pdb=" O LEU b 241 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG b 246 " --> pdb=" O GLY b 242 " (cutoff:3.500A) Processing helix chain 'b' and resid 260 through 272 removed outlier: 3.520A pdb=" N VAL b 264 " --> pdb=" O GLN b 260 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG b 265 " --> pdb=" O ALA b 261 " (cutoff:3.500A) Processing helix chain 'b' and resid 274 through 285 removed outlier: 3.573A pdb=" N GLY b 278 " --> pdb=" O LEU b 274 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS b 285 " --> pdb=" O LEU b 281 " (cutoff:3.500A) Processing helix chain 'b' and resid 296 through 307 removed outlier: 3.950A pdb=" N CYS b 300 " --> pdb=" O SER b 296 " (cutoff:3.500A) Processing helix chain 'b' and resid 310 through 327 removed outlier: 3.801A pdb=" N GLN b 326 " --> pdb=" O ARG b 322 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG b 327 " --> pdb=" O ASN b 323 " (cutoff:3.500A) Processing helix chain 'b' and resid 335 through 348 Processing helix chain 'b' and resid 381 through 398 Processing helix chain 'b' and resid 404 through 416 Processing helix chain 'b' and resid 422 through 439 Processing helix chain 'b' and resid 440 through 443 removed outlier: 3.956A pdb=" N VAL b 443 " --> pdb=" O SER b 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 440 through 443' Processing helix chain 'b' and resid 445 through 462 Processing helix chain 'b' and resid 476 through 489 Processing helix chain 'b' and resid 493 through 504 removed outlier: 3.583A pdb=" N ASP b 497 " --> pdb=" O SER b 493 " (cutoff:3.500A) Processing helix chain 'b' and resid 510 through 513 Processing helix chain 'b' and resid 514 through 524 removed outlier: 3.516A pdb=" N PHE b 521 " --> pdb=" O MET b 517 " (cutoff:3.500A) Processing helix chain 'b' and resid 527 through 538 removed outlier: 3.938A pdb=" N VAL b 536 " --> pdb=" O THR b 532 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG b 537 " --> pdb=" O ALA b 533 " (cutoff:3.500A) Processing helix chain 'b' and resid 552 through 563 removed outlier: 3.517A pdb=" N CYS b 556 " --> pdb=" O LEU b 552 " (cutoff:3.500A) Processing helix chain 'b' and resid 564 through 569 Processing helix chain 'b' and resid 573 through 583 removed outlier: 3.559A pdb=" N GLU b 583 " --> pdb=" O ARG b 579 " (cutoff:3.500A) Processing helix chain 'b' and resid 591 through 605 Processing helix chain 'b' and resid 616 through 621 Processing helix chain 'b' and resid 622 through 624 No H-bonds generated for 'chain 'b' and resid 622 through 624' Processing helix chain 'b' and resid 644 through 666 Processing helix chain 'b' and resid 680 through 686 removed outlier: 3.572A pdb=" N MET b 684 " --> pdb=" O SER b 680 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP b 685 " --> pdb=" O SER b 681 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN b 686 " --> pdb=" O SER b 682 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 680 through 686' Processing helix chain 'b' and resid 688 through 699 removed outlier: 3.617A pdb=" N GLY b 698 " --> pdb=" O ARG b 694 " (cutoff:3.500A) Processing helix chain 'b' and resid 705 through 718 Processing helix chain 'b' and resid 719 through 722 Processing helix chain 'b' and resid 723 through 731 removed outlier: 4.249A pdb=" N ILE b 728 " --> pdb=" O ASP b 725 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N CYS b 729 " --> pdb=" O ASP b 726 " (cutoff:3.500A) Processing helix chain 'b' and resid 735 through 745 Processing helix chain 'b' and resid 746 through 748 No H-bonds generated for 'chain 'b' and resid 746 through 748' Processing helix chain 'b' and resid 753 through 762 Processing helix chain 'b' and resid 767 through 779 removed outlier: 4.026A pdb=" N VAL b 771 " --> pdb=" O ASN b 767 " (cutoff:3.500A) Processing helix chain 'b' and resid 786 through 788 No H-bonds generated for 'chain 'b' and resid 786 through 788' Processing helix chain 'b' and resid 789 through 796 removed outlier: 3.745A pdb=" N ASN b 796 " --> pdb=" O VAL b 792 " (cutoff:3.500A) Processing helix chain 'b' and resid 798 through 802 Processing helix chain 'b' and resid 806 through 821 Processing helix chain 'b' and resid 824 through 836 removed outlier: 3.862A pdb=" N VAL b 830 " --> pdb=" O ARG b 826 " (cutoff:3.500A) Processing helix chain 'b' and resid 849 through 856 Processing helix chain 'b' and resid 857 through 862 Processing helix chain 'b' and resid 866 through 869 removed outlier: 3.524A pdb=" N ARG b 869 " --> pdb=" O ARG b 866 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 866 through 869' Processing helix chain 'b' and resid 870 through 901 removed outlier: 3.720A pdb=" N ILE b 876 " --> pdb=" O PRO b 872 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS b 889 " --> pdb=" O LEU b 885 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA b 890 " --> pdb=" O LEU b 886 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN b 901 " --> pdb=" O LYS b 897 " (cutoff:3.500A) Processing helix chain 'b' and resid 923 through 946 Processing helix chain 'b' and resid 949 through 954 Processing helix chain 'b' and resid 988 through 1008 removed outlier: 3.734A pdb=" N GLU b 992 " --> pdb=" O CYS b 988 " (cutoff:3.500A) Processing helix chain 'b' and resid 1008 through 1019 removed outlier: 3.763A pdb=" N ALA b1012 " --> pdb=" O ASP b1008 " (cutoff:3.500A) Processing helix chain 'b' and resid 1021 through 1023 No H-bonds generated for 'chain 'b' and resid 1021 through 1023' Processing helix chain 'b' and resid 1024 through 1032 Processing helix chain 'b' and resid 1033 through 1036 removed outlier: 4.115A pdb=" N HIS b1036 " --> pdb=" O PRO b1033 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 1033 through 1036' Processing helix chain 'b' and resid 1037 through 1046 removed outlier: 4.291A pdb=" N PHE b1041 " --> pdb=" O ILE b1037 " (cutoff:3.500A) Proline residue: b1043 - end of helix Processing helix chain 'b' and resid 1050 through 1068 removed outlier: 3.527A pdb=" N GLN b1054 " --> pdb=" O GLU b1050 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS b1063 " --> pdb=" O GLN b1059 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE b1066 " --> pdb=" O SER b1062 " (cutoff:3.500A) Processing helix chain 'b' and resid 1070 through 1091 removed outlier: 3.796A pdb=" N THR b1089 " --> pdb=" O GLY b1085 " (cutoff:3.500A) Processing helix chain 'b' and resid 1092 through 1104 Proline residue: b1102 - end of helix Processing helix chain 'b' and resid 1104 through 1114 removed outlier: 4.175A pdb=" N VAL b1108 " --> pdb=" O LEU b1104 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER b1109 " --> pdb=" O PRO b1105 " (cutoff:3.500A) Processing helix chain 'b' and resid 1117 through 1139 removed outlier: 3.519A pdb=" N SER b1134 " --> pdb=" O GLN b1130 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP b1135 " --> pdb=" O VAL b1131 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN b1139 " --> pdb=" O ASP b1135 " (cutoff:3.500A) Processing helix chain 'b' and resid 1146 through 1150 removed outlier: 4.225A pdb=" N LEU b1150 " --> pdb=" O ILE b1147 " (cutoff:3.500A) Processing helix chain 'b' and resid 1180 through 1202 Processing helix chain 'd' and resid 36 through 46 removed outlier: 3.554A pdb=" N ALA d 46 " --> pdb=" O ASP d 42 " (cutoff:3.500A) Processing helix chain 'd' and resid 50 through 60 Processing helix chain 'd' and resid 65 through 83 removed outlier: 4.098A pdb=" N TYR d 81 " --> pdb=" O LEU d 77 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS d 82 " --> pdb=" O GLU d 78 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU d 83 " --> pdb=" O HIS d 79 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 100 Processing helix chain 'd' and resid 106 through 109 removed outlier: 4.385A pdb=" N CYS d 109 " --> pdb=" O SER d 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 106 through 109' Processing helix chain 'd' and resid 110 through 120 removed outlier: 3.809A pdb=" N ASN d 120 " --> pdb=" O ASN d 116 " (cutoff:3.500A) Processing helix chain 'd' and resid 123 through 141 Processing helix chain 'd' and resid 144 through 159 Processing helix chain 'd' and resid 163 through 177 Processing helix chain 'd' and resid 196 through 203 Processing helix chain 'd' and resid 204 through 206 No H-bonds generated for 'chain 'd' and resid 204 through 206' Processing helix chain 'd' and resid 208 through 226 Processing helix chain 'd' and resid 231 through 241 removed outlier: 3.984A pdb=" N ASN d 235 " --> pdb=" O GLN d 231 " (cutoff:3.500A) Processing helix chain 'd' and resid 245 through 263 Processing helix chain 'd' and resid 279 through 292 removed outlier: 3.925A pdb=" N SER d 292 " --> pdb=" O CYS d 288 " (cutoff:3.500A) Processing helix chain 'd' and resid 295 through 308 removed outlier: 3.792A pdb=" N SER d 308 " --> pdb=" O LYS d 304 " (cutoff:3.500A) Processing helix chain 'd' and resid 313 through 320 Processing helix chain 'd' and resid 377 through 384 removed outlier: 3.697A pdb=" N GLU d 384 " --> pdb=" O VAL d 380 " (cutoff:3.500A) Processing helix chain 'd' and resid 387 through 405 Processing helix chain 'd' and resid 405 through 420 removed outlier: 3.858A pdb=" N ALA d 409 " --> pdb=" O SER d 405 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU d 410 " --> pdb=" O PRO d 406 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS d 411 " --> pdb=" O SER d 407 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP d 414 " --> pdb=" O GLU d 410 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE d 415 " --> pdb=" O LYS d 411 " (cutoff:3.500A) Processing helix chain 'd' and resid 424 through 438 Processing helix chain 'd' and resid 445 through 456 Processing helix chain 'd' and resid 460 through 473 Processing helix chain 'd' and resid 478 through 496 removed outlier: 3.778A pdb=" N ILE d 482 " --> pdb=" O THR d 478 " (cutoff:3.500A) Processing helix chain 'd' and resid 499 through 514 Processing helix chain 'd' and resid 514 through 519 removed outlier: 3.526A pdb=" N VAL d 518 " --> pdb=" O HIS d 514 " (cutoff:3.500A) Processing helix chain 'd' and resid 521 through 526 Processing helix chain 'd' and resid 541 through 558 removed outlier: 4.241A pdb=" N THR d 557 " --> pdb=" O ASN d 553 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS d 558 " --> pdb=" O ALA d 554 " (cutoff:3.500A) Processing helix chain 'd' and resid 566 through 580 Processing helix chain 'd' and resid 609 through 624 Processing helix chain 'd' and resid 628 through 648 Processing helix chain 'd' and resid 653 through 675 Processing helix chain 'd' and resid 676 through 681 removed outlier: 3.771A pdb=" N TRP d 679 " --> pdb=" O GLU d 676 " (cutoff:3.500A) Processing helix chain 'd' and resid 687 through 691 removed outlier: 4.056A pdb=" N SER d 690 " --> pdb=" O LEU d 687 " (cutoff:3.500A) Processing helix chain 'd' and resid 692 through 710 removed outlier: 3.536A pdb=" N LYS d 698 " --> pdb=" O SER d 694 " (cutoff:3.500A) Processing helix chain 'd' and resid 715 through 740 removed outlier: 4.862A pdb=" N ILE d 721 " --> pdb=" O LYS d 717 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR d 740 " --> pdb=" O VAL d 736 " (cutoff:3.500A) Processing helix chain 'd' and resid 744 through 765 Processing helix chain 'd' and resid 768 through 772 Processing helix chain 'd' and resid 775 through 783 removed outlier: 3.502A pdb=" N LYS d 779 " --> pdb=" O SER d 775 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU d 783 " --> pdb=" O LYS d 779 " (cutoff:3.500A) Processing helix chain 'd' and resid 783 through 790 removed outlier: 3.619A pdb=" N THR d 789 " --> pdb=" O PRO d 785 " (cutoff:3.500A) Processing helix chain 'd' and resid 791 through 804 removed outlier: 3.920A pdb=" N ARG d 804 " --> pdb=" O GLN d 800 " (cutoff:3.500A) Processing helix chain 'd' and resid 856 through 860 Processing helix chain 'd' and resid 878 through 880 No H-bonds generated for 'chain 'd' and resid 878 through 880' Processing helix chain 'e' and resid 291 through 303 removed outlier: 3.638A pdb=" N LEU e 301 " --> pdb=" O ILE e 297 " (cutoff:3.500A) Processing helix chain 'e' and resid 308 through 318 Processing helix chain 'e' and resid 339 through 345 removed outlier: 3.515A pdb=" N LEU e 344 " --> pdb=" O PHE e 340 " (cutoff:3.500A) Processing helix chain 'e' and resid 349 through 362 removed outlier: 4.376A pdb=" N SER e 356 " --> pdb=" O LEU e 352 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLY e 357 " --> pdb=" O GLY e 353 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU e 359 " --> pdb=" O VAL e 355 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL e 360 " --> pdb=" O SER e 356 " (cutoff:3.500A) Processing helix chain 'e' and resid 367 through 376 Processing helix chain 'e' and resid 380 through 399 removed outlier: 4.019A pdb=" N SER e 399 " --> pdb=" O VAL e 395 " (cutoff:3.500A) Processing helix chain 'e' and resid 402 through 413 Processing helix chain 'e' and resid 429 through 451 removed outlier: 3.892A pdb=" N HIS e 451 " --> pdb=" O GLN e 447 " (cutoff:3.500A) Processing helix chain 'e' and resid 471 through 476 Processing helix chain 'e' and resid 477 through 479 No H-bonds generated for 'chain 'e' and resid 477 through 479' Processing helix chain 'e' and resid 480 through 489 Processing helix chain 'e' and resid 494 through 510 removed outlier: 3.859A pdb=" N TRP e 498 " --> pdb=" O LYS e 494 " (cutoff:3.500A) Processing helix chain 'e' and resid 514 through 526 Processing helix chain 'e' and resid 528 through 543 removed outlier: 3.735A pdb=" N LEU e 534 " --> pdb=" O GLU e 530 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA e 535 " --> pdb=" O GLU e 531 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR e 536 " --> pdb=" O LEU e 532 " (cutoff:3.500A) Processing helix chain 'e' and resid 548 through 563 removed outlier: 3.928A pdb=" N LEU e 552 " --> pdb=" O GLY e 548 " (cutoff:3.500A) Processing helix chain 'e' and resid 567 through 587 Processing helix chain 'e' and resid 589 through 596 removed outlier: 3.625A pdb=" N ALA e 593 " --> pdb=" O GLY e 589 " (cutoff:3.500A) Processing helix chain 'e' and resid 598 through 605 removed outlier: 3.627A pdb=" N ALA e 605 " --> pdb=" O GLU e 601 " (cutoff:3.500A) Processing helix chain 'e' and resid 606 through 611 Processing helix chain 'e' and resid 612 through 616 Processing helix chain 'e' and resid 618 through 632 removed outlier: 3.969A pdb=" N ILE e 631 " --> pdb=" O SER e 627 " (cutoff:3.500A) Processing helix chain 'e' and resid 640 through 662 Processing helix chain 'e' and resid 663 through 666 Processing helix chain 'e' and resid 667 through 679 Processing helix chain 'e' and resid 681 through 697 Processing helix chain 'e' and resid 702 through 706 removed outlier: 3.553A pdb=" N GLY e 706 " --> pdb=" O GLU e 703 " (cutoff:3.500A) Processing helix chain 'e' and resid 727 through 735 Processing helix chain 'e' and resid 768 through 788 Processing helix chain 'e' and resid 805 through 821 Processing helix chain 'e' and resid 833 through 837 Processing helix chain 'e' and resid 840 through 854 Processing helix chain 'e' and resid 855 through 866 removed outlier: 3.729A pdb=" N GLU e 859 " --> pdb=" O PRO e 855 " (cutoff:3.500A) Processing helix chain 'e' and resid 867 through 873 removed outlier: 3.758A pdb=" N LEU e 871 " --> pdb=" O PRO e 868 " (cutoff:3.500A) Processing helix chain 'e' and resid 874 through 892 Processing helix chain 'e' and resid 900 through 917 Processing helix chain 'e' and resid 923 through 934 removed outlier: 3.555A pdb=" N ASN e 926 " --> pdb=" O ALA e 923 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET e 927 " --> pdb=" O LEU e 924 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N HIS e 928 " --> pdb=" O GLY e 925 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE e 931 " --> pdb=" O HIS e 928 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER e 932 " --> pdb=" O GLU e 929 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU e 934 " --> pdb=" O PHE e 931 " (cutoff:3.500A) Processing helix chain 'e' and resid 935 through 953 Processing helix chain 'e' and resid 956 through 958 No H-bonds generated for 'chain 'e' and resid 956 through 958' Processing helix chain 'e' and resid 983 through 995 removed outlier: 4.287A pdb=" N VAL e 987 " --> pdb=" O PRO e 983 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU e 988 " --> pdb=" O HIS e 984 " (cutoff:3.500A) Processing helix chain 'e' and resid 995 through 1000 Processing helix chain 'e' and resid 1001 through 1007 removed outlier: 4.311A pdb=" N GLY e1004 " --> pdb=" O LEU e1001 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE e1006 " --> pdb=" O SER e1003 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN e1007 " --> pdb=" O GLY e1004 " (cutoff:3.500A) Processing helix chain 'f' and resid 11 through 15 Processing helix chain 'f' and resid 23 through 42 removed outlier: 3.765A pdb=" N ASP f 42 " --> pdb=" O LEU f 38 " (cutoff:3.500A) Processing helix chain 'f' and resid 69 through 79 removed outlier: 3.698A pdb=" N ASN f 79 " --> pdb=" O ASN f 75 " (cutoff:3.500A) Processing helix chain 'f' and resid 87 through 101 Processing helix chain 'f' and resid 102 through 107 Processing helix chain 'f' and resid 154 through 158 removed outlier: 3.653A pdb=" N THR f 158 " --> pdb=" O SER f 155 " (cutoff:3.500A) Processing helix chain 'f' and resid 183 through 187 removed outlier: 4.165A pdb=" N LEU f 186 " --> pdb=" O SER f 183 " (cutoff:3.500A) Processing helix chain 'f' and resid 195 through 203 removed outlier: 4.296A pdb=" N MET f 199 " --> pdb=" O ALA f 195 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR f 203 " --> pdb=" O MET f 199 " (cutoff:3.500A) Processing helix chain 'f' and resid 212 through 226 Processing helix chain 'f' and resid 259 through 261 No H-bonds generated for 'chain 'f' and resid 259 through 261' Processing helix chain 'f' and resid 332 through 341 Processing helix chain 'f' and resid 385 through 400 Proline residue: f 391 - end of helix Processing helix chain 'f' and resid 405 through 417 removed outlier: 3.645A pdb=" N SER f 411 " --> pdb=" O LYS f 407 " (cutoff:3.500A) Processing helix chain 'f' and resid 420 through 422 No H-bonds generated for 'chain 'f' and resid 420 through 422' Processing helix chain 'f' and resid 423 through 435 Processing helix chain 'f' and resid 439 through 443 Processing helix chain 'f' and resid 449 through 473 removed outlier: 3.655A pdb=" N GLY f 472 " --> pdb=" O ASP f 468 " (cutoff:3.500A) Processing helix chain 'f' and resid 543 through 547 removed outlier: 3.569A pdb=" N ASP f 546 " --> pdb=" O ASN f 543 " (cutoff:3.500A) Processing helix chain 'f' and resid 548 through 550 No H-bonds generated for 'chain 'f' and resid 548 through 550' Processing helix chain 'f' and resid 551 through 564 Processing helix chain 'f' and resid 589 through 597 removed outlier: 3.738A pdb=" N LEU f 594 " --> pdb=" O TYR f 590 " (cutoff:3.500A) Processing helix chain 'g' and resid 22 through 31 Processing helix chain 'g' and resid 32 through 35 Processing helix chain 'g' and resid 37 through 47 Processing helix chain 'g' and resid 47 through 55 Processing helix chain 'g' and resid 57 through 75 removed outlier: 3.702A pdb=" N SER g 63 " --> pdb=" O ILE g 59 " (cutoff:3.500A) Processing helix chain 'g' and resid 76 through 90 Processing helix chain 'g' and resid 99 through 109 removed outlier: 3.529A pdb=" N PHE g 103 " --> pdb=" O ASN g 99 " (cutoff:3.500A) Processing helix chain 'g' and resid 110 through 112 No H-bonds generated for 'chain 'g' and resid 110 through 112' Processing helix chain 'g' and resid 115 through 129 Processing helix chain 'g' and resid 136 through 147 Processing helix chain 'g' and resid 151 through 169 removed outlier: 3.573A pdb=" N ALA g 167 " --> pdb=" O ALA g 163 " (cutoff:3.500A) Processing helix chain 'g' and resid 169 through 185 removed outlier: 4.156A pdb=" N GLY g 175 " --> pdb=" O ASP g 171 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN g 178 " --> pdb=" O VAL g 174 " (cutoff:3.500A) Processing helix chain 'g' and resid 190 through 198 Processing helix chain 'g' and resid 199 through 204 Processing helix chain 'g' and resid 207 through 225 removed outlier: 3.712A pdb=" N THR g 223 " --> pdb=" O GLN g 219 " (cutoff:3.500A) Processing helix chain 'g' and resid 227 through 245 Processing helix chain 'g' and resid 248 through 263 Processing helix chain 'g' and resid 265 through 283 Processing helix chain 'g' and resid 284 through 287 Processing helix chain 'g' and resid 288 through 301 Processing helix chain 'g' and resid 304 through 320 removed outlier: 3.774A pdb=" N GLY g 310 " --> pdb=" O SER g 306 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY g 320 " --> pdb=" O SER g 316 " (cutoff:3.500A) Processing helix chain 'g' and resid 322 through 328 Processing helix chain 'g' and resid 342 through 353 removed outlier: 3.748A pdb=" N TYR g 353 " --> pdb=" O GLN g 349 " (cutoff:3.500A) Processing helix chain 'g' and resid 356 through 374 removed outlier: 3.789A pdb=" N CYS g 374 " --> pdb=" O ILE g 370 " (cutoff:3.500A) Processing helix chain 'g' and resid 378 through 398 removed outlier: 4.273A pdb=" N LEU g 382 " --> pdb=" O ASP g 378 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLN g 384 " --> pdb=" O LEU g 380 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP g 385 " --> pdb=" O ALA g 381 " (cutoff:3.500A) Processing helix chain 'g' and resid 402 through 423 removed outlier: 3.858A pdb=" N ALA g 407 " --> pdb=" O PRO g 403 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR g 408 " --> pdb=" O GLY g 404 " (cutoff:3.500A) Processing helix chain 'g' and resid 426 through 439 removed outlier: 3.679A pdb=" N VAL g 430 " --> pdb=" O LEU g 426 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS g 439 " --> pdb=" O LEU g 435 " (cutoff:3.500A) Processing helix chain 'g' and resid 442 through 458 removed outlier: 3.554A pdb=" N ILE g 447 " --> pdb=" O ASP g 443 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LEU g 448 " --> pdb=" O ALA g 444 " (cutoff:3.500A) Processing helix chain 'g' and resid 460 through 466 removed outlier: 3.543A pdb=" N LEU g 463 " --> pdb=" O LEU g 460 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ASP g 465 " --> pdb=" O VAL g 462 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY g 466 " --> pdb=" O LEU g 463 " (cutoff:3.500A) Processing helix chain 'g' and resid 467 through 477 Processing helix chain 'g' and resid 485 through 501 Processing helix chain 'g' and resid 507 through 520 Processing helix chain 'g' and resid 522 through 537 removed outlier: 3.780A pdb=" N VAL g 526 " --> pdb=" O ASN g 522 " (cutoff:3.500A) Processing helix chain 'g' and resid 538 through 548 Processing helix chain 'g' and resid 555 through 575 Processing helix chain 'g' and resid 576 through 578 No H-bonds generated for 'chain 'g' and resid 576 through 578' Processing helix chain 'g' and resid 582 through 605 Processing helix chain 'g' and resid 606 through 608 No H-bonds generated for 'chain 'g' and resid 606 through 608' Processing helix chain 'g' and resid 614 through 643 removed outlier: 4.115A pdb=" N LYS g 642 " --> pdb=" O CYS g 638 " (cutoff:3.500A) Processing helix chain 'g' and resid 666 through 693 removed outlier: 4.153A pdb=" N PHE g 693 " --> pdb=" O TYR g 689 " (cutoff:3.500A) Processing helix chain 'g' and resid 696 through 721 removed outlier: 3.727A pdb=" N LEU g 720 " --> pdb=" O ALA g 716 " (cutoff:3.500A) Processing helix chain 'g' and resid 742 through 762 Processing helix chain 'g' and resid 770 through 787 removed outlier: 3.780A pdb=" N ILE g 782 " --> pdb=" O CYS g 778 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL g 787 " --> pdb=" O ALA g 783 " (cutoff:3.500A) Processing helix chain 'g' and resid 792 through 797 removed outlier: 3.747A pdb=" N PHE g 796 " --> pdb=" O GLN g 792 " (cutoff:3.500A) Processing helix chain 'g' and resid 933 through 945 Processing helix chain 'h' and resid 23 through 30 removed outlier: 3.577A pdb=" N PHE h 27 " --> pdb=" O CYS h 23 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU h 28 " --> pdb=" O TRP h 24 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU h 29 " --> pdb=" O PHE h 25 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU h 30 " --> pdb=" O GLU h 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 23 through 30' Processing helix chain 'h' and resid 32 through 37 removed outlier: 3.614A pdb=" N LYS h 36 " --> pdb=" O SER h 32 " (cutoff:3.500A) Processing helix chain 'h' and resid 48 through 59 Processing helix chain 'h' and resid 76 through 92 Processing helix chain 'h' and resid 95 through 103 Processing helix chain 'h' and resid 104 through 120 Processing helix chain 'h' and resid 136 through 157 Processing helix chain 'h' and resid 177 through 194 Processing helix chain 'h' and resid 194 through 208 Processing helix chain 'h' and resid 244 through 264 removed outlier: 3.531A pdb=" N MET h 248 " --> pdb=" O LYS h 244 " (cutoff:3.500A) Processing helix chain 'h' and resid 265 through 266 No H-bonds generated for 'chain 'h' and resid 265 through 266' Processing helix chain 'h' and resid 267 through 268 No H-bonds generated for 'chain 'h' and resid 267 through 268' Processing helix chain 'h' and resid 269 through 289 removed outlier: 4.241A pdb=" N ASN h 273 " --> pdb=" O ALA h 269 " (cutoff:3.500A) Processing helix chain 'h' and resid 298 through 313 removed outlier: 3.564A pdb=" N VAL h 311 " --> pdb=" O GLN h 307 " (cutoff:3.500A) Processing helix chain 'h' and resid 324 through 336 Processing helix chain 'h' and resid 337 through 352 removed outlier: 3.798A pdb=" N LEU h 350 " --> pdb=" O ILE h 346 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR h 351 " --> pdb=" O GLU h 347 " (cutoff:3.500A) Processing helix chain 'h' and resid 355 through 373 removed outlier: 3.677A pdb=" N GLN h 372 " --> pdb=" O LYS h 368 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY h 373 " --> pdb=" O LYS h 369 " (cutoff:3.500A) Processing helix chain 'h' and resid 376 through 395 removed outlier: 4.056A pdb=" N ILE h 380 " --> pdb=" O ALA h 376 " (cutoff:3.500A) Processing helix chain 'h' and resid 400 through 407 removed outlier: 3.553A pdb=" N ASN h 404 " --> pdb=" O SER h 400 " (cutoff:3.500A) Processing helix chain 'h' and resid 411 through 425 Processing helix chain 'h' and resid 431 through 449 removed outlier: 3.786A pdb=" N LEU h 435 " --> pdb=" O ALA h 431 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS h 436 " --> pdb=" O SER h 432 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY h 449 " --> pdb=" O ASN h 445 " (cutoff:3.500A) Processing helix chain 'h' and resid 452 through 461 removed outlier: 3.574A pdb=" N VAL h 456 " --> pdb=" O ASP h 452 " (cutoff:3.500A) Processing helix chain 'h' and resid 462 through 469 removed outlier: 3.728A pdb=" N LEU h 469 " --> pdb=" O PHE h 465 " (cutoff:3.500A) Processing helix chain 'h' and resid 472 through 483 removed outlier: 3.916A pdb=" N LEU h 476 " --> pdb=" O GLU h 472 " (cutoff:3.500A) Processing helix chain 'h' and resid 504 through 519 Processing helix chain 'h' and resid 521 through 536 Processing helix chain 'h' and resid 551 through 559 removed outlier: 4.348A pdb=" N GLY h 556 " --> pdb=" O SER h 552 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N VAL h 557 " --> pdb=" O VAL h 553 " (cutoff:3.500A) Processing helix chain 'h' and resid 563 through 583 Processing helix chain 'h' and resid 585 through 601 Processing helix chain 'h' and resid 604 through 626 Processing helix chain 'h' and resid 637 through 647 Processing helix chain 'h' and resid 656 through 670 removed outlier: 3.876A pdb=" N ALA h 660 " --> pdb=" O ARG h 656 " (cutoff:3.500A) Processing helix chain 'h' and resid 672 through 678 Processing helix chain 'h' and resid 681 through 688 removed outlier: 3.961A pdb=" N LEU h 685 " --> pdb=" O PRO h 681 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN h 686 " --> pdb=" O ALA h 682 " (cutoff:3.500A) Processing helix chain 'h' and resid 688 through 703 Processing helix chain 'h' and resid 708 through 725 removed outlier: 3.911A pdb=" N ARG h 712 " --> pdb=" O LYS h 708 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR h 713 " --> pdb=" O GLU h 709 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP h 716 " --> pdb=" O ARG h 712 " (cutoff:3.500A) Processing helix chain 'h' and resid 740 through 745 Processing helix chain 'h' and resid 753 through 763 Processing helix chain 'h' and resid 766 through 782 Processing helix chain 'h' and resid 805 through 809 Processing helix chain 'h' and resid 810 through 829 Processing helix chain 'h' and resid 832 through 846 Processing helix chain 'h' and resid 848 through 864 Processing helix chain 'h' and resid 877 through 891 Processing helix chain 'h' and resid 893 through 902 removed outlier: 3.880A pdb=" N GLN h 902 " --> pdb=" O ALA h 898 " (cutoff:3.500A) Processing helix chain 'h' and resid 908 through 917 Processing helix chain 'h' and resid 924 through 932 removed outlier: 3.560A pdb=" N TYR h 928 " --> pdb=" O MET h 925 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ASP h 930 " --> pdb=" O SER h 927 " (cutoff:3.500A) Processing helix chain 'h' and resid 934 through 948 Processing helix chain 'h' and resid 950 through 962 Processing helix chain 'h' and resid 963 through 967 Processing helix chain 'h' and resid 973 through 995 Processing helix chain 'i' and resid 31 through 38 removed outlier: 3.773A pdb=" N SER i 34 " --> pdb=" O ASP i 31 " (cutoff:3.500A) Processing helix chain 'i' and resid 46 through 51 Processing helix chain 'i' and resid 109 through 117 removed outlier: 3.595A pdb=" N THR i 117 " --> pdb=" O ILE i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 127 through 146 Processing helix chain 'i' and resid 158 through 165 removed outlier: 3.931A pdb=" N ARG i 163 " --> pdb=" O LYS i 159 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU i 164 " --> pdb=" O ASP i 160 " (cutoff:3.500A) Processing helix chain 'i' and resid 166 through 171 Processing helix chain 'i' and resid 174 through 176 No H-bonds generated for 'chain 'i' and resid 174 through 176' Processing helix chain 'i' and resid 183 through 193 removed outlier: 3.891A pdb=" N LYS i 193 " --> pdb=" O SER i 189 " (cutoff:3.500A) Processing helix chain 'i' and resid 252 through 256 Processing helix chain 'i' and resid 273 through 291 Processing helix chain 'i' and resid 303 through 320 removed outlier: 3.893A pdb=" N ASP i 307 " --> pdb=" O GLY i 303 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ASP i 317 " --> pdb=" O TYR i 313 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER i 318 " --> pdb=" O GLN i 314 " (cutoff:3.500A) Processing helix chain 'i' and resid 332 through 343 Processing helix chain 'i' and resid 344 through 347 Processing helix chain 'i' and resid 348 through 353 Processing helix chain 'i' and resid 364 through 370 removed outlier: 3.786A pdb=" N ILE i 368 " --> pdb=" O HIS i 364 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN i 369 " --> pdb=" O ALA i 365 " (cutoff:3.500A) Processing helix chain 'i' and resid 382 through 386 Processing helix chain 'i' and resid 403 through 413 removed outlier: 4.409A pdb=" N HIS i 407 " --> pdb=" O GLY i 403 " (cutoff:3.500A) Processing helix chain 'i' and resid 428 through 434 Processing helix chain 'i' and resid 435 through 437 No H-bonds generated for 'chain 'i' and resid 435 through 437' Processing helix chain 'i' and resid 453 through 465 Processing helix chain 'i' and resid 473 through 477 Processing helix chain 'i' and resid 519 through 526 removed outlier: 3.764A pdb=" N SER i 525 " --> pdb=" O GLU i 521 " (cutoff:3.500A) Processing helix chain 'k' and resid 24 through 27 Processing helix chain 'k' and resid 47 through 51 removed outlier: 3.842A pdb=" N TYR k 50 " --> pdb=" O ASP k 47 " (cutoff:3.500A) Processing helix chain 'k' and resid 56 through 61 removed outlier: 3.748A pdb=" N PHE k 60 " --> pdb=" O ARG k 56 " (cutoff:3.500A) Processing helix chain 'k' and resid 70 through 75 Processing helix chain 'k' and resid 76 through 83 Processing helix chain 'k' and resid 94 through 114 Proline residue: k 101 - end of helix Processing helix chain 'k' and resid 122 through 132 removed outlier: 3.573A pdb=" N LYS k 132 " --> pdb=" O ASP k 128 " (cutoff:3.500A) Processing helix chain 'k' and resid 214 through 231 Processing helix chain 'k' and resid 241 through 260 Processing helix chain 'k' and resid 271 through 282 Processing helix chain 'k' and resid 283 through 286 Processing helix chain 'k' and resid 287 through 293 Processing helix chain 'k' and resid 309 through 315 removed outlier: 3.739A pdb=" N ASN k 315 " --> pdb=" O ALA k 311 " (cutoff:3.500A) Processing helix chain 'k' and resid 333 through 340 Processing helix chain 'k' and resid 394 through 406 Processing helix chain 'k' and resid 416 through 431 Processing helix chain 'k' and resid 457 through 467 Processing helix chain 'k' and resid 494 through 501 Processing helix chain 'p' and resid 15 through 20 Processing helix chain 'p' and resid 21 through 23 No H-bonds generated for 'chain 'p' and resid 21 through 23' Processing helix chain 'p' and resid 24 through 34 Processing helix chain 'p' and resid 34 through 42 removed outlier: 3.852A pdb=" N ILE p 38 " --> pdb=" O LYS p 34 " (cutoff:3.500A) Processing helix chain 'p' and resid 43 through 57 removed outlier: 3.691A pdb=" N ARG p 48 " --> pdb=" O VAL p 44 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU p 52 " --> pdb=" O ARG p 48 " (cutoff:3.500A) Proline residue: p 53 - end of helix Processing helix chain 'p' and resid 64 through 75 removed outlier: 3.528A pdb=" N THR p 75 " --> pdb=" O GLU p 71 " (cutoff:3.500A) Processing helix chain 'p' and resid 76 through 81 removed outlier: 3.917A pdb=" N VAL p 80 " --> pdb=" O PHE p 76 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY p 81 " --> pdb=" O THR p 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 76 through 81' Processing helix chain 'p' and resid 82 through 88 removed outlier: 3.722A pdb=" N VAL p 86 " --> pdb=" O PRO p 83 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N HIS p 87 " --> pdb=" O GLU p 84 " (cutoff:3.500A) Processing helix chain 'p' and resid 89 through 98 Processing helix chain 'p' and resid 101 through 116 Processing helix chain 'p' and resid 117 through 119 No H-bonds generated for 'chain 'p' and resid 117 through 119' Processing helix chain 'p' and resid 120 through 137 removed outlier: 4.834A pdb=" N VAL p 129 " --> pdb=" O GLU p 125 " (cutoff:3.500A) Proline residue: p 130 - end of helix Processing helix chain 'p' and resid 140 through 155 removed outlier: 3.697A pdb=" N ARG p 144 " --> pdb=" O TRP p 140 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N SER p 152 " --> pdb=" O CYS p 148 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL p 153 " --> pdb=" O GLY p 149 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N CYS p 154 " --> pdb=" O LEU p 150 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR p 155 " --> pdb=" O PHE p 151 " (cutoff:3.500A) Processing helix chain 'p' and resid 159 through 175 removed outlier: 3.811A pdb=" N GLU p 165 " --> pdb=" O ALA p 161 " (cutoff:3.500A) Processing helix chain 'p' and resid 178 through 188 removed outlier: 3.841A pdb=" N ARG p 182 " --> pdb=" O THR p 178 " (cutoff:3.500A) Processing helix chain 'p' and resid 188 through 194 Processing helix chain 'p' and resid 197 through 214 removed outlier: 3.909A pdb=" N LYS p 202 " --> pdb=" O LEU p 198 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER p 203 " --> pdb=" O ASP p 199 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ILE p 206 " --> pdb=" O LYS p 202 " (cutoff:3.500A) Proline residue: p 207 - end of helix Processing helix chain 'p' and resid 217 through 227 removed outlier: 3.675A pdb=" N LEU p 223 " --> pdb=" O SER p 219 " (cutoff:3.500A) Processing helix chain 'p' and resid 227 through 235 Processing helix chain 'p' and resid 236 through 238 No H-bonds generated for 'chain 'p' and resid 236 through 238' Processing helix chain 'p' and resid 239 through 244 removed outlier: 3.555A pdb=" N LEU p 243 " --> pdb=" O ASP p 239 " (cutoff:3.500A) Processing helix chain 'p' and resid 244 through 253 removed outlier: 3.865A pdb=" N GLU p 253 " --> pdb=" O ARG p 249 " (cutoff:3.500A) Processing helix chain 'p' and resid 256 through 266 removed outlier: 3.578A pdb=" N ARG p 260 " --> pdb=" O SER p 256 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS p 266 " --> pdb=" O MET p 262 " (cutoff:3.500A) Processing helix chain 'p' and resid 266 through 275 removed outlier: 4.659A pdb=" N LYS p 272 " --> pdb=" O THR p 268 " (cutoff:3.500A) Processing helix chain 'p' and resid 275 through 292 removed outlier: 3.591A pdb=" N THR p 281 " --> pdb=" O GLU p 277 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N VAL p 284 " --> pdb=" O LYS p 280 " (cutoff:3.500A) Proline residue: p 285 - end of helix Processing helix chain 'p' and resid 295 through 305 removed outlier: 3.596A pdb=" N ARG p 299 " --> pdb=" O GLU p 295 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS p 305 " --> pdb=" O ALA p 301 " (cutoff:3.500A) Processing helix chain 'p' and resid 305 through 312 removed outlier: 3.556A pdb=" N ASN p 312 " --> pdb=" O GLU p 308 " (cutoff:3.500A) Processing helix chain 'p' and resid 317 through 334 removed outlier: 3.660A pdb=" N VAL p 321 " --> pdb=" O CYS p 317 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE p 322 " --> pdb=" O ARG p 318 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN p 325 " --> pdb=" O VAL p 321 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU p 327 " --> pdb=" O MET p 323 " (cutoff:3.500A) Proline residue: p 328 - end of helix removed outlier: 4.022A pdb=" N GLU p 332 " --> pdb=" O PRO p 328 " (cutoff:3.500A) Processing helix chain 'p' and resid 338 through 347 removed outlier: 3.560A pdb=" N SER p 347 " --> pdb=" O SER p 343 " (cutoff:3.500A) Processing helix chain 'p' and resid 351 through 357 removed outlier: 4.621A pdb=" N ILE p 355 " --> pdb=" O GLY p 351 " (cutoff:3.500A) Processing helix chain 'p' and resid 357 through 362 removed outlier: 3.699A pdb=" N ILE p 362 " --> pdb=" O LYS p 358 " (cutoff:3.500A) Processing helix chain 'p' and resid 364 through 374 removed outlier: 3.837A pdb=" N LEU p 368 " --> pdb=" O HIS p 364 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS p 374 " --> pdb=" O LEU p 370 " (cutoff:3.500A) Processing helix chain 'p' and resid 377 through 386 removed outlier: 3.600A pdb=" N ARG p 381 " --> pdb=" O CYS p 377 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER p 386 " --> pdb=" O LEU p 382 " (cutoff:3.500A) Processing helix chain 'p' and resid 387 through 395 removed outlier: 4.272A pdb=" N VAL p 391 " --> pdb=" O ASN p 387 " (cutoff:3.500A) Processing helix chain 'p' and resid 396 through 404 Processing helix chain 'p' and resid 404 through 412 Processing helix chain 'p' and resid 416 through 434 removed outlier: 3.732A pdb=" N ARG p 420 " --> pdb=" O LYS p 416 " (cutoff:3.500A) Proline residue: p 428 - end of helix removed outlier: 3.789A pdb=" N GLN p 433 " --> pdb=" O LEU p 429 " (cutoff:3.500A) Processing helix chain 'p' and resid 435 through 443 Processing helix chain 'p' and resid 444 through 450 Processing helix chain 'p' and resid 451 through 453 No H-bonds generated for 'chain 'p' and resid 451 through 453' Processing helix chain 'p' and resid 455 through 474 removed outlier: 3.725A pdb=" N LYS p 467 " --> pdb=" O THR p 463 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS p 468 " --> pdb=" O SER p 464 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS p 472 " --> pdb=" O LYS p 468 " (cutoff:3.500A) Processing helix chain 'p' and resid 474 through 489 removed outlier: 4.501A pdb=" N ILE p 483 " --> pdb=" O HIS p 479 " (cutoff:3.500A) Proline residue: p 484 - end of helix removed outlier: 3.725A pdb=" N MET p 489 " --> pdb=" O LYS p 485 " (cutoff:3.500A) Processing helix chain 'p' and resid 494 through 510 removed outlier: 3.579A pdb=" N ARG p 498 " --> pdb=" O ASN p 494 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLU p 510 " --> pdb=" O ASN p 506 " (cutoff:3.500A) Processing helix chain 'p' and resid 514 through 528 removed outlier: 4.824A pdb=" N LEU p 522 " --> pdb=" O THR p 518 " (cutoff:3.500A) Proline residue: p 523 - end of helix Processing helix chain 'p' and resid 529 through 531 No H-bonds generated for 'chain 'p' and resid 529 through 531' Processing helix chain 'p' and resid 533 through 548 removed outlier: 3.542A pdb=" N ASN p 539 " --> pdb=" O ASN p 535 " (cutoff:3.500A) Processing helix chain 'p' and resid 555 through 569 removed outlier: 4.790A pdb=" N LYS p 561 " --> pdb=" O GLN p 557 " (cutoff:3.500A) Proline residue: p 562 - end of helix Processing helix chain 'p' and resid 572 through 587 Processing helix chain 'q' and resid 7 through 18 Processing helix chain 'q' and resid 24 through 42 removed outlier: 3.741A pdb=" N LYS q 34 " --> pdb=" O SER q 30 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU q 37 " --> pdb=" O GLU q 33 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS q 41 " --> pdb=" O GLU q 37 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU q 42 " --> pdb=" O ILE q 38 " (cutoff:3.500A) Processing helix chain 'q' and resid 61 through 73 Processing helix chain 'q' and resid 92 through 107 Processing helix chain 'q' and resid 120 through 127 Processing helix chain 'q' and resid 128 through 138 Processing helix chain 'q' and resid 140 through 151 removed outlier: 3.614A pdb=" N LYS q 144 " --> pdb=" O ALA q 140 " (cutoff:3.500A) Processing helix chain 'q' and resid 176 through 182 removed outlier: 3.833A pdb=" N ILE q 180 " --> pdb=" O THR q 176 " (cutoff:3.500A) Processing helix chain 'q' and resid 193 through 201 Processing helix chain 'q' and resid 221 through 233 Processing helix chain 'q' and resid 264 through 268 Processing helix chain 'u' and resid 513 through 524 removed outlier: 4.272A pdb=" N UNK u 524 " --> pdb=" O UNK u 520 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1448 through 1449 Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 95 removed outlier: 7.275A pdb=" N THR A 251 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 10.417A pdb=" N LYS A 92 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 10.215A pdb=" N ILE A 249 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 190 through 194 removed outlier: 4.556A pdb=" N LEU A 198 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AA5, first strand: chain 'B' and resid 1060 through 1062 removed outlier: 3.595A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.866A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA8, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.157A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE H 56 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE H 9 " --> pdb=" O PHE H 56 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU H 58 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLU H 7 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE H 60 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N MET H 37 " --> pdb=" O SER H 32 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ARG H 111 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLY H 101 " --> pdb=" O ARG H 111 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N SER H 113 " --> pdb=" O ILE H 99 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE H 99 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TYR H 115 " --> pdb=" O TYR H 97 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 602 through 605 removed outlier: 6.766A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB2, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.789A pdb=" N VAL A 879 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB4, first strand: chain 'A' and resid 1306 through 1310 removed outlier: 3.784A pdb=" N LYS A1306 " --> pdb=" O ASP A1339 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU A1139 " --> pdb=" O THR A1338 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1243 through 1248 removed outlier: 3.820A pdb=" N ASN A1248 " --> pdb=" O VAL A1256 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL A1256 " --> pdb=" O ASN A1248 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU A1255 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE A1261 " --> pdb=" O TRP A1210 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N TRP A1210 " --> pdb=" O ILE A1261 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LEU A1211 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ILE A1175 " --> pdb=" O LEU A1211 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ARG A1213 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N THR A1173 " --> pdb=" O ARG A1213 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLU A1215 " --> pdb=" O ALA A1171 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1319 through 1322 Processing sheet with id=AB7, first strand: chain 'A' and resid 1471 through 1475 Processing sheet with id=AB8, first strand: chain 'B' and resid 65 through 67 removed outlier: 5.395A pdb=" N LEU B 86 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N THR B 131 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY B 150 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ILE B 128 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LYS B 146 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N LYS B 130 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N HIS B 144 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AC1, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC2, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.379A pdb=" N ALA B 196 " --> pdb=" O ASN B 486 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 205 through 209 removed outlier: 3.839A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC5, first strand: chain 'B' and resid 632 through 633 Processing sheet with id=AC6, first strand: chain 'B' and resid 551 through 552 removed outlier: 5.436A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 748 through 751 removed outlier: 6.654A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 748 through 751 removed outlier: 6.654A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N VAL B 907 " --> pdb=" O LYS L 46 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N MET L 15 " --> pdb=" O ILE L 28 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD1, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.261A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ILE B 965 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE B 779 " --> pdb=" O ILE B 965 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ILE B 967 " --> pdb=" O ILE B 779 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA B 781 " --> pdb=" O ILE B 967 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 827 through 829 removed outlier: 6.839A pdb=" N GLN B 838 " --> pdb=" O ASP B 891 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 865 through 867 removed outlier: 7.068A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1115 through 1119 Processing sheet with id=AD5, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id=AD6, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.627A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N TYR C 230 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N PHE C 184 " --> pdb=" O TYR C 230 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ASN C 232 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL C 182 " --> pdb=" O ASN C 232 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLU C 234 " --> pdb=" O ALA C 180 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 121 through 122 removed outlier: 6.547A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 113 through 115 Processing sheet with id=AD9, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.823A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL G 76 " --> pdb=" O TYR G 3 " (cutoff:3.500A) removed outlier: 11.217A pdb=" N LEU G 67 " --> pdb=" O ILE G 54 " (cutoff:3.500A) removed outlier: 10.318A pdb=" N ILE G 54 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N ASP G 52 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N LYS G 71 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N THR G 50 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LYS G 73 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL G 48 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.823A pdb=" N GLU D 30 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL G 76 " --> pdb=" O TYR G 3 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 60 through 63 removed outlier: 4.071A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 147 through 150 removed outlier: 6.254A pdb=" N ILE E 173 " --> pdb=" O GLN E 210 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 97 through 99 removed outlier: 5.294A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU G 83 " --> pdb=" O ILE G 147 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE G 143 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 118 through 120 removed outlier: 4.021A pdb=" N ASP G 120 " --> pdb=" O CYS G 127 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N CYS G 127 " --> pdb=" O ASP G 120 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 25 through 28 Processing sheet with id=AE7, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AE8, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AE9, first strand: chain 'U' and resid 163 through 165 Processing sheet with id=AF1, first strand: chain 'W' and resid 367 through 370 removed outlier: 3.748A pdb=" N VAL W 367 " --> pdb=" O ASN W 379 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N SER W 377 " --> pdb=" O THR W 369 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Z' and resid 438 through 439 Processing sheet with id=AF3, first strand: chain 'Z' and resid 510 through 513 removed outlier: 3.587A pdb=" N VAL Z 500 " --> pdb=" O VAL Z 513 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ILE Z 501 " --> pdb=" O VAL Z 493 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Z' and resid 539 through 543 removed outlier: 3.506A pdb=" N LEU Z 542 " --> pdb=" O THR Z 546 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N THR Z 546 " --> pdb=" O LEU Z 542 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL Z 549 " --> pdb=" O LEU Z 561 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N GLN Z 559 " --> pdb=" O VAL Z 551 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LEU Z 553 " --> pdb=" O THR Z 557 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N THR Z 557 " --> pdb=" O LEU Z 553 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Z' and resid 586 through 587 Processing sheet with id=AF6, first strand: chain 'Z' and resid 611 through 613 Processing sheet with id=AF7, first strand: chain 'Z' and resid 621 through 625 Processing sheet with id=AF8, first strand: chain 'Z' and resid 742 through 746 removed outlier: 6.266A pdb=" N GLU Z 735 " --> pdb=" O VAL Z 724 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VAL Z 724 " --> pdb=" O GLU Z 735 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'd' and resid 267 through 269 Processing sheet with id=AG1, first strand: chain 'd' and resid 821 through 824 removed outlier: 3.612A pdb=" N THR d 823 " --> pdb=" O THR d 850 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ARG d 889 " --> pdb=" O PRO d 885 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'd' and resid 835 through 838 removed outlier: 5.976A pdb=" N LEU d 835 " --> pdb=" O MET d 957 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LYS d 959 " --> pdb=" O LEU d 835 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N PHE d 837 " --> pdb=" O LYS d 959 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'd' and resid 843 through 846 Processing sheet with id=AG4, first strand: chain 'd' and resid 874 through 875 removed outlier: 3.636A pdb=" N GLY d 944 " --> pdb=" O TYR d 917 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'd' and resid 874 through 875 Processing sheet with id=AG6, first strand: chain 'e' and resid 960 through 963 Processing sheet with id=AG7, first strand: chain 'f' and resid 62 through 64 removed outlier: 6.367A pdb=" N ILE f 3 " --> pdb=" O ILE f 124 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ILE f 126 " --> pdb=" O ILE f 3 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU f 5 " --> pdb=" O ILE f 126 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILE f 128 " --> pdb=" O LEU f 5 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU f 7 " --> pdb=" O ILE f 128 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N ASP f 130 " --> pdb=" O LEU f 7 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ALA f 123 " --> pdb=" O ARG f 167 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N PHE f 169 " --> pdb=" O ALA f 123 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ILE f 125 " --> pdb=" O PHE f 169 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEU f 171 " --> pdb=" O ILE f 125 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR f 127 " --> pdb=" O LEU f 171 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU f 173 " --> pdb=" O THR f 127 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR f 129 " --> pdb=" O LEU f 173 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N TYR f 208 " --> pdb=" O LEU f 168 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ALA f 170 " --> pdb=" O TYR f 208 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N VAL f 210 " --> pdb=" O ALA f 170 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL f 172 " --> pdb=" O VAL f 210 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'f' and resid 263 through 269 removed outlier: 8.328A pdb=" N VAL f 307 " --> pdb=" O VAL f 232 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASN f 234 " --> pdb=" O VAL f 307 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N PHE f 309 " --> pdb=" O ASN f 234 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLU f 236 " --> pdb=" O PHE f 309 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N CYS f 311 " --> pdb=" O GLU f 236 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN f 349 " --> pdb=" O SER f 310 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR f 312 " --> pdb=" O CYS f 347 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N CYS f 347 " --> pdb=" O THR f 312 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP f 325 " --> pdb=" O VAL f 381 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'g' and resid 819 through 822 removed outlier: 6.585A pdb=" N ILE g 819 " --> pdb=" O LYS g 929 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU g 931 " --> pdb=" O ILE g 819 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N VAL g 821 " --> pdb=" O LEU g 931 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'g' and resid 819 through 822 removed outlier: 6.585A pdb=" N ILE g 819 " --> pdb=" O LYS g 929 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU g 931 " --> pdb=" O ILE g 819 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N VAL g 821 " --> pdb=" O LEU g 931 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'g' and resid 827 through 834 Processing sheet with id=AH3, first strand: chain 'i' and resid 194 through 197 removed outlier: 6.148A pdb=" N VAL i 123 " --> pdb=" O GLN i 195 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL i 197 " --> pdb=" O VAL i 123 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ALA i 125 " --> pdb=" O VAL i 197 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE i 99 " --> pdb=" O TYR i 124 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N THR i 126 " --> pdb=" O ILE i 99 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU i 503 " --> pdb=" O CYS i 5 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'i' and resid 68 through 71 Processing sheet with id=AH5, first strand: chain 'i' and resid 83 through 84 Processing sheet with id=AH6, first strand: chain 'i' and resid 203 through 205 removed outlier: 3.602A pdb=" N VAL i 209 " --> pdb=" O LEU i 205 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL i 260 " --> pdb=" O LYS i 233 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'i' and resid 373 through 376 removed outlier: 6.163A pdb=" N LEU i 326 " --> pdb=" O LYS i 374 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N TYR i 376 " --> pdb=" O LEU i 326 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N PHE i 328 " --> pdb=" O TYR i 376 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU i 296 " --> pdb=" O ILE i 421 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'i' and resid 529 through 530 removed outlier: 8.165A pdb=" N LEU k 492 " --> pdb=" O PRO k 453 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY k 455 " --> pdb=" O LEU k 492 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N HIS i 551 " --> pdb=" O LYS i 515 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU i 517 " --> pdb=" O HIS i 551 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'k' and resid 133 through 136 removed outlier: 5.807A pdb=" N ILE k 90 " --> pdb=" O VAL k 134 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL k 136 " --> pdb=" O ILE k 90 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N MET k 92 " --> pdb=" O VAL k 136 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL k 64 " --> pdb=" O TYR k 91 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N THR k 93 " --> pdb=" O VAL k 64 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N MET k 30 " --> pdb=" O ILE k 65 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'k' and resid 141 through 143 removed outlier: 3.673A pdb=" N LEU k 199 " --> pdb=" O SER k 172 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU k 203 " --> pdb=" O THR k 176 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU k 200 " --> pdb=" O LEU k 411 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL k 413 " --> pdb=" O LEU k 200 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N THR k 202 " --> pdb=" O VAL k 413 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU k 412 " --> pdb=" O TYR k 436 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'k' and resid 305 through 307 removed outlier: 6.676A pdb=" N ILE k 265 " --> pdb=" O LYS k 306 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'k' and resid 348 through 350 removed outlier: 6.288A pdb=" N VAL k 348 " --> pdb=" O GLU k 385 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'q' and resid 45 through 48 removed outlier: 6.228A pdb=" N GLN q 46 " --> pdb=" O LEU q 158 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL q 237 " --> pdb=" O VAL q 257 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ILE q 259 " --> pdb=" O VAL q 237 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG q 239 " --> pdb=" O ILE q 259 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'q' and resid 111 through 113 removed outlier: 6.524A pdb=" N TYR q 80 " --> pdb=" O THR q 112 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL q 52 " --> pdb=" O LEU q 278 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'q' and resid 202 through 203 5577 hydrogen bonds defined for protein. 16065 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: 55.76 Time building geometry restraints manager: 35.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 32082 1.34 - 1.46: 20564 1.46 - 1.58: 49455 1.58 - 1.70: 144 1.70 - 1.83: 891 Bond restraints: 103136 Sorted by residual: bond pdb=" C GLN L 13 " pdb=" N PRO L 14 " ideal model delta sigma weight residual 1.335 1.372 -0.037 8.70e-03 1.32e+04 1.79e+01 bond pdb=" C SER g 608 " pdb=" N THR g 609 " ideal model delta sigma weight residual 1.331 1.288 0.043 1.59e-02 3.96e+03 7.33e+00 bond pdb=" C PHE U 100 " pdb=" N PRO U 101 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.10e+00 bond pdb=" C ARG k 44 " pdb=" N PHE k 45 " ideal model delta sigma weight residual 1.331 1.264 0.067 3.12e-02 1.03e+03 4.63e+00 bond pdb=" CB MET b 435 " pdb=" CG MET b 435 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.15e+00 ... (remaining 103131 not shown) Histogram of bond angle deviations from ideal: 93.06 - 101.42: 296 101.42 - 109.77: 13231 109.77 - 118.12: 66233 118.12 - 126.48: 58786 126.48 - 134.83: 1629 Bond angle restraints: 140175 Sorted by residual: angle pdb=" C LEU h 469 " pdb=" N LYS h 470 " pdb=" CA LYS h 470 " ideal model delta sigma weight residual 121.54 132.45 -10.91 1.91e+00 2.74e-01 3.26e+01 angle pdb=" C ASN q 88 " pdb=" N ARG q 89 " pdb=" CA ARG q 89 " ideal model delta sigma weight residual 121.54 131.95 -10.41 1.91e+00 2.74e-01 2.97e+01 angle pdb=" N GLU h 719 " pdb=" CA GLU h 719 " pdb=" CB GLU h 719 " ideal model delta sigma weight residual 110.16 117.67 -7.51 1.48e+00 4.57e-01 2.57e+01 angle pdb=" N GLU a1737 " pdb=" CA GLU a1737 " pdb=" CB GLU a1737 " ideal model delta sigma weight residual 110.40 118.57 -8.17 1.63e+00 3.76e-01 2.51e+01 angle pdb=" N GLU a2072 " pdb=" CA GLU a2072 " pdb=" CB GLU a2072 " ideal model delta sigma weight residual 110.07 117.17 -7.10 1.45e+00 4.76e-01 2.40e+01 ... (remaining 140170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.37: 60369 32.37 - 64.74: 1577 64.74 - 97.11: 143 97.11 - 129.48: 0 129.48 - 161.85: 3 Dihedral angle restraints: 62092 sinusoidal: 24115 harmonic: 37977 Sorted by residual: dihedral pdb=" CA LEU a1033 " pdb=" C LEU a1033 " pdb=" N PRO a1034 " pdb=" CA PRO a1034 " ideal model delta harmonic sigma weight residual -180.00 -143.27 -36.73 0 5.00e+00 4.00e-02 5.40e+01 dihedral pdb=" CA HIS g 598 " pdb=" C HIS g 598 " pdb=" N LYS g 599 " pdb=" CA LYS g 599 " ideal model delta harmonic sigma weight residual 180.00 152.12 27.88 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA TYR i 436 " pdb=" C TYR i 436 " pdb=" N GLN i 437 " pdb=" CA GLN i 437 " ideal model delta harmonic sigma weight residual -180.00 -152.98 -27.02 0 5.00e+00 4.00e-02 2.92e+01 ... (remaining 62089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 14926 0.090 - 0.180: 1260 0.180 - 0.271: 47 0.271 - 0.361: 5 0.361 - 0.451: 1 Chirality restraints: 16239 Sorted by residual: chirality pdb=" CB ILE g 232 " pdb=" CA ILE g 232 " pdb=" CG1 ILE g 232 " pdb=" CG2 ILE g 232 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.09e+00 chirality pdb=" CB ILE A 621 " pdb=" CA ILE A 621 " pdb=" CG1 ILE A 621 " pdb=" CG2 ILE A 621 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA ASP d 745 " pdb=" N ASP d 745 " pdb=" C ASP d 745 " pdb=" CB ASP d 745 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 16236 not shown) Planarity restraints: 17889 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU i 359 " -0.072 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO i 360 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO i 360 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO i 360 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 752 " 0.035 2.00e-02 2.50e+03 2.98e-02 1.77e+01 pdb=" CG TYR B 752 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TYR B 752 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR B 752 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 752 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 752 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR B 752 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 752 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO e 568 " -0.051 5.00e-02 4.00e+02 7.68e-02 9.43e+00 pdb=" N PRO e 569 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO e 569 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO e 569 " -0.044 5.00e-02 4.00e+02 ... (remaining 17886 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.29: 39 2.29 - 2.94: 41076 2.94 - 3.60: 155146 3.60 - 4.25: 242206 4.25 - 4.90: 401086 Nonbonded interactions: 839553 Sorted by model distance: nonbonded pdb=" O GLY k 177 " pdb=" OE2 GLU k 203 " model vdw 1.638 3.040 nonbonded pdb=" OD2 ASP q 85 " pdb="MN MN q1002 " model vdw 1.837 2.320 nonbonded pdb=" OD1 ASN q 117 " pdb="MN MN q1001 " model vdw 1.926 2.320 nonbonded pdb=" O GLY k 177 " pdb=" CD GLU k 203 " model vdw 1.950 3.270 nonbonded pdb=" NE2 HIS q 167 " pdb="MN MN q1001 " model vdw 2.019 2.400 ... (remaining 839548 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 24.770 Check model and map are aligned: 1.140 Set scattering table: 0.730 Process input model: 238.390 Find NCS groups from input model: 3.640 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 276.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6237 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 : 0.004 0.067 103136 Z= 0.288 Angle : 0.777 16.154 140175 Z= 0.393 Chirality : 0.049 0.451 16239 Planarity : 0.006 0.108 17889 Dihedral : 14.555 161.848 37557 Min Nonbonded Distance : 1.638 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.04 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 0.16 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.07), residues: 12886 helix: -0.17 (0.06), residues: 6985 sheet: -0.23 (0.17), residues: 1029 loop : -1.08 (0.08), residues: 4872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP W 145 HIS 0.011 0.001 HIS g 598 PHE 0.034 0.002 PHE p 538 TYR 0.073 0.002 TYR B 752 ARG 0.012 0.000 ARG b 808 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25772 Ramachandran restraints generated. 12886 Oldfield, 0 Emsley, 12886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25772 Ramachandran restraints generated. 12886 Oldfield, 0 Emsley, 12886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 11617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 559 time to evaluate : 9.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1102 MET cc_start: 0.5563 (ptt) cc_final: 0.5262 (ttp) REVERT: E 121 MET cc_start: -0.1250 (pmm) cc_final: -0.1569 (ptp) REVERT: Z 635 MET cc_start: 0.1350 (mmp) cc_final: 0.0717 (tpt) REVERT: b 880 MET cc_start: 0.8028 (mtm) cc_final: 0.7612 (mtm) REVERT: b 1035 MET cc_start: 0.8549 (mmm) cc_final: 0.8041 (mmt) REVERT: e 844 ASP cc_start: 0.8223 (m-30) cc_final: 0.7716 (m-30) REVERT: f 532 LEU cc_start: 0.8244 (mp) cc_final: 0.8018 (mp) REVERT: g 230 MET cc_start: 0.8060 (mmm) cc_final: 0.7774 (mmm) REVERT: k 437 MET cc_start: 0.6950 (mmm) cc_final: 0.6709 (mmt) outliers start: 0 outliers final: 0 residues processed: 559 average time/residue: 0.9740 time to fit residues: 965.6001 Evaluate side-chains 435 residues out of total 11617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 435 time to evaluate : 8.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1314 random chunks: chunk 1109 optimal weight: 0.8980 chunk 995 optimal weight: 7.9990 chunk 552 optimal weight: 10.0000 chunk 340 optimal weight: 7.9990 chunk 671 optimal weight: 4.9990 chunk 532 optimal weight: 0.0040 chunk 1029 optimal weight: 7.9990 chunk 398 optimal weight: 7.9990 chunk 626 optimal weight: 4.9990 chunk 766 optimal weight: 5.9990 chunk 1193 optimal weight: 6.9990 overall best weight: 3.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 ASN ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN D 43 HIS E 133 GLN I 32 ASN I 41 ASN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 46 HIS U 187 GLN U 188 GLN W 118 HIS ** W 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 489 GLN Z 741 GLN ** a1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 285 HIS b 717 ASN ** b1002 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b1187 HIS d 231 GLN d 403 GLN d 492 ASN d 689 GLN e 770 GLN f 410 GLN g 291 ASN g 563 ASN ** g 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 884 HIS g 938 GLN h 588 HIS ** h 854 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 210 GLN ** i 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 198 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6376 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 103136 Z= 0.246 Angle : 0.590 11.807 140175 Z= 0.300 Chirality : 0.041 0.243 16239 Planarity : 0.004 0.070 17889 Dihedral : 8.677 164.533 14936 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.64 % Favored : 96.32 % Rotamer: Outliers : 0.42 % Allowed : 5.37 % Favored : 94.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 0.16 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.07), residues: 12886 helix: 1.02 (0.06), residues: 7021 sheet: -0.22 (0.16), residues: 1048 loop : -0.78 (0.09), residues: 4817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP e 902 HIS 0.011 0.001 HIS A 465 PHE 0.025 0.001 PHE h 457 TYR 0.021 0.001 TYR g 935 ARG 0.005 0.000 ARG I 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25772 Ramachandran restraints generated. 12886 Oldfield, 0 Emsley, 12886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25772 Ramachandran restraints generated. 12886 Oldfield, 0 Emsley, 12886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 11617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 440 time to evaluate : 9.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1102 MET cc_start: 0.5684 (ptt) cc_final: 0.5371 (ttp) REVERT: A 1228 MET cc_start: 0.4858 (mtt) cc_final: 0.4551 (mtt) REVERT: B 108 MET cc_start: 0.3618 (OUTLIER) cc_final: 0.1646 (tpp) REVERT: E 121 MET cc_start: -0.1116 (pmm) cc_final: -0.2117 (ptp) REVERT: U 187 GLN cc_start: 0.6612 (OUTLIER) cc_final: 0.6091 (pm20) REVERT: W 316 MET cc_start: 0.1434 (ppp) cc_final: 0.1093 (ppp) REVERT: a 1283 LYS cc_start: 0.8090 (mmmt) cc_final: 0.7672 (mmmt) REVERT: a 1286 MET cc_start: 0.8849 (ppp) cc_final: 0.8613 (ppp) REVERT: a 1464 LEU cc_start: 0.8966 (pp) cc_final: 0.8489 (tp) REVERT: a 2092 MET cc_start: 0.8174 (mmm) cc_final: 0.7884 (mtp) REVERT: b 24 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: b 485 MET cc_start: 0.8107 (tmm) cc_final: 0.7901 (tmm) REVERT: b 1122 MET cc_start: 0.8904 (mmm) cc_final: 0.8637 (mmt) REVERT: d 689 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7313 (pp30) REVERT: d 745 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.8123 (p0) REVERT: e 844 ASP cc_start: 0.8180 (m-30) cc_final: 0.7681 (m-30) REVERT: f 14 MET cc_start: 0.7766 (mmm) cc_final: 0.7440 (mmp) REVERT: f 434 MET cc_start: 0.3826 (OUTLIER) cc_final: 0.3340 (ttt) REVERT: g 230 MET cc_start: 0.8227 (mmm) cc_final: 0.7987 (mmm) outliers start: 43 outliers final: 17 residues processed: 469 average time/residue: 0.8463 time to fit residues: 710.0811 Evaluate side-chains 441 residues out of total 11617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 418 time to evaluate : 9.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1344 MET Chi-restraints excluded: chain A residue 1401 LEU Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain K residue 22 ASN Chi-restraints excluded: chain K residue 70 LYS Chi-restraints excluded: chain U residue 187 GLN Chi-restraints excluded: chain V residue 82 SER Chi-restraints excluded: chain a residue 1039 PHE Chi-restraints excluded: chain a residue 2113 ASN Chi-restraints excluded: chain a residue 2171 MET Chi-restraints excluded: chain b residue 24 GLU Chi-restraints excluded: chain b residue 339 MET Chi-restraints excluded: chain b residue 1147 ILE Chi-restraints excluded: chain d residue 689 GLN Chi-restraints excluded: chain d residue 745 ASP Chi-restraints excluded: chain e residue 609 ASP Chi-restraints excluded: chain f residue 171 LEU Chi-restraints excluded: chain f residue 410 GLN Chi-restraints excluded: chain f residue 434 MET Chi-restraints excluded: chain g residue 283 THR Chi-restraints excluded: chain g residue 696 ASP Chi-restraints excluded: chain g residue 787 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1314 random chunks: chunk 663 optimal weight: 0.3980 chunk 370 optimal weight: 30.0000 chunk 993 optimal weight: 5.9990 chunk 812 optimal weight: 5.9990 chunk 329 optimal weight: 20.0000 chunk 1195 optimal weight: 9.9990 chunk 1291 optimal weight: 7.9990 chunk 1064 optimal weight: 5.9990 chunk 1185 optimal weight: 40.0000 chunk 407 optimal weight: 20.0000 chunk 958 optimal weight: 2.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 GLN ** A1332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 GLN ** B 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 187 GLN ** W 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 489 GLN ** a1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b1002 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 926 ASN e 963 GLN e 989 HIS ** g 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 113 ASN h 781 HIS ** h 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 988 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 484 HIS ** k 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 168 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 103136 Z= 0.276 Angle : 0.581 12.046 140175 Z= 0.293 Chirality : 0.041 0.258 16239 Planarity : 0.004 0.062 17889 Dihedral : 8.536 165.002 14936 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.79 % Favored : 96.17 % Rotamer: Outliers : 0.65 % Allowed : 7.64 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.08), residues: 12886 helix: 1.41 (0.06), residues: 7032 sheet: -0.34 (0.16), residues: 1040 loop : -0.65 (0.09), residues: 4814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP e 902 HIS 0.010 0.001 HIS a1294 PHE 0.024 0.001 PHE h 866 TYR 0.020 0.001 TYR g 689 ARG 0.005 0.000 ARG p 171 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25772 Ramachandran restraints generated. 12886 Oldfield, 0 Emsley, 12886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25772 Ramachandran restraints generated. 12886 Oldfield, 0 Emsley, 12886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 11617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 423 time to evaluate : 9.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1102 MET cc_start: 0.5773 (ptt) cc_final: 0.5566 (ptt) REVERT: A 1228 MET cc_start: 0.5085 (mtt) cc_final: 0.4665 (mtt) REVERT: B 239 MET cc_start: 0.7152 (ppp) cc_final: 0.6551 (ppp) REVERT: B 529 MET cc_start: 0.5771 (OUTLIER) cc_final: 0.5376 (ppp) REVERT: E 121 MET cc_start: -0.1025 (pmm) cc_final: -0.1957 (ttm) REVERT: W 316 MET cc_start: 0.1489 (ppp) cc_final: 0.1146 (ppp) REVERT: Z 451 MET cc_start: 0.7799 (pmm) cc_final: 0.7386 (pmm) REVERT: Z 635 MET cc_start: -0.1297 (mmm) cc_final: -0.1569 (mmt) REVERT: a 1131 MET cc_start: 0.1346 (ppp) cc_final: 0.1106 (ppp) REVERT: a 2092 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7882 (mtp) REVERT: b 415 MET cc_start: 0.8638 (mmm) cc_final: 0.8432 (mpp) REVERT: b 485 MET cc_start: 0.8191 (tmm) cc_final: 0.7941 (tmm) REVERT: b 1122 MET cc_start: 0.8938 (mmm) cc_final: 0.8722 (mmt) REVERT: f 14 MET cc_start: 0.7856 (mmm) cc_final: 0.7343 (mmm) REVERT: f 434 MET cc_start: 0.3939 (OUTLIER) cc_final: 0.3410 (ttt) REVERT: g 230 MET cc_start: 0.8324 (mmm) cc_final: 0.8115 (mmm) outliers start: 67 outliers final: 24 residues processed: 475 average time/residue: 0.8667 time to fit residues: 739.4635 Evaluate side-chains 441 residues out of total 11617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 414 time to evaluate : 8.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 1344 MET Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain G residue 134 ASP Chi-restraints excluded: chain K residue 70 LYS Chi-restraints excluded: chain V residue 82 SER Chi-restraints excluded: chain a residue 2092 MET Chi-restraints excluded: chain a residue 2113 ASN Chi-restraints excluded: chain a residue 2171 MET Chi-restraints excluded: chain b residue 339 MET Chi-restraints excluded: chain b residue 1136 VAL Chi-restraints excluded: chain b residue 1147 ILE Chi-restraints excluded: chain b residue 1179 MET Chi-restraints excluded: chain e residue 578 LEU Chi-restraints excluded: chain e residue 609 ASP Chi-restraints excluded: chain f residue 171 LEU Chi-restraints excluded: chain f residue 434 MET Chi-restraints excluded: chain g residue 696 ASP Chi-restraints excluded: chain g residue 787 VAL Chi-restraints excluded: chain g residue 831 VAL Chi-restraints excluded: chain g residue 906 VAL Chi-restraints excluded: chain p residue 501 THR Chi-restraints excluded: chain q residue 156 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1314 random chunks: chunk 1181 optimal weight: 50.0000 chunk 898 optimal weight: 10.0000 chunk 620 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 570 optimal weight: 30.0000 chunk 802 optimal weight: 1.9990 chunk 1199 optimal weight: 6.9990 chunk 1270 optimal weight: 20.0000 chunk 626 optimal weight: 4.9990 chunk 1137 optimal weight: 10.0000 chunk 342 optimal weight: 50.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 GLN A1077 ASN ** A1332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN ** B 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1120 ASN E 30 GLN L 13 GLN ** W 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 463 GLN ** a1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1674 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 752 HIS b 934 GLN d 125 GLN d 148 GLN d 236 GLN ** d 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 689 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 859 ASN d 864 GLN d 884 ASN e 537 GLN e 690 GLN e 770 GLN f 19 HIS ** f 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 356 ASN g 515 GLN g 547 GLN ** g 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 988 GLN ** i 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 248 GLN p 172 ASN ** p 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6533 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 103136 Z= 0.370 Angle : 0.645 14.696 140175 Z= 0.324 Chirality : 0.042 0.273 16239 Planarity : 0.004 0.061 17889 Dihedral : 8.515 165.708 14936 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.16 % Favored : 95.79 % Rotamer: Outliers : 0.95 % Allowed : 9.58 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.08), residues: 12886 helix: 1.42 (0.06), residues: 7082 sheet: -0.35 (0.16), residues: 1023 loop : -0.66 (0.09), residues: 4781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP e 902 HIS 0.015 0.001 HIS a1271 PHE 0.035 0.002 PHE h 866 TYR 0.020 0.002 TYR L 41 ARG 0.005 0.001 ARG k 258 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25772 Ramachandran restraints generated. 12886 Oldfield, 0 Emsley, 12886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25772 Ramachandran restraints generated. 12886 Oldfield, 0 Emsley, 12886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 11617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 414 time to evaluate : 9.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1102 MET cc_start: 0.5812 (ptt) cc_final: 0.5471 (ptt) REVERT: A 1228 MET cc_start: 0.5264 (mtt) cc_final: 0.4943 (mtt) REVERT: A 1484 MET cc_start: 0.3964 (pmm) cc_final: 0.3618 (pmm) REVERT: B 108 MET cc_start: 0.4086 (tpp) cc_final: 0.3756 (tpp) REVERT: B 239 MET cc_start: 0.7280 (ppp) cc_final: 0.6649 (ppp) REVERT: B 908 MET cc_start: 0.5421 (OUTLIER) cc_final: 0.5114 (tpt) REVERT: E 121 MET cc_start: -0.1112 (pmm) cc_final: -0.1745 (ttm) REVERT: U 76 MET cc_start: 0.6564 (mmm) cc_final: 0.6362 (mmm) REVERT: W 316 MET cc_start: 0.1846 (ppp) cc_final: 0.1447 (ppp) REVERT: Z 451 MET cc_start: 0.7981 (pmm) cc_final: 0.7713 (pmm) REVERT: a 1286 MET cc_start: 0.9006 (ppp) cc_final: 0.8683 (ppp) REVERT: a 1364 MET cc_start: 0.8764 (ptt) cc_final: 0.8535 (mtm) REVERT: a 2092 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7901 (mtp) REVERT: b 188 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8408 (mm) REVERT: b 1122 MET cc_start: 0.8913 (mmm) cc_final: 0.8698 (mmt) REVERT: d 725 MET cc_start: 0.9034 (tpp) cc_final: 0.8730 (tpp) REVERT: d 768 ASP cc_start: 0.8269 (OUTLIER) cc_final: 0.8051 (p0) REVERT: f 14 MET cc_start: 0.7833 (mmm) cc_final: 0.7427 (mmm) REVERT: f 434 MET cc_start: 0.3870 (OUTLIER) cc_final: 0.3374 (ttt) REVERT: g 230 MET cc_start: 0.8374 (mmm) cc_final: 0.7978 (mmm) REVERT: g 597 TYR cc_start: 0.8689 (OUTLIER) cc_final: 0.8267 (t80) REVERT: g 798 LYS cc_start: 0.8395 (tppt) cc_final: 0.8175 (tppt) outliers start: 98 outliers final: 44 residues processed: 490 average time/residue: 0.8519 time to fit residues: 751.9933 Evaluate side-chains 460 residues out of total 11617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 410 time to evaluate : 9.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 1428 MET Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 908 MET Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain K residue 22 ASN Chi-restraints excluded: chain K residue 70 LYS Chi-restraints excluded: chain V residue 82 SER Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 463 GLN Chi-restraints excluded: chain a residue 1039 PHE Chi-restraints excluded: chain a residue 1100 MET Chi-restraints excluded: chain a residue 2092 MET Chi-restraints excluded: chain a residue 2113 ASN Chi-restraints excluded: chain a residue 2124 THR Chi-restraints excluded: chain b residue 188 LEU Chi-restraints excluded: chain b residue 262 LEU Chi-restraints excluded: chain b residue 339 MET Chi-restraints excluded: chain b residue 538 VAL Chi-restraints excluded: chain b residue 764 VAL Chi-restraints excluded: chain b residue 1136 VAL Chi-restraints excluded: chain b residue 1138 THR Chi-restraints excluded: chain b residue 1147 ILE Chi-restraints excluded: chain d residue 486 LEU Chi-restraints excluded: chain d residue 768 ASP Chi-restraints excluded: chain e residue 565 THR Chi-restraints excluded: chain e residue 578 LEU Chi-restraints excluded: chain e residue 609 ASP Chi-restraints excluded: chain e residue 914 MET Chi-restraints excluded: chain f residue 171 LEU Chi-restraints excluded: chain f residue 434 MET Chi-restraints excluded: chain g residue 271 LEU Chi-restraints excluded: chain g residue 283 THR Chi-restraints excluded: chain g residue 372 VAL Chi-restraints excluded: chain g residue 597 TYR Chi-restraints excluded: chain g residue 696 ASP Chi-restraints excluded: chain g residue 787 VAL Chi-restraints excluded: chain g residue 831 VAL Chi-restraints excluded: chain g residue 906 VAL Chi-restraints excluded: chain h residue 313 VAL Chi-restraints excluded: chain h residue 543 THR Chi-restraints excluded: chain i residue 307 ASP Chi-restraints excluded: chain k residue 62 ASP Chi-restraints excluded: chain p residue 501 THR Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 156 THR Chi-restraints excluded: chain q residue 175 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1314 random chunks: chunk 1057 optimal weight: 20.0000 chunk 720 optimal weight: 1.9990 chunk 18 optimal weight: 40.0000 chunk 945 optimal weight: 30.0000 chunk 524 optimal weight: 9.9990 chunk 1083 optimal weight: 5.9990 chunk 877 optimal weight: 3.9990 chunk 1 optimal weight: 20.0000 chunk 648 optimal weight: 0.9980 chunk 1140 optimal weight: 0.9990 chunk 320 optimal weight: 20.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 GLN I 32 ASN ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 569 HIS ** b 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 148 GLN ** d 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 689 GLN d 864 GLN e 770 GLN f 234 ASN f 363 HIS g 356 ASN ** g 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 686 GLN ** h 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 105 HIS ** i 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 165 GLN p 383 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 103136 Z= 0.207 Angle : 0.552 13.006 140175 Z= 0.276 Chirality : 0.040 0.218 16239 Planarity : 0.004 0.062 17889 Dihedral : 8.424 166.011 14936 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.76 % Favored : 96.20 % Rotamer: Outliers : 0.83 % Allowed : 10.87 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.08), residues: 12886 helix: 1.68 (0.06), residues: 7065 sheet: -0.38 (0.16), residues: 1028 loop : -0.63 (0.09), residues: 4793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP e 902 HIS 0.011 0.001 HIS a1294 PHE 0.021 0.001 PHE g 103 TYR 0.017 0.001 TYR g 771 ARG 0.004 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25772 Ramachandran restraints generated. 12886 Oldfield, 0 Emsley, 12886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25772 Ramachandran restraints generated. 12886 Oldfield, 0 Emsley, 12886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 11617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 416 time to evaluate : 9.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.1855 (ppp) cc_final: 0.1648 (ppp) REVERT: A 1228 MET cc_start: 0.5289 (mtt) cc_final: 0.4967 (mtt) REVERT: A 1484 MET cc_start: 0.4046 (pmm) cc_final: 0.3725 (pmm) REVERT: B 239 MET cc_start: 0.7287 (ppp) cc_final: 0.6754 (ppp) REVERT: B 976 MET cc_start: 0.5596 (ptp) cc_final: 0.5307 (ptp) REVERT: E 110 MET cc_start: 0.5840 (tmm) cc_final: 0.4796 (tmm) REVERT: E 121 MET cc_start: -0.1204 (pmm) cc_final: -0.1639 (ttm) REVERT: U 76 MET cc_start: 0.6740 (mmm) cc_final: 0.6470 (mmm) REVERT: W 316 MET cc_start: 0.1657 (ppp) cc_final: 0.1361 (ppp) REVERT: a 1131 MET cc_start: 0.1415 (ppp) cc_final: 0.1124 (tmm) REVERT: b 188 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8250 (mm) REVERT: b 1122 MET cc_start: 0.8884 (mmm) cc_final: 0.8652 (mmt) REVERT: b 1138 THR cc_start: 0.8840 (OUTLIER) cc_final: 0.8540 (p) REVERT: b 1199 MET cc_start: 0.8706 (ttp) cc_final: 0.8480 (tmm) REVERT: d 725 MET cc_start: 0.8930 (tpp) cc_final: 0.8612 (tpp) REVERT: d 768 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7960 (p0) REVERT: f 14 MET cc_start: 0.7823 (mmm) cc_final: 0.7327 (mmm) REVERT: f 434 MET cc_start: 0.4115 (mtm) cc_final: 0.3757 (ttt) REVERT: g 27 MET cc_start: 0.8540 (mmm) cc_final: 0.8101 (mpp) REVERT: g 230 MET cc_start: 0.8364 (mmm) cc_final: 0.8014 (mmm) REVERT: g 597 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.8126 (t80) REVERT: k 35 MET cc_start: 0.6931 (tmm) cc_final: 0.6589 (tmm) REVERT: k 319 MET cc_start: 0.6287 (tmm) cc_final: 0.5952 (tmm) outliers start: 86 outliers final: 37 residues processed: 489 average time/residue: 0.8398 time to fit residues: 742.3499 Evaluate side-chains 448 residues out of total 11617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 407 time to evaluate : 8.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 908 MET Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain K residue 22 ASN Chi-restraints excluded: chain K residue 70 LYS Chi-restraints excluded: chain M residue 1630 SER Chi-restraints excluded: chain V residue 82 SER Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain a residue 1039 PHE Chi-restraints excluded: chain a residue 2113 ASN Chi-restraints excluded: chain a residue 2124 THR Chi-restraints excluded: chain b residue 188 LEU Chi-restraints excluded: chain b residue 262 LEU Chi-restraints excluded: chain b residue 339 MET Chi-restraints excluded: chain b residue 1138 THR Chi-restraints excluded: chain b residue 1147 ILE Chi-restraints excluded: chain d residue 47 THR Chi-restraints excluded: chain d residue 486 LEU Chi-restraints excluded: chain d residue 681 VAL Chi-restraints excluded: chain d residue 704 THR Chi-restraints excluded: chain d residue 768 ASP Chi-restraints excluded: chain e residue 578 LEU Chi-restraints excluded: chain e residue 609 ASP Chi-restraints excluded: chain f residue 171 LEU Chi-restraints excluded: chain g residue 271 LEU Chi-restraints excluded: chain g residue 283 THR Chi-restraints excluded: chain g residue 597 TYR Chi-restraints excluded: chain g residue 598 HIS Chi-restraints excluded: chain g residue 696 ASP Chi-restraints excluded: chain g residue 787 VAL Chi-restraints excluded: chain g residue 831 VAL Chi-restraints excluded: chain h residue 803 ILE Chi-restraints excluded: chain h residue 821 LEU Chi-restraints excluded: chain q residue 142 VAL Chi-restraints excluded: chain q residue 156 THR Chi-restraints excluded: chain q residue 175 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1314 random chunks: chunk 427 optimal weight: 7.9990 chunk 1143 optimal weight: 9.9990 chunk 251 optimal weight: 0.1980 chunk 745 optimal weight: 3.9990 chunk 313 optimal weight: 1.9990 chunk 1271 optimal weight: 10.0000 chunk 1055 optimal weight: 50.0000 chunk 588 optimal weight: 8.9990 chunk 105 optimal weight: 0.2980 chunk 420 optimal weight: 40.0000 chunk 667 optimal weight: 10.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS A 472 HIS A1332 GLN ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 ASN W 103 GLN ** W 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 93 HIS ** d 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 356 ASN ** g 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 187 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 103136 Z= 0.214 Angle : 0.562 13.476 140175 Z= 0.279 Chirality : 0.040 0.257 16239 Planarity : 0.004 0.062 17889 Dihedral : 8.370 166.251 14936 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.90 % Favored : 96.07 % Rotamer: Outliers : 0.93 % Allowed : 11.53 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.08), residues: 12886 helix: 1.77 (0.06), residues: 7073 sheet: -0.33 (0.16), residues: 1054 loop : -0.60 (0.09), residues: 4759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP e 902 HIS 0.012 0.001 HIS A 465 PHE 0.021 0.001 PHE g 103 TYR 0.021 0.001 TYR g 771 ARG 0.006 0.000 ARG B1091 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25772 Ramachandran restraints generated. 12886 Oldfield, 0 Emsley, 12886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25772 Ramachandran restraints generated. 12886 Oldfield, 0 Emsley, 12886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 11617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 413 time to evaluate : 9.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1228 MET cc_start: 0.5324 (mtt) cc_final: 0.5016 (mtt) REVERT: A 1262 MET cc_start: 0.5587 (mmt) cc_final: 0.3667 (mpp) REVERT: E 110 MET cc_start: 0.5937 (tmm) cc_final: 0.5038 (tmm) REVERT: U 76 MET cc_start: 0.7201 (mmm) cc_final: 0.6860 (mmm) REVERT: W 316 MET cc_start: 0.1920 (ppp) cc_final: 0.1589 (ppp) REVERT: W 338 MET cc_start: 0.3032 (tpp) cc_final: 0.2779 (tpp) REVERT: a 1131 MET cc_start: 0.1432 (ppp) cc_final: 0.1120 (tmm) REVERT: a 1283 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7580 (tptt) REVERT: a 1624 MET cc_start: 0.7546 (OUTLIER) cc_final: 0.7310 (tmm) REVERT: b 1138 THR cc_start: 0.8836 (OUTLIER) cc_final: 0.8530 (p) REVERT: b 1199 MET cc_start: 0.8747 (ttp) cc_final: 0.8534 (tmm) REVERT: d 725 MET cc_start: 0.8931 (tpp) cc_final: 0.8609 (tpp) REVERT: f 14 MET cc_start: 0.7842 (mmm) cc_final: 0.7371 (mmm) REVERT: f 434 MET cc_start: 0.3921 (mtm) cc_final: 0.3414 (ttt) REVERT: g 27 MET cc_start: 0.8577 (mmm) cc_final: 0.8015 (mpp) REVERT: g 230 MET cc_start: 0.8354 (mmm) cc_final: 0.7997 (mmm) REVERT: g 597 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.8152 (t80) REVERT: k 35 MET cc_start: 0.6899 (tmm) cc_final: 0.6629 (tmm) REVERT: k 319 MET cc_start: 0.6329 (tmm) cc_final: 0.5922 (tmm) outliers start: 96 outliers final: 53 residues processed: 490 average time/residue: 0.8495 time to fit residues: 750.5796 Evaluate side-chains 466 residues out of total 11617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 409 time to evaluate : 9.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 908 MET Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain G residue 134 ASP Chi-restraints excluded: chain K residue 22 ASN Chi-restraints excluded: chain K residue 70 LYS Chi-restraints excluded: chain M residue 1630 SER Chi-restraints excluded: chain V residue 82 SER Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 448 THR Chi-restraints excluded: chain Z residue 635 MET Chi-restraints excluded: chain a residue 1039 PHE Chi-restraints excluded: chain a residue 1283 LYS Chi-restraints excluded: chain a residue 1624 MET Chi-restraints excluded: chain a residue 2113 ASN Chi-restraints excluded: chain a residue 2124 THR Chi-restraints excluded: chain b residue 262 LEU Chi-restraints excluded: chain b residue 339 MET Chi-restraints excluded: chain b residue 538 VAL Chi-restraints excluded: chain b residue 544 LEU Chi-restraints excluded: chain b residue 1136 VAL Chi-restraints excluded: chain b residue 1138 THR Chi-restraints excluded: chain b residue 1147 ILE Chi-restraints excluded: chain b residue 1179 MET Chi-restraints excluded: chain b residue 1182 ASP Chi-restraints excluded: chain d residue 486 LEU Chi-restraints excluded: chain d residue 662 THR Chi-restraints excluded: chain d residue 681 VAL Chi-restraints excluded: chain d residue 704 THR Chi-restraints excluded: chain e residue 578 LEU Chi-restraints excluded: chain e residue 609 ASP Chi-restraints excluded: chain f residue 171 LEU Chi-restraints excluded: chain g residue 271 LEU Chi-restraints excluded: chain g residue 283 THR Chi-restraints excluded: chain g residue 597 TYR Chi-restraints excluded: chain g residue 598 HIS Chi-restraints excluded: chain g residue 696 ASP Chi-restraints excluded: chain g residue 831 VAL Chi-restraints excluded: chain g residue 906 VAL Chi-restraints excluded: chain h residue 543 THR Chi-restraints excluded: chain h residue 803 ILE Chi-restraints excluded: chain h residue 821 LEU Chi-restraints excluded: chain i residue 305 ILE Chi-restraints excluded: chain i residue 307 ASP Chi-restraints excluded: chain k residue 93 THR Chi-restraints excluded: chain p residue 501 THR Chi-restraints excluded: chain q residue 156 THR Chi-restraints excluded: chain q residue 175 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1314 random chunks: chunk 1225 optimal weight: 7.9990 chunk 143 optimal weight: 30.0000 chunk 724 optimal weight: 0.6980 chunk 928 optimal weight: 0.3980 chunk 719 optimal weight: 0.7980 chunk 1070 optimal weight: 9.9990 chunk 709 optimal weight: 0.8980 chunk 1266 optimal weight: 9.9990 chunk 792 optimal weight: 8.9990 chunk 772 optimal weight: 8.9990 chunk 584 optimal weight: 40.0000 overall best weight: 2.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 GLN ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 185 GLN g 356 ASN ** g 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6477 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 103136 Z= 0.183 Angle : 0.559 19.385 140175 Z= 0.275 Chirality : 0.040 0.255 16239 Planarity : 0.004 0.062 17889 Dihedral : 8.329 166.464 14936 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.83 % Favored : 96.13 % Rotamer: Outliers : 0.86 % Allowed : 12.14 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.08), residues: 12886 helix: 1.84 (0.06), residues: 7077 sheet: -0.29 (0.16), residues: 1050 loop : -0.56 (0.09), residues: 4759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP e 902 HIS 0.013 0.001 HIS a1294 PHE 0.044 0.001 PHE B 364 TYR 0.019 0.001 TYR g 771 ARG 0.009 0.000 ARG E 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25772 Ramachandran restraints generated. 12886 Oldfield, 0 Emsley, 12886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25772 Ramachandran restraints generated. 12886 Oldfield, 0 Emsley, 12886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 11617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 414 time to evaluate : 9.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 VAL cc_start: 0.3687 (OUTLIER) cc_final: 0.3106 (t) REVERT: A 238 MET cc_start: 0.1118 (tmm) cc_final: 0.0885 (tmm) REVERT: A 1228 MET cc_start: 0.5276 (mtt) cc_final: 0.5032 (mtt) REVERT: A 1262 MET cc_start: 0.5583 (mmt) cc_final: 0.3894 (mpp) REVERT: E 110 MET cc_start: 0.6063 (tmm) cc_final: 0.5219 (mmm) REVERT: U 76 MET cc_start: 0.7370 (mmm) cc_final: 0.7060 (mmm) REVERT: W 316 MET cc_start: 0.1941 (ppp) cc_final: 0.1606 (ppp) REVERT: a 1131 MET cc_start: 0.1522 (ppp) cc_final: 0.1173 (tmm) REVERT: a 1624 MET cc_start: 0.7491 (tmm) cc_final: 0.7241 (ppp) REVERT: b 1138 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8538 (p) REVERT: d 725 MET cc_start: 0.8939 (tpp) cc_final: 0.8610 (tpp) REVERT: f 14 MET cc_start: 0.7846 (mmm) cc_final: 0.7394 (mmm) REVERT: f 317 MET cc_start: 0.4465 (ppp) cc_final: 0.3307 (ppp) REVERT: f 434 MET cc_start: 0.4005 (mtm) cc_final: 0.3532 (ttt) REVERT: g 125 MET cc_start: 0.8434 (mmm) cc_final: 0.8182 (mmm) REVERT: g 230 MET cc_start: 0.8345 (mmm) cc_final: 0.7996 (mmm) REVERT: g 597 TYR cc_start: 0.8509 (OUTLIER) cc_final: 0.8115 (t80) REVERT: i 250 MET cc_start: 0.7511 (tpt) cc_final: 0.7029 (mmm) REVERT: i 489 MET cc_start: 0.7384 (mpp) cc_final: 0.7006 (mmp) REVERT: k 319 MET cc_start: 0.6356 (tmm) cc_final: 0.5932 (tmm) REVERT: p 208 MET cc_start: 0.7822 (ptm) cc_final: 0.7608 (ptm) outliers start: 89 outliers final: 60 residues processed: 485 average time/residue: 0.8556 time to fit residues: 749.1420 Evaluate side-chains 470 residues out of total 11617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 407 time to evaluate : 9.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 1102 MET Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 908 MET Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain G residue 134 ASP Chi-restraints excluded: chain K residue 70 LYS Chi-restraints excluded: chain M residue 1630 SER Chi-restraints excluded: chain V residue 82 SER Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 416 GLN Chi-restraints excluded: chain W residue 448 THR Chi-restraints excluded: chain a residue 1039 PHE Chi-restraints excluded: chain a residue 2113 ASN Chi-restraints excluded: chain a residue 2124 THR Chi-restraints excluded: chain b residue 262 LEU Chi-restraints excluded: chain b residue 339 MET Chi-restraints excluded: chain b residue 544 LEU Chi-restraints excluded: chain b residue 725 ASP Chi-restraints excluded: chain b residue 1011 ILE Chi-restraints excluded: chain b residue 1138 THR Chi-restraints excluded: chain b residue 1147 ILE Chi-restraints excluded: chain b residue 1182 ASP Chi-restraints excluded: chain d residue 196 VAL Chi-restraints excluded: chain d residue 414 ASP Chi-restraints excluded: chain d residue 486 LEU Chi-restraints excluded: chain d residue 662 THR Chi-restraints excluded: chain d residue 681 VAL Chi-restraints excluded: chain d residue 704 THR Chi-restraints excluded: chain e residue 550 LEU Chi-restraints excluded: chain e residue 565 THR Chi-restraints excluded: chain e residue 578 LEU Chi-restraints excluded: chain e residue 609 ASP Chi-restraints excluded: chain f residue 171 LEU Chi-restraints excluded: chain g residue 271 LEU Chi-restraints excluded: chain g residue 283 THR Chi-restraints excluded: chain g residue 578 LEU Chi-restraints excluded: chain g residue 597 TYR Chi-restraints excluded: chain g residue 598 HIS Chi-restraints excluded: chain g residue 696 ASP Chi-restraints excluded: chain g residue 777 LEU Chi-restraints excluded: chain g residue 787 VAL Chi-restraints excluded: chain g residue 831 VAL Chi-restraints excluded: chain g residue 906 VAL Chi-restraints excluded: chain h residue 803 ILE Chi-restraints excluded: chain h residue 821 LEU Chi-restraints excluded: chain i residue 305 ILE Chi-restraints excluded: chain i residue 307 ASP Chi-restraints excluded: chain i residue 317 ASP Chi-restraints excluded: chain k residue 93 THR Chi-restraints excluded: chain p residue 501 THR Chi-restraints excluded: chain q residue 142 VAL Chi-restraints excluded: chain q residue 156 THR Chi-restraints excluded: chain q residue 175 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1314 random chunks: chunk 783 optimal weight: 0.4980 chunk 505 optimal weight: 40.0000 chunk 756 optimal weight: 6.9990 chunk 381 optimal weight: 50.0000 chunk 248 optimal weight: 5.9990 chunk 245 optimal weight: 8.9990 chunk 805 optimal weight: 4.9990 chunk 862 optimal weight: 8.9990 chunk 626 optimal weight: 7.9990 chunk 118 optimal weight: 50.0000 chunk 995 optimal weight: 10.0000 overall best weight: 5.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 742 ASN A 825 ASN A 861 GLN A1236 ASN ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN B 525 ASN B 842 HIS ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 585 ASN ** a1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 93 HIS d 148 GLN ** d 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 864 GLN e 452 HIS ** e 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 356 ASN ** g 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 879 GLN h 892 ASN ** h 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 13 GLN ** q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 103136 Z= 0.329 Angle : 0.638 19.730 140175 Z= 0.316 Chirality : 0.041 0.285 16239 Planarity : 0.004 0.069 17889 Dihedral : 8.390 167.136 14936 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.41 % Favored : 95.55 % Rotamer: Outliers : 0.94 % Allowed : 12.77 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.08), residues: 12886 helix: 1.67 (0.06), residues: 7104 sheet: -0.29 (0.16), residues: 1044 loop : -0.59 (0.09), residues: 4738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP e 902 HIS 0.013 0.001 HIS a1294 PHE 0.032 0.001 PHE e 570 TYR 0.022 0.002 TYR i 429 ARG 0.005 0.000 ARG k 258 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25772 Ramachandran restraints generated. 12886 Oldfield, 0 Emsley, 12886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25772 Ramachandran restraints generated. 12886 Oldfield, 0 Emsley, 12886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 11617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 410 time to evaluate : 9.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 VAL cc_start: 0.3642 (OUTLIER) cc_final: 0.3060 (t) REVERT: A 238 MET cc_start: 0.0622 (tmm) cc_final: 0.0315 (tmm) REVERT: A 1228 MET cc_start: 0.5473 (mtt) cc_final: 0.5211 (mtt) REVERT: A 1262 MET cc_start: 0.5801 (mmt) cc_final: 0.5099 (mpp) REVERT: B 1125 MET cc_start: 0.6327 (tpt) cc_final: 0.4845 (ppp) REVERT: E 110 MET cc_start: 0.6424 (tmm) cc_final: 0.5637 (mmm) REVERT: W 316 MET cc_start: 0.1856 (ppp) cc_final: 0.1526 (ppp) REVERT: W 338 MET cc_start: 0.3125 (tpp) cc_final: 0.2897 (tpp) REVERT: a 1131 MET cc_start: 0.1701 (ppp) cc_final: 0.1378 (tmm) REVERT: a 1624 MET cc_start: 0.7523 (tmm) cc_final: 0.7311 (ppp) REVERT: b 1199 MET cc_start: 0.8719 (ttp) cc_final: 0.8446 (tmm) REVERT: d 725 MET cc_start: 0.8973 (tpp) cc_final: 0.8674 (tpp) REVERT: f 14 MET cc_start: 0.7832 (mmm) cc_final: 0.7473 (mmm) REVERT: f 317 MET cc_start: 0.4572 (ppp) cc_final: 0.3373 (ppp) REVERT: f 434 MET cc_start: 0.3981 (mtm) cc_final: 0.3524 (ttt) REVERT: g 230 MET cc_start: 0.8355 (mmm) cc_final: 0.7987 (mmm) REVERT: g 597 TYR cc_start: 0.8685 (OUTLIER) cc_final: 0.8240 (t80) REVERT: i 250 MET cc_start: 0.7844 (tpt) cc_final: 0.7532 (mmm) REVERT: i 489 MET cc_start: 0.7444 (mpp) cc_final: 0.7197 (mmt) REVERT: k 319 MET cc_start: 0.6139 (tmm) cc_final: 0.5672 (tmm) REVERT: p 208 MET cc_start: 0.7800 (ptm) cc_final: 0.7555 (ptm) outliers start: 97 outliers final: 69 residues processed: 492 average time/residue: 0.8693 time to fit residues: 773.7069 Evaluate side-chains 478 residues out of total 11617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 407 time to evaluate : 9.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 908 MET Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 134 ASP Chi-restraints excluded: chain K residue 70 LYS Chi-restraints excluded: chain M residue 1630 SER Chi-restraints excluded: chain V residue 82 SER Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 448 THR Chi-restraints excluded: chain a residue 2113 ASN Chi-restraints excluded: chain a residue 2124 THR Chi-restraints excluded: chain b residue 262 LEU Chi-restraints excluded: chain b residue 339 MET Chi-restraints excluded: chain b residue 538 VAL Chi-restraints excluded: chain b residue 794 THR Chi-restraints excluded: chain b residue 1011 ILE Chi-restraints excluded: chain b residue 1136 VAL Chi-restraints excluded: chain b residue 1138 THR Chi-restraints excluded: chain b residue 1147 ILE Chi-restraints excluded: chain b residue 1182 ASP Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 196 VAL Chi-restraints excluded: chain d residue 414 ASP Chi-restraints excluded: chain d residue 486 LEU Chi-restraints excluded: chain d residue 662 THR Chi-restraints excluded: chain d residue 681 VAL Chi-restraints excluded: chain d residue 704 THR Chi-restraints excluded: chain d residue 843 VAL Chi-restraints excluded: chain e residue 550 LEU Chi-restraints excluded: chain e residue 578 LEU Chi-restraints excluded: chain e residue 609 ASP Chi-restraints excluded: chain f residue 171 LEU Chi-restraints excluded: chain f residue 202 VAL Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain g residue 283 THR Chi-restraints excluded: chain g residue 597 TYR Chi-restraints excluded: chain g residue 598 HIS Chi-restraints excluded: chain g residue 696 ASP Chi-restraints excluded: chain g residue 722 LEU Chi-restraints excluded: chain g residue 777 LEU Chi-restraints excluded: chain g residue 787 VAL Chi-restraints excluded: chain g residue 831 VAL Chi-restraints excluded: chain g residue 906 VAL Chi-restraints excluded: chain h residue 543 THR Chi-restraints excluded: chain h residue 803 ILE Chi-restraints excluded: chain h residue 821 LEU Chi-restraints excluded: chain i residue 160 ASP Chi-restraints excluded: chain i residue 305 ILE Chi-restraints excluded: chain i residue 307 ASP Chi-restraints excluded: chain i residue 317 ASP Chi-restraints excluded: chain k residue 62 ASP Chi-restraints excluded: chain k residue 93 THR Chi-restraints excluded: chain p residue 501 THR Chi-restraints excluded: chain p residue 540 VAL Chi-restraints excluded: chain q residue 142 VAL Chi-restraints excluded: chain q residue 156 THR Chi-restraints excluded: chain q residue 175 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1314 random chunks: chunk 1152 optimal weight: 3.9990 chunk 1213 optimal weight: 50.0000 chunk 1106 optimal weight: 5.9990 chunk 1180 optimal weight: 30.0000 chunk 1212 optimal weight: 20.0000 chunk 710 optimal weight: 7.9990 chunk 514 optimal weight: 10.0000 chunk 926 optimal weight: 1.9990 chunk 362 optimal weight: 0.7980 chunk 1066 optimal weight: 10.0000 chunk 1116 optimal weight: 1.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 93 HIS ** b 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 148 GLN ** d 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 864 GLN ** e 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 926 ASN ** g 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 549 ASN ** q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 103136 Z= 0.213 Angle : 0.582 15.278 140175 Z= 0.287 Chirality : 0.040 0.306 16239 Planarity : 0.004 0.067 17889 Dihedral : 8.347 167.435 14936 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.98 % Favored : 95.97 % Rotamer: Outliers : 0.76 % Allowed : 13.10 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.08), residues: 12886 helix: 1.80 (0.06), residues: 7100 sheet: -0.32 (0.16), residues: 1055 loop : -0.56 (0.10), residues: 4731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP e 902 HIS 0.008 0.001 HIS C 265 PHE 0.025 0.001 PHE i 394 TYR 0.030 0.001 TYR L 17 ARG 0.003 0.000 ARG b 564 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25772 Ramachandran restraints generated. 12886 Oldfield, 0 Emsley, 12886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25772 Ramachandran restraints generated. 12886 Oldfield, 0 Emsley, 12886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 11617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 412 time to evaluate : 9.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 VAL cc_start: 0.3543 (OUTLIER) cc_final: 0.2968 (t) REVERT: A 238 MET cc_start: 0.0729 (tmm) cc_final: 0.0476 (tmm) REVERT: A 1228 MET cc_start: 0.5315 (mtt) cc_final: 0.5038 (mtt) REVERT: A 1262 MET cc_start: 0.5804 (mmt) cc_final: 0.5155 (mpp) REVERT: B 525 ASN cc_start: 0.7754 (OUTLIER) cc_final: 0.7453 (m-40) REVERT: B 1125 MET cc_start: 0.6113 (tpt) cc_final: 0.4540 (ppp) REVERT: E 110 MET cc_start: 0.6429 (tmm) cc_final: 0.5640 (mmm) REVERT: W 316 MET cc_start: 0.1845 (ppp) cc_final: 0.1506 (ppp) REVERT: a 1131 MET cc_start: 0.1628 (ppp) cc_final: 0.1301 (tmm) REVERT: a 1624 MET cc_start: 0.7439 (tmm) cc_final: 0.7205 (ppp) REVERT: b 1138 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8545 (p) REVERT: d 725 MET cc_start: 0.8970 (tpp) cc_final: 0.8618 (tpp) REVERT: f 14 MET cc_start: 0.7752 (mmm) cc_final: 0.7393 (mmm) REVERT: f 317 MET cc_start: 0.4550 (ppp) cc_final: 0.3363 (ppp) REVERT: f 434 MET cc_start: 0.4054 (mtm) cc_final: 0.3591 (ttt) REVERT: g 125 MET cc_start: 0.8420 (mmm) cc_final: 0.8193 (mmm) REVERT: g 230 MET cc_start: 0.8362 (mmm) cc_final: 0.8038 (mmm) REVERT: g 597 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.8147 (t80) REVERT: i 1 MET cc_start: 0.7121 (tmm) cc_final: 0.6811 (ttp) REVERT: i 250 MET cc_start: 0.7766 (tpt) cc_final: 0.7495 (mmm) REVERT: i 441 MET cc_start: 0.6236 (tpp) cc_final: 0.5802 (mmm) REVERT: k 319 MET cc_start: 0.6462 (tmm) cc_final: 0.5929 (tmm) REVERT: p 521 MET cc_start: 0.8110 (mmp) cc_final: 0.7892 (mpp) outliers start: 78 outliers final: 63 residues processed: 479 average time/residue: 0.8752 time to fit residues: 754.2422 Evaluate side-chains 471 residues out of total 11617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 404 time to evaluate : 9.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 908 MET Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain K residue 70 LYS Chi-restraints excluded: chain M residue 1630 SER Chi-restraints excluded: chain V residue 82 SER Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 448 THR Chi-restraints excluded: chain a residue 2113 ASN Chi-restraints excluded: chain a residue 2124 THR Chi-restraints excluded: chain b residue 262 LEU Chi-restraints excluded: chain b residue 339 MET Chi-restraints excluded: chain b residue 538 VAL Chi-restraints excluded: chain b residue 544 LEU Chi-restraints excluded: chain b residue 1011 ILE Chi-restraints excluded: chain b residue 1136 VAL Chi-restraints excluded: chain b residue 1138 THR Chi-restraints excluded: chain b residue 1147 ILE Chi-restraints excluded: chain b residue 1182 ASP Chi-restraints excluded: chain d residue 196 VAL Chi-restraints excluded: chain d residue 414 ASP Chi-restraints excluded: chain d residue 486 LEU Chi-restraints excluded: chain d residue 662 THR Chi-restraints excluded: chain d residue 681 VAL Chi-restraints excluded: chain d residue 704 THR Chi-restraints excluded: chain d residue 843 VAL Chi-restraints excluded: chain e residue 550 LEU Chi-restraints excluded: chain e residue 578 LEU Chi-restraints excluded: chain e residue 609 ASP Chi-restraints excluded: chain e residue 914 MET Chi-restraints excluded: chain f residue 171 LEU Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain g residue 283 THR Chi-restraints excluded: chain g residue 597 TYR Chi-restraints excluded: chain g residue 598 HIS Chi-restraints excluded: chain g residue 696 ASP Chi-restraints excluded: chain g residue 777 LEU Chi-restraints excluded: chain g residue 787 VAL Chi-restraints excluded: chain g residue 831 VAL Chi-restraints excluded: chain g residue 906 VAL Chi-restraints excluded: chain h residue 543 THR Chi-restraints excluded: chain h residue 803 ILE Chi-restraints excluded: chain h residue 821 LEU Chi-restraints excluded: chain i residue 305 ILE Chi-restraints excluded: chain i residue 307 ASP Chi-restraints excluded: chain i residue 317 ASP Chi-restraints excluded: chain k residue 62 ASP Chi-restraints excluded: chain k residue 93 THR Chi-restraints excluded: chain p residue 501 THR Chi-restraints excluded: chain q residue 142 VAL Chi-restraints excluded: chain q residue 156 THR Chi-restraints excluded: chain q residue 175 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1314 random chunks: chunk 1176 optimal weight: 6.9990 chunk 774 optimal weight: 8.9990 chunk 1247 optimal weight: 7.9990 chunk 761 optimal weight: 3.9990 chunk 592 optimal weight: 20.0000 chunk 867 optimal weight: 4.9990 chunk 1309 optimal weight: 0.9990 chunk 1204 optimal weight: 20.0000 chunk 1042 optimal weight: 7.9990 chunk 108 optimal weight: 30.0000 chunk 805 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 GLN ** A 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 ASN ** K 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 40 ASN ** U 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 294 GLN ** W 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 93 HIS ** b 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 148 GLN d 492 ASN ** d 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 864 GLN ** e 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 438 ASN ** h 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 549 ASN ** q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 103136 Z= 0.285 Angle : 0.627 15.980 140175 Z= 0.309 Chirality : 0.041 0.337 16239 Planarity : 0.004 0.067 17889 Dihedral : 8.360 167.979 14936 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.42 % Favored : 95.53 % Rotamer: Outliers : 0.71 % Allowed : 13.31 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.08), residues: 12886 helix: 1.73 (0.06), residues: 7110 sheet: -0.38 (0.16), residues: 1055 loop : -0.56 (0.10), residues: 4721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP e 902 HIS 0.009 0.001 HIS C 265 PHE 0.024 0.001 PHE h 866 TYR 0.027 0.001 TYR g 771 ARG 0.005 0.000 ARG U 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25772 Ramachandran restraints generated. 12886 Oldfield, 0 Emsley, 12886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25772 Ramachandran restraints generated. 12886 Oldfield, 0 Emsley, 12886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 11617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 408 time to evaluate : 9.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.0808 (tmm) cc_final: 0.0463 (tmm) REVERT: A 329 MET cc_start: 0.6312 (tpp) cc_final: 0.5582 (tpp) REVERT: A 1228 MET cc_start: 0.5497 (mtt) cc_final: 0.5193 (mtt) REVERT: A 1262 MET cc_start: 0.5867 (mmt) cc_final: 0.5308 (mpp) REVERT: B 840 MET cc_start: 0.1452 (mmm) cc_final: 0.1135 (mmp) REVERT: B 1125 MET cc_start: 0.6057 (tpt) cc_final: 0.4527 (ppp) REVERT: D 90 LYS cc_start: 0.1751 (OUTLIER) cc_final: 0.1423 (pttm) REVERT: E 110 MET cc_start: 0.6488 (tmm) cc_final: 0.5654 (mmm) REVERT: U 92 MET cc_start: 0.5759 (mmm) cc_final: 0.5434 (mmm) REVERT: W 316 MET cc_start: 0.1914 (ppp) cc_final: 0.1564 (ppp) REVERT: a 1286 MET cc_start: 0.8934 (ppp) cc_final: 0.8635 (ppp) REVERT: a 1624 MET cc_start: 0.7461 (tmm) cc_final: 0.7219 (ppp) REVERT: b 743 MET cc_start: 0.8681 (tpp) cc_final: 0.8373 (tpp) REVERT: d 725 MET cc_start: 0.8964 (tpp) cc_final: 0.8646 (tpp) REVERT: f 14 MET cc_start: 0.7788 (mmm) cc_final: 0.7422 (mmm) REVERT: f 317 MET cc_start: 0.4592 (ppp) cc_final: 0.3382 (ppp) REVERT: f 434 MET cc_start: 0.4084 (mtm) cc_final: 0.3608 (ttt) REVERT: g 230 MET cc_start: 0.8354 (mmm) cc_final: 0.8016 (mmm) REVERT: g 597 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.8224 (t80) REVERT: i 1 MET cc_start: 0.7147 (tmm) cc_final: 0.6865 (ttp) REVERT: i 250 MET cc_start: 0.7845 (tpt) cc_final: 0.7567 (mmm) REVERT: i 441 MET cc_start: 0.6353 (tpp) cc_final: 0.5523 (mmm) REVERT: k 319 MET cc_start: 0.6359 (tmm) cc_final: 0.5745 (tmm) REVERT: p 521 MET cc_start: 0.8073 (mmp) cc_final: 0.7780 (mpp) outliers start: 73 outliers final: 65 residues processed: 469 average time/residue: 0.8504 time to fit residues: 718.6288 Evaluate side-chains 470 residues out of total 11617 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 403 time to evaluate : 9.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 908 MET Chi-restraints excluded: chain B residue 965 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain D residue 90 LYS Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain K residue 70 LYS Chi-restraints excluded: chain M residue 1630 SER Chi-restraints excluded: chain V residue 82 SER Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 448 THR Chi-restraints excluded: chain a residue 2113 ASN Chi-restraints excluded: chain a residue 2124 THR Chi-restraints excluded: chain b residue 262 LEU Chi-restraints excluded: chain b residue 339 MET Chi-restraints excluded: chain b residue 538 VAL Chi-restraints excluded: chain b residue 544 LEU Chi-restraints excluded: chain b residue 1011 ILE Chi-restraints excluded: chain b residue 1136 VAL Chi-restraints excluded: chain b residue 1138 THR Chi-restraints excluded: chain b residue 1147 ILE Chi-restraints excluded: chain b residue 1182 ASP Chi-restraints excluded: chain d residue 196 VAL Chi-restraints excluded: chain d residue 414 ASP Chi-restraints excluded: chain d residue 486 LEU Chi-restraints excluded: chain d residue 662 THR Chi-restraints excluded: chain d residue 681 VAL Chi-restraints excluded: chain d residue 704 THR Chi-restraints excluded: chain d residue 843 VAL Chi-restraints excluded: chain e residue 550 LEU Chi-restraints excluded: chain e residue 578 LEU Chi-restraints excluded: chain e residue 609 ASP Chi-restraints excluded: chain e residue 914 MET Chi-restraints excluded: chain f residue 171 LEU Chi-restraints excluded: chain g residue 283 THR Chi-restraints excluded: chain g residue 286 THR Chi-restraints excluded: chain g residue 597 TYR Chi-restraints excluded: chain g residue 598 HIS Chi-restraints excluded: chain g residue 696 ASP Chi-restraints excluded: chain g residue 777 LEU Chi-restraints excluded: chain g residue 787 VAL Chi-restraints excluded: chain g residue 831 VAL Chi-restraints excluded: chain g residue 906 VAL Chi-restraints excluded: chain h residue 543 THR Chi-restraints excluded: chain h residue 803 ILE Chi-restraints excluded: chain h residue 821 LEU Chi-restraints excluded: chain i residue 160 ASP Chi-restraints excluded: chain i residue 305 ILE Chi-restraints excluded: chain i residue 307 ASP Chi-restraints excluded: chain i residue 317 ASP Chi-restraints excluded: chain k residue 62 ASP Chi-restraints excluded: chain k residue 93 THR Chi-restraints excluded: chain p residue 501 THR Chi-restraints excluded: chain p residue 540 VAL Chi-restraints excluded: chain q residue 142 VAL Chi-restraints excluded: chain q residue 156 THR Chi-restraints excluded: chain q residue 175 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1314 random chunks: chunk 639 optimal weight: 0.8980 chunk 828 optimal weight: 7.9990 chunk 1110 optimal weight: 0.9980 chunk 319 optimal weight: 30.0000 chunk 961 optimal weight: 0.6980 chunk 153 optimal weight: 0.0870 chunk 289 optimal weight: 20.0000 chunk 1044 optimal weight: 30.0000 chunk 436 optimal weight: 50.0000 chunk 1072 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 overall best weight: 1.5360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 HIS ** A1445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 749 HIS ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 44 ASN ** U 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 27 GLN b 93 HIS b 622 GLN d 148 GLN d 492 ASN ** d 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 864 GLN e 499 GLN ** e 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 362 HIS ** g 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 579 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 549 ASN ** q 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.070311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.042212 restraints weight = 818790.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.041031 restraints weight = 496834.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.041053 restraints weight = 446349.788| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3287 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 33 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 34 | |-----------------------------------------------------------------------------| r_final: 0.3287 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 103136 Z= 0.166 Angle : 0.585 16.371 140175 Z= 0.286 Chirality : 0.040 0.271 16239 Planarity : 0.004 0.067 17889 Dihedral : 8.302 168.134 14936 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.83 % Favored : 96.12 % Rotamer: Outliers : 0.67 % Allowed : 13.52 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.08), residues: 12886 helix: 1.88 (0.06), residues: 7094 sheet: -0.40 (0.16), residues: 1064 loop : -0.53 (0.10), residues: 4728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP e 902 HIS 0.008 0.001 HIS C 265 PHE 0.028 0.001 PHE B 47 TYR 0.027 0.001 TYR L 17 ARG 0.006 0.000 ARG A1345 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17141.29 seconds wall clock time: 309 minutes 38.21 seconds (18578.21 seconds total)