Starting phenix.real_space_refine on Sat Dec 28 15:15:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tmt_26002/12_2024/7tmt_26002.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tmt_26002/12_2024/7tmt_26002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tmt_26002/12_2024/7tmt_26002.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tmt_26002/12_2024/7tmt_26002.map" model { file = "/net/cci-nas-00/data/ceres_data/7tmt_26002/12_2024/7tmt_26002.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tmt_26002/12_2024/7tmt_26002.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 144 5.16 5 C 33489 2.51 5 N 9607 2.21 5 O 10191 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 53433 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 4545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4545 Classifications: {'peptide': 593} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 562} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3688 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 448} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 4541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4541 Classifications: {'peptide': 593} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 562} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP%COO:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 3690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3690 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 448} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "E" Number of atoms: 4578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4578 Classifications: {'peptide': 593} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 562} Chain: "F" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3712 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 451} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'HIS:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1202 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 170} Link IDs: {'PTRANS': 6, 'TRANS': 214} Unresolved non-hydrogen bonds: 562 Unresolved non-hydrogen angles: 697 Unresolved non-hydrogen dihedrals: 436 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 1, 'ASN:plan1': 14, 'ASP:plan': 12, 'PHE:plan': 3, 'GLU:plan': 27, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 283 Chain: "H" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 587 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 1, 'TRANS': 110} Unresolved non-hydrogen bonds: 293 Unresolved non-hydrogen angles: 361 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 147 Chain: "I" Number of atoms: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1324 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 136} Link IDs: {'PTRANS': 6, 'TRANS': 214} Unresolved non-hydrogen bonds: 443 Unresolved non-hydrogen angles: 554 Unresolved non-hydrogen dihedrals: 342 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 2, 'ASN:plan1': 13, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 22, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 244 Chain: "J" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 584 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 1, 'TRANS': 109} Unresolved non-hydrogen bonds: 292 Unresolved non-hydrogen angles: 360 Unresolved non-hydrogen dihedrals: 236 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 151 Chain: "K" Number of atoms: 1332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1332 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 146} Link IDs: {'PTRANS': 6, 'TRANS': 217} Unresolved non-hydrogen bonds: 462 Unresolved non-hydrogen angles: 580 Unresolved non-hydrogen dihedrals: 352 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 2, 'ASN:plan1': 15, 'ASP:plan': 12, 'PHE:plan': 1, 'GLU:plan': 24, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 235 Chain: "L" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 594 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 1, 'TRANS': 109} Unresolved non-hydrogen bonds: 281 Unresolved non-hydrogen angles: 347 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 142 Chain: "M" Number of atoms: 1444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1444 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 3, 'TRANS': 219} Unresolved non-hydrogen bonds: 358 Unresolved non-hydrogen angles: 455 Unresolved non-hydrogen dihedrals: 281 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 204 Chain: "N" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 581 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 109} Unresolved non-hydrogen bonds: 359 Unresolved non-hydrogen angles: 458 Unresolved non-hydrogen dihedrals: 286 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 9, 'PHE:plan': 7, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 207 Chain: "O" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 1792 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 301} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 337} Chain breaks: 1 Unresolved non-hydrogen bonds: 1080 Unresolved non-hydrogen angles: 1381 Unresolved non-hydrogen dihedrals: 888 Unresolved non-hydrogen chiralities: 109 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 6, 'TYR:plan': 12, 'ASN:plan1': 21, 'TRP:plan': 3, 'ASP:plan': 18, 'PHE:plan': 20, 'GLU:plan': 27, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 590 Chain: "P" Number of atoms: 2197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 2197 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 396} Link IDs: {'PTRANS': 9, 'TRANS': 428} Chain breaks: 2 Unresolved non-hydrogen bonds: 1393 Unresolved non-hydrogen angles: 1777 Unresolved non-hydrogen dihedrals: 1129 Unresolved non-hydrogen chiralities: 151 Planarities with less than four sites: {'GLN:plan1': 24, 'ASP:plan': 29, 'TYR:plan': 11, 'ASN:plan1': 24, 'TRP:plan': 5, 'HIS:plan': 10, 'PHE:plan': 16, 'GLU:plan': 32, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 721 Chain: "a" Number of atoms: 4317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 4317 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 492} Link IDs: {'PTRANS': 21, 'TRANS': 712} Chain breaks: 2 Unresolved non-hydrogen bonds: 1686 Unresolved non-hydrogen angles: 2146 Unresolved non-hydrogen dihedrals: 1346 Unresolved non-hydrogen chiralities: 201 Planarities with less than four sites: {'GLN:plan1': 24, 'HIS:plan': 8, 'TYR:plan': 17, 'ASN:plan1': 21, 'TRP:plan': 1, 'ASP:plan': 35, 'PHE:plan': 23, 'GLU:plan': 38, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 837 Chain: "b" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 315 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 1, 'TRANS': 50} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 16 Chain: "c" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1165 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 111} Link IDs: {'PTRANS': 2, 'TRANS': 195} Unresolved non-hydrogen bonds: 315 Unresolved non-hydrogen angles: 409 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'HIS:plan': 1, 'GLN%COO:plan1': 1, 'ASN:plan1': 4, 'ASP:plan': 3, 'PHE:plan': 6, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 88 Chain: "d" Number of atoms: 2209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2209 Classifications: {'peptide': 343} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 190} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 333} Unresolved non-hydrogen bonds: 586 Unresolved non-hydrogen angles: 752 Unresolved non-hydrogen dihedrals: 446 Unresolved non-hydrogen chiralities: 72 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 7, 'TYR:plan': 5, 'ASN:plan1': 14, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 21, 'TYR%COO:plan': 1, 'ASP:plan': 19} Unresolved non-hydrogen planarities: 311 Chain: "e" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 428 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 3, 'TRANS': 60} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "f" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 358 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 2, 'TRANS': 60} Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 181 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 68 Chain: "g" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 911 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 306 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 73 Chain: "h" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 872 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 275 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 90 Chain: "i" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 957 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 243 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 76 Chain: "j" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 926 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 284 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 61 Chain: "k" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 902 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 245 Unresolved non-hydrogen angles: 323 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 4, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 76 Chain: "l" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 922 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 293 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 67 Chain: "m" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 932 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 211 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "n" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 871 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 277 Unresolved non-hydrogen angles: 363 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 97 Chain: "o" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 930 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 6, 'TRANS': 151} Unresolved non-hydrogen bonds: 225 Unresolved non-hydrogen angles: 290 Unresolved non-hydrogen dihedrals: 173 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 2, 'ASP:plan': 2, 'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 23.71, per 1000 atoms: 0.44 Number of scatterers: 53433 At special positions: 0 Unit cell: (142.998, 187.46, 260.762, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 144 16.00 P 2 15.00 O 10191 8.00 N 9607 7.00 C 33489 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.85 Conformation dependent library (CDL) restraints added in 6.6 seconds 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15198 Finding SS restraints... Secondary structure from input PDB file: 304 helices and 45 sheets defined 64.5% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.73 Creating SS restraints... Processing helix chain 'A' and resid 113 through 119 Processing helix chain 'A' and resid 237 through 243 Processing helix chain 'A' and resid 261 through 272 removed outlier: 3.955A pdb=" N ILE A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 297 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 310 through 313 Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 331 through 346 removed outlier: 3.528A pdb=" N GLN A 346 " --> pdb=" O TYR A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 372 removed outlier: 3.791A pdb=" N TRP A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 394 Processing helix chain 'A' and resid 425 through 435 Processing helix chain 'A' and resid 442 through 448 Processing helix chain 'A' and resid 467 through 475 removed outlier: 3.977A pdb=" N SER A 473 " --> pdb=" O LYS A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 502 removed outlier: 4.035A pdb=" N GLN A 497 " --> pdb=" O GLU A 493 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 507 Processing helix chain 'A' and resid 508 through 525 Processing helix chain 'A' and resid 539 through 563 Processing helix chain 'A' and resid 566 through 574 Processing helix chain 'A' and resid 574 through 584 Processing helix chain 'A' and resid 585 through 587 No H-bonds generated for 'chain 'A' and resid 585 through 587' Processing helix chain 'A' and resid 588 through 591 Processing helix chain 'A' and resid 592 through 616 removed outlier: 3.794A pdb=" N ASP A 616 " --> pdb=" O ALA A 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 21 removed outlier: 4.142A pdb=" N GLN B 18 " --> pdb=" O ALA B 15 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN B 21 " --> pdb=" O GLN B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 144 Processing helix chain 'B' and resid 155 through 160 removed outlier: 3.533A pdb=" N THR B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 191 removed outlier: 4.151A pdb=" N ALA B 185 " --> pdb=" O ASN B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 202 through 206 removed outlier: 4.311A pdb=" N GLU B 206 " --> pdb=" O GLY B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 232 removed outlier: 3.881A pdb=" N PHE B 224 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN B 232 " --> pdb=" O ASP B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 238 removed outlier: 3.717A pdb=" N GLU B 236 " --> pdb=" O GLY B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 269 Proline residue: B 256 - end of helix Processing helix chain 'B' and resid 280 through 295 removed outlier: 3.539A pdb=" N TYR B 284 " --> pdb=" O ASP B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 304 removed outlier: 3.589A pdb=" N GLY B 303 " --> pdb=" O GLY B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 306 No H-bonds generated for 'chain 'B' and resid 305 through 306' Processing helix chain 'B' and resid 307 through 317 removed outlier: 4.203A pdb=" N ILE B 315 " --> pdb=" O ASP B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 354 Processing helix chain 'B' and resid 361 through 367 removed outlier: 3.607A pdb=" N LYS B 367 " --> pdb=" O GLN B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 387 removed outlier: 3.712A pdb=" N ILE B 387 " --> pdb=" O LYS B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 417 Processing helix chain 'B' and resid 426 through 443 Processing helix chain 'B' and resid 453 through 466 Processing helix chain 'B' and resid 477 through 485 removed outlier: 4.241A pdb=" N GLU B 483 " --> pdb=" O LYS B 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 119 Processing helix chain 'C' and resid 237 through 243 Processing helix chain 'C' and resid 261 through 272 removed outlier: 3.570A pdb=" N GLN C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 297 Processing helix chain 'C' and resid 298 through 300 No H-bonds generated for 'chain 'C' and resid 298 through 300' Processing helix chain 'C' and resid 310 through 313 Processing helix chain 'C' and resid 325 through 345 removed outlier: 4.413A pdb=" N ILE C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR C 334 " --> pdb=" O GLU C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 372 removed outlier: 3.795A pdb=" N TRP C 360 " --> pdb=" O SER C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 393 Processing helix chain 'C' and resid 425 through 433 removed outlier: 3.827A pdb=" N GLY C 433 " --> pdb=" O THR C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 448 Processing helix chain 'C' and resid 467 through 475 removed outlier: 4.123A pdb=" N SER C 473 " --> pdb=" O LYS C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 500 Processing helix chain 'C' and resid 503 through 507 removed outlier: 4.099A pdb=" N ALA C 506 " --> pdb=" O GLY C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 525 Processing helix chain 'C' and resid 539 through 563 Processing helix chain 'C' and resid 566 through 574 Processing helix chain 'C' and resid 574 through 584 Processing helix chain 'C' and resid 585 through 587 No H-bonds generated for 'chain 'C' and resid 585 through 587' Processing helix chain 'C' and resid 588 through 591 Processing helix chain 'C' and resid 592 through 616 removed outlier: 3.944A pdb=" N GLY C 598 " --> pdb=" O LYS C 594 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP C 616 " --> pdb=" O ALA C 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 20 Processing helix chain 'D' and resid 155 through 160 Processing helix chain 'D' and resid 179 through 191 Processing helix chain 'D' and resid 200 through 205 removed outlier: 4.024A pdb=" N HIS D 204 " --> pdb=" O VAL D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 233 Processing helix chain 'D' and resid 234 through 238 removed outlier: 4.072A pdb=" N THR D 238 " --> pdb=" O LEU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 253 Processing helix chain 'D' and resid 254 through 269 Processing helix chain 'D' and resid 280 through 295 removed outlier: 3.645A pdb=" N TYR D 284 " --> pdb=" O ASP D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 317 removed outlier: 4.378A pdb=" N ILE D 315 " --> pdb=" O ASP D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 341 removed outlier: 3.752A pdb=" N ASP D 341 " --> pdb=" O PRO D 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 338 through 341' Processing helix chain 'D' and resid 344 through 354 removed outlier: 3.725A pdb=" N TYR D 352 " --> pdb=" O ASP D 348 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE D 353 " --> pdb=" O LEU D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 367 Processing helix chain 'D' and resid 382 through 386 removed outlier: 3.540A pdb=" N SER D 385 " --> pdb=" O LEU D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 420 Processing helix chain 'D' and resid 421 through 425 Processing helix chain 'D' and resid 426 through 443 Processing helix chain 'D' and resid 453 through 466 Processing helix chain 'D' and resid 467 through 468 No H-bonds generated for 'chain 'D' and resid 467 through 468' Processing helix chain 'D' and resid 469 through 473 removed outlier: 3.681A pdb=" N LEU D 473 " --> pdb=" O LYS D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 485 Processing helix chain 'E' and resid 111 through 120 removed outlier: 3.511A pdb=" N ILE E 115 " --> pdb=" O PRO E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 243 Processing helix chain 'E' and resid 261 through 273 Processing helix chain 'E' and resid 287 through 297 removed outlier: 4.577A pdb=" N VAL E 293 " --> pdb=" O GLU E 289 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU E 294 " --> pdb=" O MET E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 345 removed outlier: 4.050A pdb=" N ALA E 331 " --> pdb=" O ALA E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 372 removed outlier: 3.696A pdb=" N TRP E 360 " --> pdb=" O SER E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 380 Processing helix chain 'E' and resid 381 through 382 No H-bonds generated for 'chain 'E' and resid 381 through 382' Processing helix chain 'E' and resid 383 through 394 Processing helix chain 'E' and resid 418 through 422 Processing helix chain 'E' and resid 425 through 432 Processing helix chain 'E' and resid 442 through 448 removed outlier: 3.888A pdb=" N ARG E 448 " --> pdb=" O LYS E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 475 Processing helix chain 'E' and resid 477 through 503 removed outlier: 4.014A pdb=" N LEU E 501 " --> pdb=" O GLN E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 525 Processing helix chain 'E' and resid 539 through 564 Processing helix chain 'E' and resid 566 through 574 removed outlier: 4.487A pdb=" N ASP E 572 " --> pdb=" O SER E 568 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER E 573 " --> pdb=" O LYS E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 584 Processing helix chain 'E' and resid 585 through 587 No H-bonds generated for 'chain 'E' and resid 585 through 587' Processing helix chain 'E' and resid 588 through 591 Processing helix chain 'E' and resid 592 through 615 removed outlier: 3.541A pdb=" N THR E 615 " --> pdb=" O PHE E 611 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 18 Processing helix chain 'F' and resid 155 through 160 removed outlier: 3.524A pdb=" N THR F 160 " --> pdb=" O SER F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 191 Processing helix chain 'F' and resid 218 through 231 Processing helix chain 'F' and resid 249 through 252 Processing helix chain 'F' and resid 253 through 268 removed outlier: 4.223A pdb=" N ARG F 257 " --> pdb=" O ILE F 253 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR F 261 " --> pdb=" O ARG F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 295 removed outlier: 3.532A pdb=" N ARG F 295 " --> pdb=" O VAL F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 317 Processing helix chain 'F' and resid 344 through 354 Processing helix chain 'F' and resid 361 through 368 removed outlier: 3.568A pdb=" N HIS F 365 " --> pdb=" O ASP F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 421 Processing helix chain 'F' and resid 426 through 443 Processing helix chain 'F' and resid 453 through 466 Processing helix chain 'F' and resid 469 through 473 removed outlier: 3.639A pdb=" N LEU F 473 " --> pdb=" O LYS F 470 " (cutoff:3.500A) Processing helix chain 'F' and resid 477 through 485 Processing helix chain 'G' and resid 9 through 113 removed outlier: 3.756A pdb=" N VAL G 51 " --> pdb=" O LYS G 47 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN G 53 " --> pdb=" O ASN G 49 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS G 65 " --> pdb=" O ASN G 61 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN G 112 " --> pdb=" O SER G 108 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASN G 113 " --> pdb=" O GLY G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 133 Proline residue: G 119 - end of helix Processing helix chain 'G' and resid 142 through 144 No H-bonds generated for 'chain 'G' and resid 142 through 144' Processing helix chain 'G' and resid 145 through 164 removed outlier: 5.074A pdb=" N ASP G 154 " --> pdb=" O GLU G 150 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ASP G 155 " --> pdb=" O SER G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 214 removed outlier: 3.640A pdb=" N GLU G 212 " --> pdb=" O LYS G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 223 Processing helix chain 'H' and resid 4 through 104 removed outlier: 3.770A pdb=" N GLY H 78 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ASP H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ASP H 93 " --> pdb=" O LYS H 89 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS H 96 " --> pdb=" O ASP H 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 113 removed outlier: 3.666A pdb=" N ASN I 113 " --> pdb=" O GLY I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 132 Proline residue: I 119 - end of helix Processing helix chain 'I' and resid 145 through 152 Processing helix chain 'I' and resid 152 through 164 Processing helix chain 'I' and resid 202 through 214 removed outlier: 3.984A pdb=" N LYS I 208 " --> pdb=" O GLU I 204 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 220 Processing helix chain 'J' and resid 3 through 64 removed outlier: 3.546A pdb=" N TYR J 46 " --> pdb=" O GLU J 42 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU J 58 " --> pdb=" O LEU J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 104 removed outlier: 3.577A pdb=" N GLU J 79 " --> pdb=" O GLY J 75 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ASP J 92 " --> pdb=" O GLU J 88 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ASP J 93 " --> pdb=" O LYS J 89 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU J 100 " --> pdb=" O LYS J 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 113 removed outlier: 3.907A pdb=" N GLY K 60 " --> pdb=" O ASN K 56 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASN K 61 " --> pdb=" O ASN K 57 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE K 80 " --> pdb=" O THR K 76 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN K 113 " --> pdb=" O GLY K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 133 Proline residue: K 119 - end of helix Processing helix chain 'K' and resid 144 through 164 removed outlier: 4.573A pdb=" N LEU K 148 " --> pdb=" O ARG K 144 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ASP K 154 " --> pdb=" O GLU K 150 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ASP K 155 " --> pdb=" O SER K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 214 removed outlier: 4.006A pdb=" N LYS K 208 " --> pdb=" O GLU K 204 " (cutoff:3.500A) Processing helix chain 'K' and resid 214 through 224 Processing helix chain 'L' and resid 3 through 104 removed outlier: 3.668A pdb=" N VAL L 65 " --> pdb=" O ASN L 61 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY L 66 " --> pdb=" O ALA L 62 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS L 70 " --> pdb=" O GLY L 66 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY L 78 " --> pdb=" O ALA L 74 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU L 79 " --> pdb=" O GLY L 75 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ASP L 92 " --> pdb=" O GLU L 88 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASP L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS L 96 " --> pdb=" O ASP L 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 11 through 76 removed outlier: 4.291A pdb=" N MET M 61 " --> pdb=" O MET M 57 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 84 Processing helix chain 'M' and resid 126 through 172 removed outlier: 4.206A pdb=" N GLN M 130 " --> pdb=" O GLY M 126 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE M 156 " --> pdb=" O LEU M 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 187 Proline residue: M 179 - end of helix Processing helix chain 'M' and resid 187 through 218 Processing helix chain 'M' and resid 219 through 224 Processing helix chain 'N' and resid 15 through 22 Processing helix chain 'N' and resid 40 through 44 removed outlier: 3.820A pdb=" N GLY N 43 " --> pdb=" O TYR N 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 60 removed outlier: 3.791A pdb=" N ILE N 50 " --> pdb=" O THR N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 75 Processing helix chain 'N' and resid 76 through 84 Processing helix chain 'N' and resid 106 through 116 Processing helix chain 'O' and resid 29 through 41 Processing helix chain 'O' and resid 57 through 89 removed outlier: 3.545A pdb=" N LEU O 89 " --> pdb=" O ILE O 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 111 Processing helix chain 'O' and resid 126 through 166 removed outlier: 3.664A pdb=" N LYS O 166 " --> pdb=" O ALA O 162 " (cutoff:3.500A) Processing helix chain 'O' and resid 202 through 212 removed outlier: 3.884A pdb=" N THR O 212 " --> pdb=" O LYS O 208 " (cutoff:3.500A) Processing helix chain 'O' and resid 227 through 231 Processing helix chain 'O' and resid 239 through 241 No H-bonds generated for 'chain 'O' and resid 239 through 241' Processing helix chain 'O' and resid 242 through 252 removed outlier: 4.106A pdb=" N ALA O 250 " --> pdb=" O PHE O 246 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU O 252 " --> pdb=" O THR O 248 " (cutoff:3.500A) Processing helix chain 'O' and resid 263 through 320 removed outlier: 3.897A pdb=" N VAL O 297 " --> pdb=" O LYS O 293 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N PHE O 300 " --> pdb=" O TYR O 296 " (cutoff:3.500A) Processing helix chain 'O' and resid 333 through 335 No H-bonds generated for 'chain 'O' and resid 333 through 335' Processing helix chain 'O' and resid 336 through 348 removed outlier: 3.520A pdb=" N LYS O 341 " --> pdb=" O LEU O 337 " (cutoff:3.500A) Processing helix chain 'P' and resid 11 through 21 removed outlier: 4.525A pdb=" N ARG P 17 " --> pdb=" O PHE P 13 " (cutoff:3.500A) Processing helix chain 'P' and resid 24 through 28 removed outlier: 3.836A pdb=" N TRP P 27 " --> pdb=" O SER P 24 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP P 28 " --> pdb=" O VAL P 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 24 through 28' Processing helix chain 'P' and resid 29 through 34 Processing helix chain 'P' and resid 37 through 48 Processing helix chain 'P' and resid 76 through 87 Processing helix chain 'P' and resid 89 through 106 Processing helix chain 'P' and resid 109 through 120 Processing helix chain 'P' and resid 121 through 131 removed outlier: 4.100A pdb=" N GLU P 125 " --> pdb=" O PRO P 121 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLN P 126 " --> pdb=" O LYS P 122 " (cutoff:3.500A) Processing helix chain 'P' and resid 135 through 151 Processing helix chain 'P' and resid 157 through 166 Processing helix chain 'P' and resid 167 through 176 Processing helix chain 'P' and resid 179 through 194 Processing helix chain 'P' and resid 196 through 206 removed outlier: 3.657A pdb=" N VAL P 202 " --> pdb=" O GLU P 198 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU P 205 " --> pdb=" O ASP P 201 " (cutoff:3.500A) Processing helix chain 'P' and resid 207 through 209 No H-bonds generated for 'chain 'P' and resid 207 through 209' Processing helix chain 'P' and resid 210 through 221 removed outlier: 3.548A pdb=" N LEU P 214 " --> pdb=" O PHE P 210 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA P 221 " --> pdb=" O ILE P 217 " (cutoff:3.500A) Processing helix chain 'P' and resid 237 through 254 removed outlier: 4.307A pdb=" N SER P 246 " --> pdb=" O LEU P 242 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU P 247 " --> pdb=" O GLN P 243 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU P 249 " --> pdb=" O HIS P 245 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE P 250 " --> pdb=" O SER P 246 " (cutoff:3.500A) Processing helix chain 'P' and resid 256 through 267 removed outlier: 3.697A pdb=" N GLN P 265 " --> pdb=" O ASN P 261 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS P 266 " --> pdb=" O GLU P 262 " (cutoff:3.500A) Processing helix chain 'P' and resid 267 through 281 removed outlier: 4.135A pdb=" N LYS P 279 " --> pdb=" O LEU P 275 " (cutoff:3.500A) Processing helix chain 'P' and resid 283 through 299 Processing helix chain 'P' and resid 304 through 317 removed outlier: 4.132A pdb=" N LYS P 310 " --> pdb=" O LYS P 306 " (cutoff:3.500A) Processing helix chain 'P' and resid 317 through 328 removed outlier: 4.303A pdb=" N THR P 321 " --> pdb=" O ASN P 317 " (cutoff:3.500A) Processing helix chain 'P' and resid 332 through 346 Processing helix chain 'P' and resid 346 through 355 removed outlier: 3.747A pdb=" N TYR P 350 " --> pdb=" O LEU P 346 " (cutoff:3.500A) Processing helix chain 'P' and resid 355 through 365 Processing helix chain 'P' and resid 371 through 374 Processing helix chain 'P' and resid 375 through 380 Processing helix chain 'P' and resid 380 through 408 removed outlier: 4.336A pdb=" N ILE P 384 " --> pdb=" O TRP P 380 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS P 389 " --> pdb=" O ASP P 385 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ASP P 390 " --> pdb=" O GLU P 386 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASN P 391 " --> pdb=" O PHE P 387 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ILE P 394 " --> pdb=" O ASP P 390 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N PHE P 395 " --> pdb=" O ASN P 391 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU P 398 " --> pdb=" O ILE P 394 " (cutoff:3.500A) Processing helix chain 'P' and resid 413 through 434 Processing helix chain 'P' and resid 434 through 444 removed outlier: 3.653A pdb=" N ILE P 438 " --> pdb=" O LEU P 434 " (cutoff:3.500A) Processing helix chain 'P' and resid 445 through 453 Processing helix chain 'P' and resid 458 through 478 Processing helix chain 'a' and resid 25 through 37 Processing helix chain 'a' and resid 44 through 48 removed outlier: 3.707A pdb=" N LYS a 47 " --> pdb=" O LEU a 44 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL a 48 " --> pdb=" O ASN a 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 44 through 48' Processing helix chain 'a' and resid 49 through 53 Processing helix chain 'a' and resid 55 through 79 Processing helix chain 'a' and resid 84 through 99 removed outlier: 4.006A pdb=" N THR a 88 " --> pdb=" O TYR a 84 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR a 91 " --> pdb=" O ASP a 87 " (cutoff:3.500A) Processing helix chain 'a' and resid 106 through 142 removed outlier: 3.805A pdb=" N GLN a 140 " --> pdb=" O ASN a 136 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG a 142 " --> pdb=" O LEU a 138 " (cutoff:3.500A) Processing helix chain 'a' and resid 195 through 207 Processing helix chain 'a' and resid 242 through 256 Processing helix chain 'a' and resid 266 through 326 removed outlier: 4.019A pdb=" N GLU a 305 " --> pdb=" O ALA a 301 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ASP a 307 " --> pdb=" O ALA a 303 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N SER a 308 " --> pdb=" O LYS a 304 " (cutoff:3.500A) Processing helix chain 'a' and resid 345 through 360 Processing helix chain 'a' and resid 387 through 396 Processing helix chain 'a' and resid 408 through 424 removed outlier: 4.225A pdb=" N ILE a 412 " --> pdb=" O GLY a 408 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL a 413 " --> pdb=" O LEU a 409 " (cutoff:3.500A) Proline residue: a 416 - end of helix removed outlier: 3.614A pdb=" N MET a 422 " --> pdb=" O MET a 418 " (cutoff:3.500A) Processing helix chain 'a' and resid 425 through 442 removed outlier: 4.099A pdb=" N ASN a 442 " --> pdb=" O SER a 438 " (cutoff:3.500A) Processing helix chain 'a' and resid 442 through 449 Processing helix chain 'a' and resid 454 through 461 Processing helix chain 'a' and resid 463 through 479 Processing helix chain 'a' and resid 527 through 562 removed outlier: 3.863A pdb=" N LYS a 538 " --> pdb=" O SER a 534 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE a 562 " --> pdb=" O ASN a 558 " (cutoff:3.500A) Processing helix chain 'a' and resid 564 through 596 removed outlier: 4.606A pdb=" N ILE a 573 " --> pdb=" O ILE a 569 " (cutoff:3.500A) Proline residue: a 574 - end of helix removed outlier: 4.961A pdb=" N TYR a 585 " --> pdb=" O GLY a 581 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP a 594 " --> pdb=" O ILE a 590 " (cutoff:3.500A) Processing helix chain 'a' and resid 597 through 602 Processing helix chain 'a' and resid 607 through 618 Processing helix chain 'a' and resid 627 through 651 removed outlier: 3.973A pdb=" N LYS a 632 " --> pdb=" O PRO a 628 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE a 645 " --> pdb=" O ALA a 641 " (cutoff:3.500A) Proline residue: a 646 - end of helix Processing helix chain 'a' and resid 711 through 733 removed outlier: 3.550A pdb=" N GLN a 715 " --> pdb=" O ILE a 711 " (cutoff:3.500A) Processing helix chain 'a' and resid 733 through 759 removed outlier: 4.202A pdb=" N TRP a 737 " --> pdb=" O TYR a 733 " (cutoff:3.500A) Processing helix chain 'a' and resid 763 through 788 removed outlier: 3.592A pdb=" N ALA a 772 " --> pdb=" O PHE a 768 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA a 775 " --> pdb=" O VAL a 771 " (cutoff:3.500A) Processing helix chain 'a' and resid 788 through 804 Processing helix chain 'a' and resid 804 through 810 Processing helix chain 'b' and resid 220 through 245 removed outlier: 4.073A pdb=" N CYS b 226 " --> pdb=" O GLY b 222 " (cutoff:3.500A) Processing helix chain 'b' and resid 250 through 255 Processing helix chain 'c' and resid 17 through 38 Processing helix chain 'c' and resid 41 through 51 removed outlier: 3.802A pdb=" N ILE c 45 " --> pdb=" O HIS c 41 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN c 46 " --> pdb=" O GLY c 42 " (cutoff:3.500A) Processing helix chain 'c' and resid 55 through 91 removed outlier: 3.861A pdb=" N VAL c 91 " --> pdb=" O ILE c 87 " (cutoff:3.500A) Processing helix chain 'c' and resid 93 through 100 removed outlier: 3.591A pdb=" N THR c 97 " --> pdb=" O ALA c 93 " (cutoff:3.500A) Processing helix chain 'c' and resid 100 through 125 removed outlier: 3.726A pdb=" N ILE c 117 " --> pdb=" O TYR c 113 " (cutoff:3.500A) Processing helix chain 'c' and resid 130 through 175 removed outlier: 4.051A pdb=" N LEU c 139 " --> pdb=" O SER c 135 " (cutoff:3.500A) Processing helix chain 'c' and resid 177 through 209 removed outlier: 4.269A pdb=" N VAL c 186 " --> pdb=" O VAL c 182 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ILE c 187 " --> pdb=" O LYS c 183 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU c 188 " --> pdb=" O ILE c 184 " (cutoff:3.500A) Processing helix chain 'd' and resid 5 through 22 removed outlier: 3.985A pdb=" N ASP d 9 " --> pdb=" O TYR d 5 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N PHE d 12 " --> pdb=" O ILE d 8 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ILE d 13 " --> pdb=" O ASP d 9 " (cutoff:3.500A) Processing helix chain 'd' and resid 26 through 36 Processing helix chain 'd' and resid 38 through 49 Processing helix chain 'd' and resid 52 through 57 removed outlier: 4.583A pdb=" N LEU d 55 " --> pdb=" O GLY d 52 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 86 Processing helix chain 'd' and resid 89 through 112 removed outlier: 3.784A pdb=" N TYR d 102 " --> pdb=" O ILE d 98 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP d 105 " --> pdb=" O GLY d 101 " (cutoff:3.500A) Processing helix chain 'd' and resid 120 through 127 Processing helix chain 'd' and resid 128 through 132 Processing helix chain 'd' and resid 135 through 142 Processing helix chain 'd' and resid 144 through 154 Processing helix chain 'd' and resid 158 through 165 removed outlier: 3.525A pdb=" N CYS d 165 " --> pdb=" O TYR d 161 " (cutoff:3.500A) Processing helix chain 'd' and resid 179 through 200 Processing helix chain 'd' and resid 203 through 228 removed outlier: 4.238A pdb=" N LEU d 228 " --> pdb=" O ALA d 224 " (cutoff:3.500A) Processing helix chain 'd' and resid 234 through 242 removed outlier: 3.596A pdb=" N ASP d 240 " --> pdb=" O ASP d 236 " (cutoff:3.500A) Processing helix chain 'd' and resid 250 through 259 removed outlier: 3.945A pdb=" N HIS d 255 " --> pdb=" O LEU d 251 " (cutoff:3.500A) Processing helix chain 'd' and resid 261 through 270 removed outlier: 3.596A pdb=" N VAL d 265 " --> pdb=" O ASP d 261 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG d 266 " --> pdb=" O PHE d 262 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU d 269 " --> pdb=" O VAL d 265 " (cutoff:3.500A) Processing helix chain 'd' and resid 283 through 302 removed outlier: 3.773A pdb=" N GLN d 302 " --> pdb=" O ASP d 298 " (cutoff:3.500A) Processing helix chain 'd' and resid 306 through 332 removed outlier: 4.072A pdb=" N TRP d 310 " --> pdb=" O ILE d 306 " (cutoff:3.500A) Processing helix chain 'd' and resid 337 through 341 removed outlier: 4.040A pdb=" N TYR d 341 " --> pdb=" O ILE d 338 " (cutoff:3.500A) Processing helix chain 'e' and resid 5 through 24 Processing helix chain 'e' and resid 29 through 57 removed outlier: 4.367A pdb=" N HIS e 57 " --> pdb=" O LEU e 53 " (cutoff:3.500A) Processing helix chain 'f' and resid 12 through 34 removed outlier: 4.028A pdb=" N LEU f 16 " --> pdb=" O CYS f 12 " (cutoff:3.500A) Processing helix chain 'f' and resid 37 through 41 Processing helix chain 'f' and resid 47 through 70 Processing helix chain 'g' and resid 7 through 46 removed outlier: 3.919A pdb=" N PHE g 11 " --> pdb=" O VAL g 7 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE g 21 " --> pdb=" O CYS g 17 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY g 38 " --> pdb=" O LYS g 34 " (cutoff:3.500A) Processing helix chain 'g' and resid 47 through 50 Processing helix chain 'g' and resid 51 through 52 No H-bonds generated for 'chain 'g' and resid 51 through 52' Processing helix chain 'g' and resid 53 through 77 removed outlier: 4.195A pdb=" N VAL g 57 " --> pdb=" O ASN g 53 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER g 77 " --> pdb=" O LEU g 73 " (cutoff:3.500A) Processing helix chain 'g' and resid 83 through 122 Processing helix chain 'g' and resid 125 through 155 removed outlier: 3.660A pdb=" N LEU g 131 " --> pdb=" O VAL g 127 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU g 139 " --> pdb=" O PHE g 135 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY g 140 " --> pdb=" O ALA g 136 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR g 155 " --> pdb=" O ASN g 151 " (cutoff:3.500A) Processing helix chain 'h' and resid 8 through 44 removed outlier: 4.111A pdb=" N PHE h 12 " --> pdb=" O TYR h 8 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY h 13 " --> pdb=" O ALA h 9 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR h 24 " --> pdb=" O ALA h 20 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL h 44 " --> pdb=" O CYS h 40 " (cutoff:3.500A) Processing helix chain 'h' and resid 46 through 51 Processing helix chain 'h' and resid 54 through 78 removed outlier: 3.959A pdb=" N SER h 77 " --> pdb=" O LEU h 73 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU h 78 " --> pdb=" O VAL h 74 " (cutoff:3.500A) Processing helix chain 'h' and resid 83 through 122 Processing helix chain 'h' and resid 125 through 156 removed outlier: 3.866A pdb=" N LEU h 139 " --> pdb=" O PHE h 135 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY h 140 " --> pdb=" O ALA h 136 " (cutoff:3.500A) Processing helix chain 'i' and resid 8 through 46 removed outlier: 4.388A pdb=" N ILE i 15 " --> pdb=" O PHE i 11 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR i 24 " --> pdb=" O ALA i 20 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA i 41 " --> pdb=" O VAL i 37 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL i 44 " --> pdb=" O CYS i 40 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU i 45 " --> pdb=" O ALA i 41 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 54 Processing helix chain 'i' and resid 54 through 78 Processing helix chain 'i' and resid 83 through 122 Processing helix chain 'i' and resid 122 through 155 removed outlier: 3.653A pdb=" N PHE i 126 " --> pdb=" O GLN i 122 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY i 128 " --> pdb=" O ARG i 124 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE i 130 " --> pdb=" O PHE i 126 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LEU i 131 " --> pdb=" O VAL i 127 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE i 132 " --> pdb=" O GLY i 128 " (cutoff:3.500A) Processing helix chain 'j' and resid 7 through 44 removed outlier: 4.280A pdb=" N PHE j 11 " --> pdb=" O VAL j 7 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N THR j 24 " --> pdb=" O ALA j 20 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER j 25 " --> pdb=" O ILE j 21 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL j 44 " --> pdb=" O CYS j 40 " (cutoff:3.500A) Processing helix chain 'j' and resid 46 through 53 Processing helix chain 'j' and resid 53 through 78 removed outlier: 4.676A pdb=" N VAL j 57 " --> pdb=" O ASN j 53 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE j 63 " --> pdb=" O MET j 59 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA j 64 " --> pdb=" O ALA j 60 " (cutoff:3.500A) Processing helix chain 'j' and resid 83 through 120 Processing helix chain 'j' and resid 125 through 155 removed outlier: 3.858A pdb=" N THR j 155 " --> pdb=" O ASN j 151 " (cutoff:3.500A) Processing helix chain 'k' and resid 8 through 44 removed outlier: 3.784A pdb=" N SER k 25 " --> pdb=" O ILE k 21 " (cutoff:3.500A) Processing helix chain 'k' and resid 46 through 50 Processing helix chain 'k' and resid 51 through 52 No H-bonds generated for 'chain 'k' and resid 51 through 52' Processing helix chain 'k' and resid 53 through 78 removed outlier: 4.347A pdb=" N VAL k 57 " --> pdb=" O ASN k 53 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER k 77 " --> pdb=" O LEU k 73 " (cutoff:3.500A) Processing helix chain 'k' and resid 83 through 120 removed outlier: 3.683A pdb=" N SER k 120 " --> pdb=" O VAL k 116 " (cutoff:3.500A) Processing helix chain 'k' and resid 123 through 155 removed outlier: 4.204A pdb=" N VAL k 127 " --> pdb=" O PRO k 123 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR k 155 " --> pdb=" O ASN k 151 " (cutoff:3.500A) Processing helix chain 'l' and resid 8 through 46 removed outlier: 3.527A pdb=" N PHE l 12 " --> pdb=" O TYR l 8 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N CYS l 17 " --> pdb=" O GLY l 13 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR l 24 " --> pdb=" O ALA l 20 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY l 38 " --> pdb=" O LYS l 34 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA l 41 " --> pdb=" O VAL l 37 " (cutoff:3.500A) Processing helix chain 'l' and resid 47 through 50 Processing helix chain 'l' and resid 54 through 77 removed outlier: 3.589A pdb=" N ILE l 63 " --> pdb=" O MET l 59 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA l 64 " --> pdb=" O ALA l 60 " (cutoff:3.500A) Processing helix chain 'l' and resid 83 through 121 removed outlier: 4.408A pdb=" N GLN l 121 " --> pdb=" O ARG l 117 " (cutoff:3.500A) Processing helix chain 'l' and resid 124 through 154 removed outlier: 4.501A pdb=" N GLY l 128 " --> pdb=" O ARG l 124 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE l 135 " --> pdb=" O LEU l 131 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA l 136 " --> pdb=" O ILE l 132 " (cutoff:3.500A) Processing helix chain 'm' and resid 8 through 43 removed outlier: 3.731A pdb=" N THR m 24 " --> pdb=" O ALA m 20 " (cutoff:3.500A) Processing helix chain 'm' and resid 46 through 50 Processing helix chain 'm' and resid 51 through 53 No H-bonds generated for 'chain 'm' and resid 51 through 53' Processing helix chain 'm' and resid 54 through 78 Processing helix chain 'm' and resid 83 through 122 removed outlier: 3.684A pdb=" N GLN m 121 " --> pdb=" O ARG m 117 " (cutoff:3.500A) Processing helix chain 'm' and resid 125 through 155 removed outlier: 3.800A pdb=" N LEU m 131 " --> pdb=" O VAL m 127 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE m 132 " --> pdb=" O GLY m 128 " (cutoff:3.500A) Processing helix chain 'n' and resid 8 through 46 removed outlier: 4.263A pdb=" N PHE n 12 " --> pdb=" O TYR n 8 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLY n 13 " --> pdb=" O ALA n 9 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR n 24 " --> pdb=" O ALA n 20 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL n 44 " --> pdb=" O CYS n 40 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU n 45 " --> pdb=" O ALA n 41 " (cutoff:3.500A) Processing helix chain 'n' and resid 49 through 78 removed outlier: 4.713A pdb=" N VAL n 55 " --> pdb=" O PHE n 51 " (cutoff:3.500A) Proline residue: n 56 - end of helix removed outlier: 3.688A pdb=" N GLY n 67 " --> pdb=" O ILE n 63 " (cutoff:3.500A) Processing helix chain 'n' and resid 84 through 122 removed outlier: 3.862A pdb=" N ALA n 114 " --> pdb=" O ILE n 110 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG n 117 " --> pdb=" O ASP n 113 " (cutoff:3.500A) Processing helix chain 'n' and resid 124 through 158 removed outlier: 4.265A pdb=" N GLY n 128 " --> pdb=" O ARG n 124 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE n 135 " --> pdb=" O LEU n 131 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA n 136 " --> pdb=" O ILE n 132 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR n 155 " --> pdb=" O ASN n 151 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN n 156 " --> pdb=" O SER n 152 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP n 157 " --> pdb=" O ARG n 153 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL n 158 " --> pdb=" O ALA n 154 " (cutoff:3.500A) Processing helix chain 'o' and resid 14 through 52 removed outlier: 3.846A pdb=" N SER o 30 " --> pdb=" O ALA o 26 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE o 51 " --> pdb=" O GLY o 47 " (cutoff:3.500A) Processing helix chain 'o' and resid 53 through 56 Processing helix chain 'o' and resid 57 through 58 No H-bonds generated for 'chain 'o' and resid 57 through 58' Processing helix chain 'o' and resid 59 through 82 removed outlier: 4.312A pdb=" N VAL o 63 " --> pdb=" O SER o 59 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY o 82 " --> pdb=" O VAL o 78 " (cutoff:3.500A) Processing helix chain 'o' and resid 91 through 127 Processing helix chain 'o' and resid 128 through 129 No H-bonds generated for 'chain 'o' and resid 128 through 129' Processing helix chain 'o' and resid 130 through 132 No H-bonds generated for 'chain 'o' and resid 130 through 132' Processing helix chain 'o' and resid 133 through 164 removed outlier: 4.056A pdb=" N LEU o 139 " --> pdb=" O VAL o 135 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU o 147 " --> pdb=" O PHE o 143 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY o 148 " --> pdb=" O SER o 144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 31 removed outlier: 6.359A pdb=" N ILE A 36 " --> pdb=" O TYR A 28 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL A 30 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL A 34 " --> pdb=" O VAL A 30 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 34 through 38 current: chain 'A' and resid 56 through 64 removed outlier: 6.112A pdb=" N VAL A 60 " --> pdb=" O GLN A 71 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN A 71 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 62 " --> pdb=" O THR A 69 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 67 through 72 current: chain 'B' and resid 38 through 41 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 41 current: chain 'B' and resid 62 through 71 removed outlier: 6.464A pdb=" N ILE B 76 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE B 70 " --> pdb=" O ARG B 74 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARG B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 74 through 79 current: chain 'C' and resid 34 through 38 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 34 through 38 current: chain 'C' and resid 67 through 71 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 67 through 71 current: chain 'E' and resid 34 through 37 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 68 through 71 current: chain 'F' and resid 38 through 41 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 38 through 41 current: chain 'F' and resid 62 through 71 removed outlier: 5.496A pdb=" N VAL F 67 " --> pdb=" O GLN F 78 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLN F 78 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU F 69 " --> pdb=" O ILE F 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 96 Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 105 removed outlier: 6.801A pdb=" N ILE A 279 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ASP A 355 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL A 281 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N MET A 352 " --> pdb=" O VAL A 413 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ALA A 415 " --> pdb=" O MET A 352 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ALA A 354 " --> pdb=" O ALA A 415 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N THR A 252 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL A 416 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ILE A 254 " --> pdb=" O VAL A 416 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 170 through 172 removed outlier: 4.184A pdb=" N GLY A 159 " --> pdb=" O ILE A 172 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 151 through 152 removed outlier: 6.679A pdb=" N GLU A 199 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE A 202 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 398 through 399 Processing sheet with id=AA7, first strand: chain 'B' and resid 101 through 104 Processing sheet with id=AA8, first strand: chain 'B' and resid 151 through 152 Processing sheet with id=AA9, first strand: chain 'B' and resid 172 through 174 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 172 through 174 current: chain 'B' and resid 241 through 244 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 241 through 244 current: chain 'B' and resid 328 through 336 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 356 through 357 Processing sheet with id=AB2, first strand: chain 'C' and resid 47 through 51 removed outlier: 4.911A pdb=" N LYS C 90 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N LYS C 50 " --> pdb=" O THR C 88 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N THR C 88 " --> pdb=" O LYS C 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 104 through 105 removed outlier: 5.971A pdb=" N ILE C 278 " --> pdb=" O THR C 316 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL C 318 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TYR C 280 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASN C 320 " --> pdb=" O TYR C 280 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N GLY C 282 " --> pdb=" O ASN C 320 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 160 through 161 Processing sheet with id=AB5, first strand: chain 'C' and resid 151 through 152 removed outlier: 6.770A pdb=" N GLU C 199 " --> pdb=" O THR C 183 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ILE C 185 " --> pdb=" O ILE C 197 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ILE C 197 " --> pdb=" O ILE C 185 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 225 through 226 removed outlier: 4.039A pdb=" N GLU C 225 " --> pdb=" O VAL C 399 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 437 through 438 Processing sheet with id=AB8, first strand: chain 'D' and resid 26 through 27 Processing sheet with id=AB9, first strand: chain 'D' and resid 31 through 35 removed outlier: 5.647A pdb=" N VAL D 31 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLU D 42 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE D 70 " --> pdb=" O ARG D 74 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE D 76 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLU D 51 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE D 52 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU D 94 " --> pdb=" O ASN D 54 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 101 through 104 removed outlier: 3.521A pdb=" N ASP D 130 " --> pdb=" O VAL D 104 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 113 through 114 removed outlier: 6.291A pdb=" N PHE D 113 " --> pdb=" O LEU D 242 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N LEU D 244 " --> pdb=" O PHE D 113 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET D 215 " --> pdb=" O THR D 279 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 335 through 336 removed outlier: 6.552A pdb=" N PHE D 173 " --> pdb=" O VAL D 360 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 273 through 276 Processing sheet with id=AC5, first strand: chain 'E' and resid 93 through 96 Processing sheet with id=AC6, first strand: chain 'E' and resid 104 through 105 removed outlier: 6.518A pdb=" N ILE E 278 " --> pdb=" O THR E 316 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL E 318 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N TYR E 280 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASN E 320 " --> pdb=" O TYR E 280 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLY E 282 " --> pdb=" O ASN E 320 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE E 279 " --> pdb=" O ILE E 353 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N MET E 352 " --> pdb=" O VAL E 413 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N ALA E 415 " --> pdb=" O MET E 352 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA E 354 " --> pdb=" O ALA E 415 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR E 252 " --> pdb=" O ALA E 414 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 170 through 173 Processing sheet with id=AC8, first strand: chain 'E' and resid 151 through 152 removed outlier: 6.624A pdb=" N GLU E 199 " --> pdb=" O THR E 183 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 225 through 226 removed outlier: 3.825A pdb=" N GLU E 225 " --> pdb=" O VAL E 399 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 301 through 302 removed outlier: 3.826A pdb=" N GLU E 309 " --> pdb=" O THR E 302 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 144 through 145 removed outlier: 3.563A pdb=" N ILE F 145 " --> pdb=" O ARG F 321 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG F 321 " --> pdb=" O ILE F 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 151 through 152 Processing sheet with id=AD4, first strand: chain 'F' and resid 334 through 336 removed outlier: 5.946A pdb=" N ILE F 172 " --> pdb=" O LEU F 335 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 215 through 217 Processing sheet with id=AD6, first strand: chain 'F' and resid 273 through 274 Processing sheet with id=AD7, first strand: chain 'G' and resid 171 through 174 Processing sheet with id=AD8, first strand: chain 'I' and resid 171 through 174 removed outlier: 3.588A pdb=" N ALA I 137 " --> pdb=" O GLU I 171 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 171 through 174 removed outlier: 3.611A pdb=" N ALA K 137 " --> pdb=" O GLU K 171 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS K 140 " --> pdb=" O VAL K 189 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 65 through 66 removed outlier: 7.451A pdb=" N ALA N 65 " --> pdb=" O ILE N 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'O' and resid 14 through 16 removed outlier: 4.256A pdb=" N ILE O 14 " --> pdb=" O LYS O 328 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'a' and resid 40 through 41 removed outlier: 3.722A pdb=" N ILE a 367 " --> pdb=" O TYR a 20 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'a' and resid 233 through 235 removed outlier: 4.086A pdb=" N THR a 188 " --> pdb=" O TYR a 261 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL a 190 " --> pdb=" O ASN a 259 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN a 259 " --> pdb=" O VAL a 190 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'a' and resid 212 through 214 removed outlier: 3.758A pdb=" N PHE a 212 " --> pdb=" O PHE a 239 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE a 239 " --> pdb=" O PHE a 212 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE a 237 " --> pdb=" O LYS a 214 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'a' and resid 222 through 223 Processing sheet with id=AE7, first strand: chain 'a' and resid 378 through 379 Processing sheet with id=AE8, first strand: chain 'a' and resid 494 through 495 Processing sheet with id=AE9, first strand: chain 'a' and resid 506 through 507 removed outlier: 3.671A pdb=" N ILE a 506 " --> pdb=" O ARG e 64 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG e 64 " --> pdb=" O ILE a 506 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 4053 hydrogen bonds defined for protein. 11868 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: 19.73 Time building geometry restraints manager: 13.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 12915 1.33 - 1.45: 10543 1.45 - 1.57: 30613 1.57 - 1.69: 3 1.69 - 1.81: 247 Bond restraints: 54321 Sorted by residual: bond pdb=" CA THR C 130 " pdb=" C THR C 130 " ideal model delta sigma weight residual 1.524 1.554 -0.030 1.26e-02 6.30e+03 5.68e+00 bond pdb=" CB MET A 607 " pdb=" CG MET A 607 " ideal model delta sigma weight residual 1.520 1.450 0.070 3.00e-02 1.11e+03 5.39e+00 bond pdb=" N THR C 130 " pdb=" CA THR C 130 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.41e-02 5.03e+03 4.08e+00 bond pdb=" C ASP M 218 " pdb=" O ASP M 218 " ideal model delta sigma weight residual 1.234 1.209 0.025 1.40e-02 5.10e+03 3.19e+00 bond pdb=" N ASP C 129 " pdb=" CA ASP C 129 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.21e-02 6.83e+03 3.17e+00 ... (remaining 54316 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 73087 2.14 - 4.29: 1078 4.29 - 6.43: 154 6.43 - 8.58: 24 8.58 - 10.72: 3 Bond angle restraints: 74346 Sorted by residual: angle pdb=" N VAL D 375 " pdb=" CA VAL D 375 " pdb=" C VAL D 375 " ideal model delta sigma weight residual 110.42 118.78 -8.36 9.60e-01 1.09e+00 7.58e+01 angle pdb=" N ASP C 129 " pdb=" CA ASP C 129 " pdb=" C ASP C 129 " ideal model delta sigma weight residual 111.28 118.95 -7.67 1.09e+00 8.42e-01 4.95e+01 angle pdb=" N THR M 214 " pdb=" CA THR M 214 " pdb=" C THR M 214 " ideal model delta sigma weight residual 111.36 104.71 6.65 1.09e+00 8.42e-01 3.73e+01 angle pdb=" C ASN O 95 " pdb=" CA ASN O 95 " pdb=" CB ASN O 95 " ideal model delta sigma weight residual 117.23 110.31 6.92 1.36e+00 5.41e-01 2.59e+01 angle pdb=" C GLU O 189 " pdb=" CA GLU O 189 " pdb=" CB GLU O 189 " ideal model delta sigma weight residual 116.54 110.73 5.81 1.15e+00 7.56e-01 2.55e+01 ... (remaining 74341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.82: 31398 28.82 - 57.64: 660 57.64 - 86.46: 58 86.46 - 115.28: 12 115.28 - 144.10: 2 Dihedral angle restraints: 32130 sinusoidal: 8526 harmonic: 23604 Sorted by residual: dihedral pdb=" O1B ADP E 701 " pdb=" O3A ADP E 701 " pdb=" PB ADP E 701 " pdb=" PA ADP E 701 " ideal model delta sinusoidal sigma weight residual 300.00 155.90 144.10 1 2.00e+01 2.50e-03 4.34e+01 dihedral pdb=" C5' ADP E 701 " pdb=" O5' ADP E 701 " pdb=" PA ADP E 701 " pdb=" O2A ADP E 701 " ideal model delta sinusoidal sigma weight residual -60.00 66.21 -126.21 1 2.00e+01 2.50e-03 3.82e+01 dihedral pdb=" CA LEU M 217 " pdb=" C LEU M 217 " pdb=" N ASP M 218 " pdb=" CA ASP M 218 " ideal model delta harmonic sigma weight residual 180.00 151.67 28.33 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 32127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 6894 0.055 - 0.109: 1675 0.109 - 0.164: 175 0.164 - 0.219: 9 0.219 - 0.273: 2 Chirality restraints: 8755 Sorted by residual: chirality pdb=" CB ILE F 102 " pdb=" CA ILE F 102 " pdb=" CG1 ILE F 102 " pdb=" CG2 ILE F 102 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB ILE M 185 " pdb=" CA ILE M 185 " pdb=" CG1 ILE M 185 " pdb=" CG2 ILE M 185 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA TRP c 147 " pdb=" N TRP c 147 " pdb=" C TRP c 147 " pdb=" CB TRP c 147 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 8752 not shown) Planarity restraints: 10052 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP a 802 " -0.026 2.00e-02 2.50e+03 2.64e-02 1.74e+01 pdb=" CG TRP a 802 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 TRP a 802 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP a 802 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP a 802 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP a 802 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP a 802 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 802 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 802 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP a 802 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 95 " 0.026 2.00e-02 2.50e+03 2.42e-02 1.02e+01 pdb=" CG PHE D 95 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE D 95 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE D 95 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 95 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE D 95 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE D 95 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL i 55 " -0.045 5.00e-02 4.00e+02 6.63e-02 7.04e+00 pdb=" N PRO i 56 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO i 56 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO i 56 " -0.037 5.00e-02 4.00e+02 ... (remaining 10049 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 726 2.67 - 3.23: 56411 3.23 - 3.78: 88546 3.78 - 4.34: 107864 4.34 - 4.90: 179230 Nonbonded interactions: 432777 Sorted by model distance: nonbonded pdb=" OD1 ASP D 114 " pdb=" N GLY D 115 " model vdw 2.109 3.120 nonbonded pdb=" O GLY I 186 " pdb=" OG1 THR I 202 " model vdw 2.196 3.040 nonbonded pdb=" OH TYR F 284 " pdb=" OD2 ASP F 311 " model vdw 2.197 3.040 nonbonded pdb=" OH TYR c 57 " pdb=" O ALA c 128 " model vdw 2.206 3.040 nonbonded pdb=" OE2 GLU C 74 " pdb=" NH2 ARG C 110 " model vdw 2.208 3.120 ... (remaining 432772 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 24 through 128 or (resid 129 and (name N or name CA or nam \ e C or name O or name CB )) or resid 130 through 193 or (resid 194 and (name N o \ r name CA or name C or name O or name CB )) or resid 195 through 261 or (resid 2 \ 62 through 270 and (name N or name CA or name C or name O or name CB )) or resid \ 271 through 273 or (resid 274 through 277 and (name N or name CA or name C or n \ ame O or name CB )) or resid 278 through 615 or (resid 616 and (name N or name C \ A or name C or name O or name CB or name OXT)))) selection = (chain 'C' and (resid 24 through 284 or (resid 285 and (name N or name CA or nam \ e C or name O or name CB )) or resid 286 through 308 or (resid 309 and (name N o \ r name CA or name C or name O or name CB )) or resid 310 through 354 or (resid 3 \ 55 and (name N or name CA or name C or name O or name CB )) or resid 356 through \ 421 or (resid 422 and (name N or name CA or name C or name O or name CB )) or r \ esid 423 through 589 or (resid 590 through 591 and (name N or name CA or name C \ or name O or name CB )) or resid 592 or (resid 593 through 595 and (name N or na \ me CA or name C or name O or name CB )) or resid 596 through 616)) selection = (chain 'E' and (resid 24 through 128 or (resid 129 and (name N or name CA or nam \ e C or name O or name CB )) or resid 130 through 193 or (resid 194 and (name N o \ r name CA or name C or name O or name CB )) or resid 195 through 261 or (resid 2 \ 62 through 270 and (name N or name CA or name C or name O or name CB )) or resid \ 271 through 273 or (resid 274 through 277 and (name N or name CA or name C or n \ ame O or name CB )) or resid 278 through 284 or (resid 285 and (name N or name C \ A or name C or name O or name CB )) or resid 286 through 308 or (resid 309 and ( \ name N or name CA or name C or name O or name CB )) or resid 310 through 354 or \ (resid 355 and (name N or name CA or name C or name O or name CB )) or resid 356 \ through 421 or (resid 422 and (name N or name CA or name C or name O or name CB \ )) or resid 423 through 589 or (resid 590 through 591 and (name N or name CA or \ name C or name O or name CB )) or resid 592 or (resid 593 through 595 and (name \ N or name CA or name C or name O or name CB )) or resid 596 through 615 or (res \ id 616 and (name N or name CA or name C or name O or name CB or name OXT)))) } ncs_group { reference = (chain 'B' and (resid 14 through 192 or (resid 193 through 195 and (name N or na \ me CA or name C or name O or name CB )) or resid 196 through 487)) selection = (chain 'D' and (resid 14 through 105 or (resid 106 and (name N or name CA or nam \ e C or name O or name CB )) or resid 107 through 481 or (resid 482 and (name N o \ r name CA or name C or name O or name CB )) or resid 483 through 487)) selection = (chain 'F' and (resid 14 through 105 or (resid 106 and (name N or name CA or nam \ e C or name O or name CB )) or resid 107 through 204 or (resid 205 and (name N o \ r name CA or name C or name O or name CB )) or resid 206 through 481 or (resid 4 \ 82 and (name N or name CA or name C or name O or name CB )) or resid 483 through \ 487)) } ncs_group { reference = (chain 'G' and (resid 9 through 162 or (resid 163 through 164 and (name N or nam \ e CA or name C or name O or name CB )) or resid 165 or (resid 166 through 167 an \ d (name N or name CA or name C or name O or name CB )) or resid 168 through 198 \ or (resid 199 through 206 and (name N or name CA or name C or name O or name CB \ )) or resid 207 through 208 or (resid 209 through 215 and (name N or name CA or \ name C or name O or name CB )) or resid 216 through 222 or (resid 223 and (name \ N or name CA or name C or name O or name CB )) or resid 224 through 228)) selection = (chain 'I' and (resid 9 through 81 or (resid 82 through 97 and (name N or name C \ A or name C or name O or name CB )) or (resid 98 through 108 and (name N or name \ CA or name C or name O or name CB )) or resid 109 through 117 or (resid 118 and \ (name N or name CA or name C or name O or name CB )) or resid 119 or (resid 120 \ through 134 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 35 or (resid 136 through 137 and (name N or name CA or name C or name O or name \ CB )) or resid 138 through 147 or (resid 148 through 152 and (name N or name CA \ or name C or name O or name CB )) or resid 153 or (resid 154 through 156 and (na \ me N or name CA or name C or name O or name CB )) or resid 157 or (resid 158 thr \ ough 159 and (name N or name CA or name C or name O or name CB )) or resid 160 t \ hrough 162 or (resid 163 through 164 and (name N or name CA or name C or name O \ or name CB )) or resid 165 through 169 or (resid 170 through 177 and (name N or \ name CA or name C or name O or name CB )) or resid 178 or (resid 179 through 185 \ and (name N or name CA or name C or name O or name CB )) or (resid 186 through \ 206 and (name N or name CA or name C or name O or name CB )) or resid 207 throug \ h 214 or (resid 215 and (name N or name CA or name C or name O or name CB )) or \ resid 216 through 219 or (resid 220 and (name N or name CA or name C or name O o \ r name CB )) or resid 221 or (resid 222 through 223 and (name N or name CA or na \ me C or name O or name CB )) or resid 224 through 228)) selection = (chain 'K' and (resid 9 through 61 or (resid 62 through 97 and (name N or name C \ A or name C or name O or name CB )) or (resid 98 through 108 and (name N or name \ CA or name C or name O or name CB )) or (resid 109 through 116 and (name N or n \ ame CA or name C or name O or name CB )) or resid 117 or (resid 118 and (name N \ or name CA or name C or name O or name CB )) or resid 119 through 120 or (resid \ 121 through 134 and (name N or name CA or name C or name O or name CB )) or resi \ d 135 or (resid 136 through 137 and (name N or name CA or name C or name O or na \ me CB )) or resid 138 through 141 or (resid 142 through 152 and (name N or name \ CA or name C or name O or name CB )) or resid 153 through 157 or (resid 158 thro \ ugh 159 and (name N or name CA or name C or name O or name CB )) or resid 160 th \ rough 165 or (resid 166 through 167 and (name N or name CA or name C or name O o \ r name CB )) or resid 168 through 171 or (resid 172 through 177 and (name N or n \ ame CA or name C or name O or name CB )) or resid 178 through 180 or (resid 181 \ through 185 and (name N or name CA or name C or name O or name CB )) or (resid 1 \ 86 through 206 and (name N or name CA or name C or name O or name CB )) or resid \ 207 through 219 or (resid 220 and (name N or name CA or name C or name O or nam \ e CB )) or resid 221 through 228)) } ncs_group { reference = (chain 'H' and (resid 2 through 95 or (resid 96 through 103 and (name N or name \ CA or name C or name O or name CB )) or resid 104 through 109 or (resid 110 thro \ ugh 112 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'J' and (resid 2 through 88 or (resid 89 and (name N or name CA or name C \ or name O or name CB )) or resid 90 through 97 or (resid 98 through 103 and (na \ me N or name CA or name C or name O or name CB )) or resid 104 through 112)) selection = (chain 'L' and ((resid 2 through 83 and (name N or name CA or name C or name O o \ r name CB )) or resid 84 or (resid 85 through 89 and (name N or name CA or name \ C or name O or name CB )) or resid 90 through 97 or (resid 98 through 103 and (n \ ame N or name CA or name C or name O or name CB )) or resid 104 through 109 or ( \ resid 110 through 112 and (name N or name CA or name C or name O or name CB )))) \ } ncs_group { reference = (chain 'g' and ((resid 1 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 or (resid 7 through 9 and (name N or name CA or name C or \ name O or name CB )) or resid 10 or (resid 11 through 12 and (name N or name CA \ or name C or name O or name CB )) or (resid 13 through 46 and (name N or name C \ A or name C or name O or name CB )) or resid 47 through 51 or (resid 52 through \ 55 and (name N or name CA or name C or name O or name CB )) or resid 56 or (resi \ d 57 through 60 and (name N or name CA or name C or name O or name CB )) or (res \ id 61 through 66 and (name N or name CA or name C or name O or name CB )) or (re \ sid 67 through 78 and (name N or name CA or name C or name O or name CB )) or re \ sid 79 or (resid 80 through 86 and (name N or name CA or name C or name O or nam \ e CB )) or resid 87 or (resid 88 through 91 and (name N or name CA or name C or \ name O or name CB )) or (resid 92 through 108 and (name N or name CA or name C o \ r name O or name CB )) or (resid 109 through 122 and (name N or name CA or name \ C or name O or name CB )) or resid 123 through 125 or (resid 126 through 127 and \ (name N or name CA or name C or name O or name CB )) or (resid 128 through 139 \ and (name N or name CA or name C or name O or name CB )) or (resid 140 through 1 \ 59 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'h' and (resid 1 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 50 or (resid 51 through 55 and (nam \ e N or name CA or name C or name O or name CB )) or resid 56 through 77 or (resi \ d 78 and (name N or name CA or name C or name O or name CB )) or resid 79 or (re \ sid 80 through 86 and (name N or name CA or name C or name O or name CB )) or re \ sid 87 or (resid 88 through 91 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 92 through 104 and (name N or name CA or name C or name O or n \ ame CB )) or resid 105 or (resid 106 through 108 and (name N or name CA or name \ C or name O or name CB )) or (resid 109 through 117 and (name N or name CA or na \ me C or name O or name CB )) or resid 118 through 125 or (resid 126 through 127 \ and (name N or name CA or name C or name O or name CB )) or (resid 128 through 1 \ 39 and (name N or name CA or name C or name O or name CB )) or resid 140 or (res \ id 141 through 142 and (name N or name CA or name C or name O or name CB )) or r \ esid 143 or (resid 144 through 159 and (name N or name CA or name C or name O or \ name CB )))) selection = (chain 'i' and ((resid 1 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 or (resid 7 through 9 and (name N or name CA or name C or \ name O or name CB )) or resid 10 through 11 or (resid 12 and (name N or name CA \ or name C or name O or name CB )) or (resid 13 through 26 and (name N or name C \ A or name C or name O or name CB )) or (resid 27 through 30 and (name N or name \ CA or name C or name O or name CB )) or resid 31 or (resid 32 through 35 and (na \ me N or name CA or name C or name O or name CB )) or resid 36 or (resid 37 and ( \ name N or name CA or name C or name O or name CB )) or resid 38 or (resid 39 thr \ ough 46 and (name N or name CA or name C or name O or name CB )) or resid 47 thr \ ough 48 or (resid 49 through 55 and (name N or name CA or name C or name O or na \ me CB )) or resid 56 through 57 or (resid 58 through 60 and (name N or name CA o \ r name C or name O or name CB )) or (resid 61 through 66 and (name N or name CA \ or name C or name O or name CB )) or resid 67 or (resid 68 through 78 and (name \ N or name CA or name C or name O or name CB )) or resid 79 or (resid 80 through \ 86 and (name N or name CA or name C or name O or name CB )) or resid 87 or (resi \ d 88 through 91 and (name N or name CA or name C or name O or name CB )) or (res \ id 92 through 97 and (name N or name CA or name C or name O or name CB )) or res \ id 98 or (resid 99 through 100 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 101 through 108 and (name N or name CA or name C or name O or \ name CB )) or resid 109 or (resid 110 through 111 and (name N or name CA or name \ C or name O or name CB )) or resid 112 or (resid 113 through 114 and (name N or \ name CA or name C or name O or name CB )) or resid 115 or (resid 116 through 11 \ 7 and (name N or name CA or name C or name O or name CB )) or (resid 118 through \ 122 and (name N or name CA or name C or name O or name CB )) or resid 123 throu \ gh 129 or (resid 130 through 139 and (name N or name CA or name C or name O or n \ ame CB )) or (resid 140 through 159 and (name N or name CA or name C or name O o \ r name CB )))) selection = (chain 'j' and ((resid 1 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 or (resid 7 through 9 and (name N or name CA or name C or \ name O or name CB )) or resid 10 or (resid 11 through 12 and (name N or name CA \ or name C or name O or name CB )) or (resid 13 through 30 and (name N or name C \ A or name C or name O or name CB )) or (resid 31 through 46 and (name N or name \ CA or name C or name O or name CB )) or resid 47 or (resid 48 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 or (resid 57 throu \ gh 60 and (name N or name CA or name C or name O or name CB )) or (resid 61 thro \ ugh 66 and (name N or name CA or name C or name O or name CB )) or (resid 67 thr \ ough 78 and (name N or name CA or name C or name O or name CB )) or resid 79 or \ (resid 80 through 86 and (name N or name CA or name C or name O or name CB )) or \ resid 87 or (resid 88 through 91 and (name N or name CA or name C or name O or \ name CB )) or (resid 92 through 100 and (name N or name CA or name C or name O o \ r name CB )) or (resid 101 through 108 and (name N or name CA or name C or name \ O or name CB )) or resid 109 or (resid 110 through 111 and (name N or name CA or \ name C or name O or name CB )) or (resid 112 through 117 and (name N or name CA \ or name C or name O or name CB )) or resid 118 through 123 or (resid 124 throug \ h 127 and (name N or name CA or name C or name O or name CB )) or (resid 128 thr \ ough 139 and (name N or name CA or name C or name O or name CB )) or (resid 140 \ through 159 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'k' and ((resid 1 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 through 39 or (resid 40 through 46 and (name N or name CA \ or name C or name O or name CB )) or resid 47 or (resid 48 through 55 and (name \ N or name CA or name C or name O or name CB )) or resid 56 through 58 or (resid \ 59 through 60 and (name N or name CA or name C or name O or name CB )) or (resi \ d 61 through 66 and (name N or name CA or name C or name O or name CB )) or (res \ id 67 through 78 and (name N or name CA or name C or name O or name CB )) or res \ id 79 or (resid 80 through 86 and (name N or name CA or name C or name O or name \ CB )) or resid 87 or (resid 88 through 91 and (name N or name CA or name C or n \ ame O or name CB )) or (resid 92 through 100 and (name N or name CA or name C or \ name O or name CB )) or (resid 101 through 108 and (name N or name CA or name C \ or name O or name CB )) or (resid 109 through 114 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 115 through 122 and (name N or name CA or \ name C or name O or name CB )) or resid 123 or (resid 124 through 127 and (name \ N or name CA or name C or name O or name CB )) or (resid 128 through 139 and (na \ me N or name CA or name C or name O or name CB )) or (resid 140 through 142 and \ (name N or name CA or name C or name O or name CB )) or resid 143 or (resid 144 \ through 159 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'l' and ((resid 1 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 or (resid 7 through 9 and (name N or name CA or name C or \ name O or name CB )) or resid 10 or (resid 11 through 12 and (name N or name CA \ or name C or name O or name CB )) or (resid 13 through 26 and (name N or name C \ A or name C or name O or name CB )) or (resid 27 through 30 and (name N or name \ CA or name C or name O or name CB )) or (resid 31 through 35 and (name N or name \ CA or name C or name O or name CB )) or (resid 36 through 46 and (name N or nam \ e CA or name C or name O or name CB )) or resid 47 through 50 or (resid 51 throu \ gh 55 and (name N or name CA or name C or name O or name CB )) or resid 56 throu \ gh 58 or (resid 59 through 60 and (name N or name CA or name C or name O or name \ CB )) or (resid 61 through 66 and (name N or name CA or name C or name O or nam \ e CB )) or resid 67 or (resid 68 through 78 and (name N or name CA or name C or \ name O or name CB )) or resid 79 or (resid 80 through 86 and (name N or name CA \ or name C or name O or name CB )) or (resid 87 through 91 and (name N or name CA \ or name C or name O or name CB )) or (resid 92 through 111 and (name N or name \ CA or name C or name O or name CB )) or (resid 112 through 122 and (name N or na \ me CA or name C or name O or name CB )) or resid 123 through 125 or (resid 126 t \ hrough 127 and (name N or name CA or name C or name O or name CB )) or (resid 12 \ 8 through 139 and (name N or name CA or name C or name O or name CB )) or (resid \ 140 through 142 and (name N or name CA or name C or name O or name CB )) or (re \ sid 143 through 159 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'm' and ((resid 1 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 through 7 or (resid 8 through 9 and (name N or name CA or \ name C or name O or name CB )) or resid 10 or (resid 11 through 12 and (name N \ or name CA or name C or name O or name CB )) or (resid 13 through 15 and (name N \ or name CA or name C or name O or name CB )) or (resid 16 through 30 and (name \ N or name CA or name C or name O or name CB )) or (resid 31 through 35 and (name \ N or name CA or name C or name O or name CB )) or (resid 36 through 46 and (nam \ e N or name CA or name C or name O or name CB )) or resid 47 through 49 or (resi \ d 50 through 55 and (name N or name CA or name C or name O or name CB )) or resi \ d 56 through 58 or (resid 59 through 60 and (name N or name CA or name C or name \ O or name CB )) or (resid 61 through 66 and (name N or name CA or name C or nam \ e O or name CB )) or resid 67 or (resid 68 through 78 and (name N or name CA or \ name C or name O or name CB )) or (resid 79 through 86 and (name N or name CA or \ name C or name O or name CB )) or resid 87 or (resid 88 through 91 and (name N \ or name CA or name C or name O or name CB )) or (resid 92 through 108 and (name \ N or name CA or name C or name O or name CB )) or (resid 109 through 117 and (na \ me N or name CA or name C or name O or name CB )) or (resid 118 through 122 and \ (name N or name CA or name C or name O or name CB )) or resid 123 or (resid 124 \ through 127 and (name N or name CA or name C or name O or name CB )) or (resid 1 \ 28 through 139 and (name N or name CA or name C or name O or name CB )) or (resi \ d 140 through 142 and (name N or name CA or name C or name O or name CB )) or (r \ esid 143 through 159 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'n' and ((resid 1 through 5 and (name N or name CA or name C or name O or \ name CB )) or resid 6 or (resid 7 through 9 and (name N or name CA or name C or \ name O or name CB )) or resid 10 through 11 or (resid 12 and (name N or name CA \ or name C or name O or name CB )) or (resid 13 through 26 and (name N or name C \ A or name C or name O or name CB )) or (resid 27 through 35 and (name N or name \ CA or name C or name O or name CB )) or (resid 36 through 46 and (name N or name \ CA or name C or name O or name CB )) or resid 47 through 56 or (resid 57 throug \ h 60 and (name N or name CA or name C or name O or name CB )) or (resid 61 throu \ gh 66 and (name N or name CA or name C or name O or name CB )) or (resid 67 thro \ ugh 78 and (name N or name CA or name C or name O or name CB )) or (resid 79 thr \ ough 86 and (name N or name CA or name C or name O or name CB )) or (resid 87 th \ rough 117 and (name N or name CA or name C or name O or name CB )) or (resid 118 \ through 122 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 23 or (resid 124 through 127 and (name N or name CA or name C or name O or name \ CB )) or (resid 128 through 139 and (name N or name CA or name C or name O or na \ me CB )) or (resid 140 through 142 and (name N or name CA or name C or name O or \ name CB )) or resid 143 or (resid 144 through 159 and (name N or name CA or nam \ e C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 1.670 Check model and map are aligned: 0.310 Set scattering table: 0.410 Process input model: 96.360 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 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 : 0.005 0.070 54321 Z= 0.346 Angle : 0.652 10.721 74346 Z= 0.362 Chirality : 0.045 0.273 8755 Planarity : 0.005 0.066 10052 Dihedral : 12.453 144.097 16932 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.71 % Favored : 95.19 % Rotamer: Outliers : 0.19 % Allowed : 0.60 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: 1.20 (0.10), residues: 8149 helix: 2.26 (0.08), residues: 4848 sheet: -2.68 (0.19), residues: 636 loop : -1.08 (0.12), residues: 2665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP a 802 HIS 0.023 0.002 HIS F 344 PHE 0.054 0.002 PHE D 95 TYR 0.034 0.002 TYR k 66 ARG 0.011 0.001 ARG i 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 6931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 857 time to evaluate : 4.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 ASP cc_start: 0.8610 (p0) cc_final: 0.8162 (p0) REVERT: A 547 MET cc_start: 0.8833 (mtp) cc_final: 0.8276 (mtp) REVERT: B 363 GLN cc_start: 0.8153 (tp-100) cc_final: 0.7943 (tp-100) REVERT: C 64 ASP cc_start: 0.7965 (m-30) cc_final: 0.7515 (t0) REVERT: C 359 ARG cc_start: 0.8773 (mmp80) cc_final: 0.8495 (mmp80) REVERT: C 362 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7293 (tm-30) REVERT: C 465 ASN cc_start: 0.8777 (p0) cc_final: 0.8542 (p0) REVERT: C 497 GLN cc_start: 0.8422 (tm-30) cc_final: 0.8206 (tm-30) REVERT: C 516 ASP cc_start: 0.8274 (t70) cc_final: 0.8059 (t0) REVERT: D 361 ASP cc_start: 0.7897 (t70) cc_final: 0.7109 (t0) REVERT: E 59 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7379 (mt-10) REVERT: E 292 GLU cc_start: 0.8133 (pp20) cc_final: 0.7683 (pp20) REVERT: E 451 PHE cc_start: 0.8049 (m-10) cc_final: 0.7742 (m-10) REVERT: E 494 GLU cc_start: 0.8003 (pt0) cc_final: 0.7778 (pt0) REVERT: E 524 ASP cc_start: 0.8113 (m-30) cc_final: 0.7904 (m-30) REVERT: F 23 LYS cc_start: 0.8958 (mptt) cc_final: 0.8712 (mptt) REVERT: I 205 GLU cc_start: 0.8633 (pp20) cc_final: 0.8368 (tm-30) REVERT: L 82 GLU cc_start: 0.9087 (tm-30) cc_final: 0.8815 (tm-30) REVERT: M 12 ARG cc_start: 0.7933 (tpt-90) cc_final: 0.7673 (tpp80) REVERT: M 182 GLU cc_start: 0.7809 (tp30) cc_final: 0.7258 (tp30) REVERT: a 536 LYS cc_start: 0.9000 (mtmm) cc_final: 0.8738 (mtmm) REVERT: a 733 TYR cc_start: 0.8380 (m-80) cc_final: 0.7856 (m-80) REVERT: a 735 ARG cc_start: 0.8863 (ptm-80) cc_final: 0.8534 (ptm-80) REVERT: a 737 TRP cc_start: 0.8709 (t60) cc_final: 0.8483 (t60) REVERT: a 796 HIS cc_start: 0.8481 (m-70) cc_final: 0.8121 (m-70) REVERT: a 806 MET cc_start: 0.7970 (mpp) cc_final: 0.7685 (mpp) REVERT: d 314 LYS cc_start: 0.5586 (mmtp) cc_final: 0.4758 (tptt) REVERT: f 57 LEU cc_start: 0.7747 (tp) cc_final: 0.7519 (tp) REVERT: g 46 ARG cc_start: 0.8823 (tmm-80) cc_final: 0.8110 (tmm-80) REVERT: g 59 MET cc_start: 0.9088 (mmp) cc_final: 0.8846 (mtp) REVERT: g 84 LEU cc_start: 0.6363 (tp) cc_final: 0.6096 (tp) REVERT: i 99 LEU cc_start: 0.9118 (mt) cc_final: 0.8846 (mt) REVERT: m 66 TYR cc_start: 0.8329 (m-80) cc_final: 0.7896 (m-80) REVERT: o 118 MET cc_start: 0.8801 (tpp) cc_final: 0.8503 (tpp) outliers start: 7 outliers final: 1 residues processed: 861 average time/residue: 0.5340 time to fit residues: 757.3814 Evaluate side-chains 773 residues out of total 6931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 772 time to evaluate : 4.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 216 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 680 optimal weight: 20.0000 chunk 610 optimal weight: 10.0000 chunk 338 optimal weight: 6.9990 chunk 208 optimal weight: 2.9990 chunk 412 optimal weight: 20.0000 chunk 326 optimal weight: 5.9990 chunk 631 optimal weight: 20.0000 chunk 244 optimal weight: 0.7980 chunk 384 optimal weight: 0.0770 chunk 470 optimal weight: 50.0000 chunk 731 optimal weight: 0.5980 overall best weight: 2.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 ASN ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN F 29 ASN M 183 ASN ** a 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 287 HIS d 334 GLN ** e 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 151 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 54321 Z= 0.293 Angle : 0.593 11.530 74346 Z= 0.313 Chirality : 0.044 0.211 8755 Planarity : 0.004 0.059 10052 Dihedral : 5.153 131.691 8653 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.94 % Favored : 96.02 % Rotamer: Outliers : 1.47 % Allowed : 10.21 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: 1.27 (0.10), residues: 8149 helix: 2.27 (0.07), residues: 4887 sheet: -2.67 (0.19), residues: 651 loop : -1.00 (0.13), residues: 2611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP a 594 HIS 0.025 0.001 HIS F 344 PHE 0.072 0.002 PHE h 88 TYR 0.061 0.002 TYR k 66 ARG 0.007 0.001 ARG C 238 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 6931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 824 time to evaluate : 4.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ARG cc_start: 0.7769 (ttt90) cc_final: 0.7279 (ttt90) REVERT: A 123 TYR cc_start: 0.9229 (m-80) cc_final: 0.8939 (m-80) REVERT: A 547 MET cc_start: 0.8729 (mtp) cc_final: 0.8197 (mtp) REVERT: B 311 ASP cc_start: 0.8109 (m-30) cc_final: 0.7831 (t0) REVERT: B 412 ASP cc_start: 0.7493 (p0) cc_final: 0.7264 (p0) REVERT: C 64 ASP cc_start: 0.7867 (m-30) cc_final: 0.7495 (t0) REVERT: C 230 ASP cc_start: 0.8636 (p0) cc_final: 0.8364 (p0) REVERT: C 290 MET cc_start: 0.8722 (mmm) cc_final: 0.8458 (mmm) REVERT: C 304 MET cc_start: 0.3641 (OUTLIER) cc_final: 0.3093 (ppp) REVERT: C 359 ARG cc_start: 0.8741 (mmp80) cc_final: 0.8466 (mmp80) REVERT: C 362 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7373 (tm-30) REVERT: C 366 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7869 (pt0) REVERT: C 497 GLN cc_start: 0.8393 (tm-30) cc_final: 0.8148 (tm-30) REVERT: C 516 ASP cc_start: 0.8284 (t70) cc_final: 0.8070 (t0) REVERT: C 538 CYS cc_start: 0.8987 (t) cc_final: 0.8562 (t) REVERT: E 59 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7511 (mt-10) REVERT: E 105 TYR cc_start: 0.9243 (m-10) cc_final: 0.8643 (m-10) REVERT: E 494 GLU cc_start: 0.7991 (pt0) cc_final: 0.7762 (pt0) REVERT: E 524 ASP cc_start: 0.7952 (m-30) cc_final: 0.7745 (m-30) REVERT: F 23 LYS cc_start: 0.8962 (mptt) cc_final: 0.8590 (mptt) REVERT: F 353 ILE cc_start: 0.9414 (OUTLIER) cc_final: 0.9096 (mp) REVERT: I 122 GLN cc_start: 0.7872 (mm110) cc_final: 0.6645 (mm-40) REVERT: I 205 GLU cc_start: 0.8616 (pp20) cc_final: 0.8386 (tm-30) REVERT: L 82 GLU cc_start: 0.9073 (tm-30) cc_final: 0.8728 (tm-30) REVERT: M 12 ARG cc_start: 0.8021 (tpt-90) cc_final: 0.7680 (tpp80) REVERT: M 34 ARG cc_start: 0.7951 (mtm110) cc_final: 0.7323 (ttp-110) REVERT: M 57 MET cc_start: 0.5921 (mmt) cc_final: 0.4170 (tmm) REVERT: M 182 GLU cc_start: 0.7933 (tp30) cc_final: 0.7209 (tp30) REVERT: M 201 TYR cc_start: 0.8373 (t80) cc_final: 0.8155 (t80) REVERT: a 422 MET cc_start: 0.8318 (ptp) cc_final: 0.7714 (mtm) REVERT: a 527 ASN cc_start: 0.7879 (t0) cc_final: 0.7483 (t0) REVERT: a 536 LYS cc_start: 0.8918 (mtmm) cc_final: 0.8471 (mtmm) REVERT: a 733 TYR cc_start: 0.8438 (m-80) cc_final: 0.7899 (m-80) REVERT: a 735 ARG cc_start: 0.8703 (ptm-80) cc_final: 0.8165 (ptm-80) REVERT: a 737 TRP cc_start: 0.8839 (t60) cc_final: 0.8400 (t60) REVERT: a 778 PHE cc_start: 0.7647 (t80) cc_final: 0.7440 (t80) REVERT: a 796 HIS cc_start: 0.8459 (m-70) cc_final: 0.8168 (m-70) REVERT: a 806 MET cc_start: 0.8208 (mpp) cc_final: 0.7746 (mpp) REVERT: c 61 ASN cc_start: 0.9276 (m-40) cc_final: 0.8717 (t0) REVERT: d 49 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8389 (p) REVERT: d 69 GLN cc_start: 0.5935 (tp40) cc_final: 0.5637 (tp40) REVERT: d 314 LYS cc_start: 0.5576 (mmtp) cc_final: 0.4784 (tptt) REVERT: e 47 MET cc_start: 0.7817 (tpp) cc_final: 0.7581 (tpp) REVERT: f 57 LEU cc_start: 0.7763 (tp) cc_final: 0.7532 (tp) REVERT: g 46 ARG cc_start: 0.8704 (tmm-80) cc_final: 0.7980 (tmm-80) REVERT: h 78 LEU cc_start: 0.6739 (pp) cc_final: 0.6406 (tp) REVERT: i 99 LEU cc_start: 0.9110 (mt) cc_final: 0.8871 (mt) REVERT: k 135 PHE cc_start: 0.8868 (t80) cc_final: 0.8632 (t80) REVERT: l 85 TYR cc_start: 0.6053 (t80) cc_final: 0.5727 (t80) REVERT: m 34 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8670 (pttm) REVERT: m 126 PHE cc_start: 0.6903 (t80) cc_final: 0.6171 (t80) REVERT: n 142 TYR cc_start: 0.7973 (m-10) cc_final: 0.7688 (m-10) REVERT: o 72 TYR cc_start: 0.8205 (OUTLIER) cc_final: 0.7904 (m-80) REVERT: o 118 MET cc_start: 0.8798 (tpp) cc_final: 0.8519 (tpp) outliers start: 54 outliers final: 37 residues processed: 842 average time/residue: 0.5420 time to fit residues: 751.3103 Evaluate side-chains 821 residues out of total 6931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 778 time to evaluate : 4.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 529 ASN Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 24 TYR Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain M residue 8 VAL Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 209 LYS Chi-restraints excluded: chain M residue 214 THR Chi-restraints excluded: chain a residue 470 VAL Chi-restraints excluded: chain b residue 232 LEU Chi-restraints excluded: chain c residue 35 TYR Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain e residue 51 THR Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 70 VAL Chi-restraints excluded: chain h residue 141 LEU Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain m residue 34 LYS Chi-restraints excluded: chain m residue 130 ILE Chi-restraints excluded: chain n residue 149 LEU Chi-restraints excluded: chain o residue 63 VAL Chi-restraints excluded: chain o residue 72 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 406 optimal weight: 50.0000 chunk 227 optimal weight: 0.0370 chunk 609 optimal weight: 10.0000 chunk 498 optimal weight: 20.0000 chunk 201 optimal weight: 3.9990 chunk 733 optimal weight: 20.0000 chunk 792 optimal weight: 10.0000 chunk 653 optimal weight: 9.9990 chunk 727 optimal weight: 0.8980 chunk 249 optimal weight: 7.9990 chunk 588 optimal weight: 20.0000 overall best weight: 4.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 ASN E 53 HIS F 135 ASN M 55 GLN ** a 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 151 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 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 : 0.008 0.078 54321 Z= 0.543 Angle : 0.693 11.056 74346 Z= 0.366 Chirality : 0.047 0.234 8755 Planarity : 0.005 0.061 10052 Dihedral : 5.335 135.147 8649 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.97 % Favored : 94.98 % Rotamer: Outliers : 2.89 % Allowed : 14.88 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: 1.05 (0.10), residues: 8149 helix: 2.16 (0.07), residues: 4876 sheet: -2.84 (0.18), residues: 649 loop : -1.19 (0.12), residues: 2624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP a 737 HIS 0.019 0.002 HIS F 344 PHE 0.053 0.002 PHE h 88 TYR 0.052 0.002 TYR n 66 ARG 0.007 0.001 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 6931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 793 time to evaluate : 4.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ARG cc_start: 0.7903 (ttt90) cc_final: 0.7527 (ttt90) REVERT: A 308 LYS cc_start: 0.8031 (tptt) cc_final: 0.7341 (tmtt) REVERT: A 547 MET cc_start: 0.8879 (mtp) cc_final: 0.8438 (mtp) REVERT: B 311 ASP cc_start: 0.8243 (m-30) cc_final: 0.7830 (t0) REVERT: B 337 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8311 (mpp) REVERT: B 412 ASP cc_start: 0.7674 (p0) cc_final: 0.7423 (p0) REVERT: C 83 ASP cc_start: 0.8496 (m-30) cc_final: 0.8276 (m-30) REVERT: C 230 ASP cc_start: 0.8686 (p0) cc_final: 0.8356 (p0) REVERT: C 279 ILE cc_start: 0.9395 (OUTLIER) cc_final: 0.9133 (mm) REVERT: C 362 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7424 (tm-30) REVERT: C 497 GLN cc_start: 0.8389 (tm-30) cc_final: 0.8092 (tm-30) REVERT: C 516 ASP cc_start: 0.8413 (t70) cc_final: 0.8043 (t0) REVERT: C 538 CYS cc_start: 0.8898 (t) cc_final: 0.8496 (t) REVERT: D 219 LEU cc_start: 0.9203 (tp) cc_final: 0.9002 (tt) REVERT: D 311 ASP cc_start: 0.8287 (t0) cc_final: 0.7934 (t70) REVERT: E 373 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7327 (pp20) REVERT: E 569 LYS cc_start: 0.8193 (tmmt) cc_final: 0.7932 (tmmt) REVERT: F 23 LYS cc_start: 0.8919 (mptt) cc_final: 0.8562 (mptt) REVERT: F 353 ILE cc_start: 0.9464 (mp) cc_final: 0.9158 (mp) REVERT: F 416 MET cc_start: 0.8309 (tpp) cc_final: 0.8009 (tpp) REVERT: L 82 GLU cc_start: 0.9076 (tm-30) cc_final: 0.8692 (tm-30) REVERT: M 12 ARG cc_start: 0.8082 (tpt-90) cc_final: 0.7641 (tpp80) REVERT: M 34 ARG cc_start: 0.8031 (mtm110) cc_final: 0.7299 (mtp-110) REVERT: M 182 GLU cc_start: 0.7991 (tp30) cc_final: 0.7308 (tp30) REVERT: a 527 ASN cc_start: 0.7977 (t0) cc_final: 0.7524 (t0) REVERT: a 572 PHE cc_start: 0.7982 (t80) cc_final: 0.7674 (t80) REVERT: a 594 TRP cc_start: 0.7876 (m-10) cc_final: 0.7530 (m-10) REVERT: a 735 ARG cc_start: 0.8809 (ptm-80) cc_final: 0.8592 (ptm-80) REVERT: a 737 TRP cc_start: 0.8946 (t60) cc_final: 0.8597 (t60) REVERT: a 802 TRP cc_start: 0.8700 (m-90) cc_final: 0.8154 (m-90) REVERT: a 806 MET cc_start: 0.8352 (mpp) cc_final: 0.7820 (mpp) REVERT: c 61 ASN cc_start: 0.9301 (m-40) cc_final: 0.8792 (t0) REVERT: c 124 LYS cc_start: 0.8775 (tptm) cc_final: 0.8474 (tptm) REVERT: d 69 GLN cc_start: 0.6156 (tp40) cc_final: 0.5777 (tp40) REVERT: d 92 ARG cc_start: 0.8642 (tpt170) cc_final: 0.8232 (tpm170) REVERT: d 191 ASP cc_start: 0.8502 (t0) cc_final: 0.7793 (t0) REVERT: d 314 LYS cc_start: 0.5542 (mmtp) cc_final: 0.4706 (tptt) REVERT: e 47 MET cc_start: 0.7949 (tpp) cc_final: 0.7673 (tpp) REVERT: f 57 LEU cc_start: 0.7749 (tp) cc_final: 0.7505 (tp) REVERT: g 46 ARG cc_start: 0.8718 (tmm-80) cc_final: 0.8111 (tmm-80) REVERT: g 59 MET cc_start: 0.9209 (mmp) cc_final: 0.8772 (mtp) REVERT: h 78 LEU cc_start: 0.6761 (pp) cc_final: 0.6427 (tp) REVERT: i 46 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7642 (ptp-170) REVERT: i 99 LEU cc_start: 0.9160 (mt) cc_final: 0.8921 (mt) REVERT: l 46 ARG cc_start: 0.8641 (tmm-80) cc_final: 0.8167 (tmm-80) REVERT: m 34 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8658 (pttm) REVERT: m 126 PHE cc_start: 0.7078 (t80) cc_final: 0.6344 (t80) REVERT: n 142 TYR cc_start: 0.8045 (m-10) cc_final: 0.7730 (m-10) REVERT: o 72 TYR cc_start: 0.8265 (OUTLIER) cc_final: 0.7932 (m-80) REVERT: o 118 MET cc_start: 0.8814 (tpp) cc_final: 0.8550 (tpp) REVERT: o 152 MET cc_start: 0.6977 (mmm) cc_final: 0.6759 (tpp) outliers start: 106 outliers final: 80 residues processed: 849 average time/residue: 0.5373 time to fit residues: 755.2699 Evaluate side-chains 852 residues out of total 6931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 766 time to evaluate : 4.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 540 ILE Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 24 TYR Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 341 GLU Chi-restraints excluded: chain E residue 373 GLU Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 543 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 135 ASN Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 112 ASN Chi-restraints excluded: chain I residue 138 ILE Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain M residue 209 LYS Chi-restraints excluded: chain a residue 198 THR Chi-restraints excluded: chain a residue 379 THR Chi-restraints excluded: chain a residue 470 VAL Chi-restraints excluded: chain b residue 232 LEU Chi-restraints excluded: chain c residue 35 TYR Chi-restraints excluded: chain c residue 143 TYR Chi-restraints excluded: chain c residue 190 PHE Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 240 ASP Chi-restraints excluded: chain d residue 272 VAL Chi-restraints excluded: chain d residue 306 ILE Chi-restraints excluded: chain e residue 51 THR Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain g residue 70 VAL Chi-restraints excluded: chain h residue 141 LEU Chi-restraints excluded: chain i residue 46 ARG Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 110 ILE Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 144 LEU Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain k residue 40 CYS Chi-restraints excluded: chain l residue 68 LEU Chi-restraints excluded: chain m residue 34 LYS Chi-restraints excluded: chain m residue 130 ILE Chi-restraints excluded: chain n residue 149 LEU Chi-restraints excluded: chain o residue 63 VAL Chi-restraints excluded: chain o residue 72 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 724 optimal weight: 9.9990 chunk 551 optimal weight: 7.9990 chunk 380 optimal weight: 30.0000 chunk 81 optimal weight: 0.7980 chunk 349 optimal weight: 5.9990 chunk 492 optimal weight: 10.0000 chunk 735 optimal weight: 8.9990 chunk 779 optimal weight: 20.0000 chunk 384 optimal weight: 0.6980 chunk 697 optimal weight: 9.9990 chunk 209 optimal weight: 0.8980 overall best weight: 3.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 349 ASN F 135 ASN M 55 GLN ** a 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 22 ASN ** i 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 54321 Z= 0.403 Angle : 0.627 13.031 74346 Z= 0.329 Chirality : 0.045 0.456 8755 Planarity : 0.004 0.063 10052 Dihedral : 5.224 132.980 8649 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.53 % Favored : 95.42 % Rotamer: Outliers : 3.39 % Allowed : 17.09 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: 1.12 (0.10), residues: 8149 helix: 2.22 (0.07), residues: 4876 sheet: -2.93 (0.18), residues: 646 loop : -1.15 (0.12), residues: 2627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP a 737 HIS 0.011 0.001 HIS F 344 PHE 0.044 0.002 PHE h 88 TYR 0.046 0.002 TYR j 66 ARG 0.006 0.001 ARG g 153 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 6931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 791 time to evaluate : 5.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ARG cc_start: 0.7856 (ttt90) cc_final: 0.7543 (ttt90) REVERT: A 547 MET cc_start: 0.8856 (mtp) cc_final: 0.8358 (mtp) REVERT: B 51 GLU cc_start: 0.8297 (tt0) cc_final: 0.8023 (tt0) REVERT: B 311 ASP cc_start: 0.8106 (m-30) cc_final: 0.7799 (t0) REVERT: B 337 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8207 (mpp) REVERT: C 83 ASP cc_start: 0.8497 (m-30) cc_final: 0.8293 (m-30) REVERT: C 279 ILE cc_start: 0.9370 (OUTLIER) cc_final: 0.9104 (mm) REVERT: C 304 MET cc_start: 0.3807 (OUTLIER) cc_final: 0.3134 (ppp) REVERT: C 497 GLN cc_start: 0.8330 (tm-30) cc_final: 0.8045 (tm-30) REVERT: C 516 ASP cc_start: 0.8312 (t70) cc_final: 0.7922 (t0) REVERT: C 538 CYS cc_start: 0.8916 (t) cc_final: 0.8508 (t) REVERT: D 219 LEU cc_start: 0.9195 (tp) cc_final: 0.8956 (tt) REVERT: D 260 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8609 (mm) REVERT: D 311 ASP cc_start: 0.8303 (t0) cc_final: 0.8095 (t70) REVERT: E 374 MET cc_start: 0.6289 (ptp) cc_final: 0.5959 (ptp) REVERT: E 494 GLU cc_start: 0.8050 (pt0) cc_final: 0.7831 (pt0) REVERT: E 569 LYS cc_start: 0.8193 (tmmt) cc_final: 0.7932 (tmmt) REVERT: F 23 LYS cc_start: 0.8930 (mptt) cc_final: 0.8573 (mptt) REVERT: F 353 ILE cc_start: 0.9437 (OUTLIER) cc_final: 0.9095 (mp) REVERT: F 416 MET cc_start: 0.8352 (tpp) cc_final: 0.8085 (tpp) REVERT: L 82 GLU cc_start: 0.9076 (tm-30) cc_final: 0.8689 (tm-30) REVERT: M 12 ARG cc_start: 0.8094 (tpt-90) cc_final: 0.7662 (tpp80) REVERT: M 57 MET cc_start: 0.6247 (mmt) cc_final: 0.4517 (tmm) REVERT: M 182 GLU cc_start: 0.7962 (tp30) cc_final: 0.7305 (tp30) REVERT: a 478 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8169 (tp) REVERT: a 527 ASN cc_start: 0.7938 (t0) cc_final: 0.7507 (t0) REVERT: a 594 TRP cc_start: 0.7852 (m-10) cc_final: 0.7598 (m-10) REVERT: a 737 TRP cc_start: 0.8959 (t60) cc_final: 0.8668 (t60) REVERT: a 778 PHE cc_start: 0.7747 (t80) cc_final: 0.7458 (t80) REVERT: a 802 TRP cc_start: 0.8766 (m-10) cc_final: 0.8299 (m-90) REVERT: a 806 MET cc_start: 0.8175 (mpp) cc_final: 0.7705 (mpp) REVERT: c 124 LYS cc_start: 0.8808 (tptm) cc_final: 0.8557 (tptm) REVERT: d 69 GLN cc_start: 0.6116 (tp40) cc_final: 0.5729 (tp40) REVERT: d 92 ARG cc_start: 0.8558 (tpt170) cc_final: 0.8086 (tpm170) REVERT: d 191 ASP cc_start: 0.8473 (t0) cc_final: 0.8091 (t0) REVERT: d 260 GLN cc_start: 0.6750 (tm-30) cc_final: 0.6058 (tm-30) REVERT: d 312 TRP cc_start: 0.6552 (t60) cc_final: 0.6103 (t60) REVERT: d 314 LYS cc_start: 0.5513 (mmtp) cc_final: 0.4698 (tptt) REVERT: d 336 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7491 (tm-30) REVERT: e 47 MET cc_start: 0.8021 (tpp) cc_final: 0.7773 (tpp) REVERT: f 57 LEU cc_start: 0.7739 (tp) cc_final: 0.7484 (tp) REVERT: g 46 ARG cc_start: 0.8731 (tmm-80) cc_final: 0.8180 (tmm-80) REVERT: g 59 MET cc_start: 0.9254 (mmp) cc_final: 0.8705 (mtp) REVERT: h 78 LEU cc_start: 0.6680 (pp) cc_final: 0.6350 (tp) REVERT: h 117 ARG cc_start: 0.8025 (mmm160) cc_final: 0.7624 (mmm160) REVERT: i 46 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7788 (ptt-90) REVERT: i 68 LEU cc_start: 0.8272 (mt) cc_final: 0.8056 (mp) REVERT: i 99 LEU cc_start: 0.9142 (mt) cc_final: 0.8901 (mt) REVERT: j 88 PHE cc_start: 0.8061 (t80) cc_final: 0.7814 (t80) REVERT: k 135 PHE cc_start: 0.8849 (t80) cc_final: 0.8628 (t80) REVERT: l 46 ARG cc_start: 0.8614 (tmm-80) cc_final: 0.8195 (tmm-80) REVERT: m 34 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8596 (pttm) REVERT: m 126 PHE cc_start: 0.7065 (t80) cc_final: 0.6356 (t80) REVERT: m 133 LEU cc_start: 0.8448 (tt) cc_final: 0.8176 (tp) REVERT: n 142 TYR cc_start: 0.8008 (m-10) cc_final: 0.7748 (m-10) REVERT: o 72 TYR cc_start: 0.8232 (OUTLIER) cc_final: 0.7948 (m-80) REVERT: o 118 MET cc_start: 0.8768 (tpp) cc_final: 0.8500 (tpp) REVERT: o 152 MET cc_start: 0.6948 (mmm) cc_final: 0.6716 (tpp) outliers start: 124 outliers final: 89 residues processed: 856 average time/residue: 0.5377 time to fit residues: 763.3818 Evaluate side-chains 868 residues out of total 6931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 770 time to evaluate : 4.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 24 TYR Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain M residue 209 LYS Chi-restraints excluded: chain a residue 188 THR Chi-restraints excluded: chain a residue 198 THR Chi-restraints excluded: chain a residue 379 THR Chi-restraints excluded: chain a residue 478 LEU Chi-restraints excluded: chain b residue 232 LEU Chi-restraints excluded: chain c residue 35 TYR Chi-restraints excluded: chain c residue 143 TYR Chi-restraints excluded: chain c residue 185 LEU Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 240 ASP Chi-restraints excluded: chain d residue 272 VAL Chi-restraints excluded: chain d residue 306 ILE Chi-restraints excluded: chain e residue 51 THR Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 70 VAL Chi-restraints excluded: chain h residue 141 LEU Chi-restraints excluded: chain i residue 46 ARG Chi-restraints excluded: chain i residue 49 LEU Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 110 ILE Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 144 LEU Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain k residue 40 CYS Chi-restraints excluded: chain k residue 144 LEU Chi-restraints excluded: chain l residue 68 LEU Chi-restraints excluded: chain m residue 3 GLU Chi-restraints excluded: chain m residue 34 LYS Chi-restraints excluded: chain m residue 130 ILE Chi-restraints excluded: chain n residue 149 LEU Chi-restraints excluded: chain o residue 63 VAL Chi-restraints excluded: chain o residue 72 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 648 optimal weight: 5.9990 chunk 442 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 580 optimal weight: 6.9990 chunk 321 optimal weight: 20.0000 chunk 664 optimal weight: 2.9990 chunk 538 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 397 optimal weight: 6.9990 chunk 699 optimal weight: 5.9990 chunk 196 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 55 GLN ** a 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 559 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 54321 Z= 0.459 Angle : 0.651 13.503 74346 Z= 0.342 Chirality : 0.046 0.311 8755 Planarity : 0.004 0.062 10052 Dihedral : 5.253 134.137 8649 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.98 % Favored : 94.97 % Rotamer: Outliers : 4.48 % Allowed : 18.10 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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 (0.10), residues: 8149 helix: 2.20 (0.07), residues: 4872 sheet: -2.97 (0.18), residues: 643 loop : -1.18 (0.12), residues: 2634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP a 737 HIS 0.015 0.002 HIS F 344 PHE 0.053 0.002 PHE h 88 TYR 0.055 0.002 TYR j 66 ARG 0.008 0.001 ARG d 84 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 960 residues out of total 6931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 796 time to evaluate : 4.744 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: A 123 TYR cc_start: 0.9255 (m-80) cc_final: 0.9016 (m-80) REVERT: A 308 LYS cc_start: 0.7960 (tptt) cc_final: 0.7195 (tmtt) REVERT: A 547 MET cc_start: 0.8901 (mtp) cc_final: 0.8440 (mtp) REVERT: B 51 GLU cc_start: 0.8305 (tt0) cc_final: 0.8033 (tt0) REVERT: B 311 ASP cc_start: 0.8194 (m-30) cc_final: 0.7825 (t0) REVERT: B 337 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8291 (mpp) REVERT: B 422 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7340 (tm-30) REVERT: C 40 MET cc_start: 0.8304 (mmm) cc_final: 0.8098 (mmm) REVERT: C 83 ASP cc_start: 0.8518 (m-30) cc_final: 0.8275 (m-30) REVERT: C 230 ASP cc_start: 0.8548 (p0) cc_final: 0.8330 (p0) REVERT: C 279 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.9097 (mm) REVERT: C 296 GLU cc_start: 0.8099 (tp30) cc_final: 0.7691 (tp30) REVERT: C 304 MET cc_start: 0.3817 (OUTLIER) cc_final: 0.3147 (ppp) REVERT: C 496 GLU cc_start: 0.7414 (tm-30) cc_final: 0.7183 (tm-30) REVERT: C 497 GLN cc_start: 0.8329 (tm-30) cc_final: 0.8044 (tm-30) REVERT: C 516 ASP cc_start: 0.8283 (t70) cc_final: 0.7928 (t0) REVERT: C 538 CYS cc_start: 0.8899 (t) cc_final: 0.8512 (t) REVERT: D 244 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9019 (mt) REVERT: D 260 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8594 (mm) REVERT: E 569 LYS cc_start: 0.8201 (tmmt) cc_final: 0.7952 (tmmt) REVERT: F 23 LYS cc_start: 0.8944 (mptt) cc_final: 0.8526 (mptt) REVERT: F 344 HIS cc_start: 0.8419 (t-90) cc_final: 0.8196 (t-170) REVERT: F 353 ILE cc_start: 0.9442 (OUTLIER) cc_final: 0.9094 (mp) REVERT: F 416 MET cc_start: 0.8371 (tpp) cc_final: 0.8113 (tpp) REVERT: L 82 GLU cc_start: 0.9080 (tm-30) cc_final: 0.8673 (tm-30) REVERT: M 12 ARG cc_start: 0.8120 (tpt-90) cc_final: 0.7681 (tpp80) REVERT: M 34 ARG cc_start: 0.8364 (ttp-110) cc_final: 0.7969 (ttp-110) REVERT: M 55 GLN cc_start: 0.7182 (OUTLIER) cc_final: 0.6870 (pp30) REVERT: M 57 MET cc_start: 0.6477 (mmt) cc_final: 0.4747 (tmm) REVERT: M 164 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8506 (ptmt) REVERT: M 182 GLU cc_start: 0.8011 (tp30) cc_final: 0.7326 (tp30) REVERT: a 478 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8159 (tp) REVERT: a 527 ASN cc_start: 0.7952 (t0) cc_final: 0.7525 (t0) REVERT: a 594 TRP cc_start: 0.7850 (m-10) cc_final: 0.7537 (m-10) REVERT: a 735 ARG cc_start: 0.8798 (ptm-80) cc_final: 0.8558 (ptm-80) REVERT: a 737 TRP cc_start: 0.8971 (t60) cc_final: 0.8732 (t60) REVERT: a 778 PHE cc_start: 0.7750 (t80) cc_final: 0.7461 (t80) REVERT: a 802 TRP cc_start: 0.8770 (m-10) cc_final: 0.8332 (m-90) REVERT: a 806 MET cc_start: 0.8259 (mpp) cc_final: 0.7954 (mpp) REVERT: c 61 ASN cc_start: 0.9356 (OUTLIER) cc_final: 0.8810 (t0) REVERT: c 124 LYS cc_start: 0.8876 (tptm) cc_final: 0.8606 (tptm) REVERT: d 69 GLN cc_start: 0.6132 (tp40) cc_final: 0.5746 (tp40) REVERT: d 92 ARG cc_start: 0.8615 (tpt170) cc_final: 0.7636 (tpm170) REVERT: d 191 ASP cc_start: 0.8500 (t0) cc_final: 0.8046 (t0) REVERT: d 260 GLN cc_start: 0.6822 (tm-30) cc_final: 0.6107 (tm-30) REVERT: d 312 TRP cc_start: 0.6650 (t60) cc_final: 0.6132 (t60) REVERT: d 314 LYS cc_start: 0.5528 (mmtp) cc_final: 0.4676 (tptt) REVERT: d 336 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7479 (tm-30) REVERT: e 47 MET cc_start: 0.7964 (tpp) cc_final: 0.7653 (tpp) REVERT: f 57 LEU cc_start: 0.7690 (tp) cc_final: 0.7420 (tp) REVERT: g 46 ARG cc_start: 0.8797 (tmm-80) cc_final: 0.8289 (tmm-80) REVERT: h 78 LEU cc_start: 0.6813 (pp) cc_final: 0.6461 (tp) REVERT: i 68 LEU cc_start: 0.8278 (mt) cc_final: 0.8023 (mm) REVERT: i 99 LEU cc_start: 0.9159 (mt) cc_final: 0.8926 (mt) REVERT: j 88 PHE cc_start: 0.8034 (t80) cc_final: 0.7725 (t80) REVERT: l 4 LEU cc_start: 0.2054 (OUTLIER) cc_final: 0.1227 (tp) REVERT: m 34 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8569 (pttm) REVERT: m 133 LEU cc_start: 0.8543 (tt) cc_final: 0.8294 (tp) REVERT: n 22 ILE cc_start: 0.8341 (mm) cc_final: 0.8004 (tp) REVERT: o 72 TYR cc_start: 0.8241 (m-10) cc_final: 0.7967 (m-80) REVERT: o 90 TYR cc_start: 0.4751 (t80) cc_final: 0.4285 (t80) REVERT: o 93 PHE cc_start: 0.6630 (t80) cc_final: 0.6360 (t80) REVERT: o 118 MET cc_start: 0.8801 (tpp) cc_final: 0.8543 (tpp) outliers start: 164 outliers final: 119 residues processed: 890 average time/residue: 0.5630 time to fit residues: 839.2172 Evaluate side-chains 902 residues out of total 6931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 771 time to evaluate : 4.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 24 TYR Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 341 GLU Chi-restraints excluded: chain E residue 377 ASP Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain E residue 543 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 112 ASN Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain I residue 172 ILE Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 55 GLN Chi-restraints excluded: chain M residue 164 LYS Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain M residue 209 LYS Chi-restraints excluded: chain a residue 188 THR Chi-restraints excluded: chain a residue 198 THR Chi-restraints excluded: chain a residue 379 THR Chi-restraints excluded: chain a residue 470 VAL Chi-restraints excluded: chain a residue 478 LEU Chi-restraints excluded: chain b residue 232 LEU Chi-restraints excluded: chain c residue 35 TYR Chi-restraints excluded: chain c residue 61 ASN Chi-restraints excluded: chain c residue 143 TYR Chi-restraints excluded: chain c residue 185 LEU Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 240 ASP Chi-restraints excluded: chain d residue 272 VAL Chi-restraints excluded: chain d residue 306 ILE Chi-restraints excluded: chain e residue 39 LEU Chi-restraints excluded: chain e residue 51 THR Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 70 VAL Chi-restraints excluded: chain h residue 141 LEU Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 110 ILE Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 144 LEU Chi-restraints excluded: chain j residue 40 CYS Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain k residue 40 CYS Chi-restraints excluded: chain k residue 70 VAL Chi-restraints excluded: chain k residue 144 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 68 LEU Chi-restraints excluded: chain m residue 34 LYS Chi-restraints excluded: chain m residue 130 ILE Chi-restraints excluded: chain n residue 149 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 262 optimal weight: 2.9990 chunk 701 optimal weight: 30.0000 chunk 154 optimal weight: 5.9990 chunk 457 optimal weight: 20.0000 chunk 192 optimal weight: 0.9990 chunk 779 optimal weight: 20.0000 chunk 647 optimal weight: 30.0000 chunk 361 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 257 optimal weight: 2.9990 chunk 409 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 55 GLN ** a 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 333 ASN h 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 54321 Z= 0.356 Angle : 0.611 13.511 74346 Z= 0.320 Chirality : 0.044 0.336 8755 Planarity : 0.004 0.060 10052 Dihedral : 5.175 131.515 8649 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.49 % Favored : 95.46 % Rotamer: Outliers : 4.04 % Allowed : 19.74 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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 (0.10), residues: 8149 helix: 2.29 (0.07), residues: 4866 sheet: -2.91 (0.18), residues: 656 loop : -1.16 (0.12), residues: 2627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP a 737 HIS 0.010 0.001 HIS F 344 PHE 0.055 0.002 PHE h 88 TYR 0.059 0.002 TYR j 66 ARG 0.006 0.001 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 6931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 789 time to evaluate : 4.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 547 MET cc_start: 0.8868 (mtp) cc_final: 0.8359 (mtp) REVERT: B 51 GLU cc_start: 0.8279 (tt0) cc_final: 0.7994 (tt0) REVERT: B 311 ASP cc_start: 0.8223 (m-30) cc_final: 0.7819 (t0) REVERT: B 337 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8283 (mpp) REVERT: B 416 MET cc_start: 0.8097 (mmm) cc_final: 0.7831 (mmm) REVERT: B 422 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7361 (tm-30) REVERT: C 83 ASP cc_start: 0.8505 (m-30) cc_final: 0.8271 (m-30) REVERT: C 230 ASP cc_start: 0.8598 (p0) cc_final: 0.8363 (p0) REVERT: C 279 ILE cc_start: 0.9348 (OUTLIER) cc_final: 0.9076 (mm) REVERT: C 304 MET cc_start: 0.3870 (OUTLIER) cc_final: 0.3182 (ppp) REVERT: C 497 GLN cc_start: 0.8335 (tm-30) cc_final: 0.8032 (tm-30) REVERT: C 516 ASP cc_start: 0.8251 (t70) cc_final: 0.7900 (t0) REVERT: C 538 CYS cc_start: 0.8920 (t) cc_final: 0.8506 (t) REVERT: D 244 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8993 (mt) REVERT: E 40 MET cc_start: 0.9005 (mmm) cc_final: 0.8599 (mmm) REVERT: E 105 TYR cc_start: 0.9270 (m-80) cc_final: 0.8851 (m-10) REVERT: E 569 LYS cc_start: 0.8186 (tmmt) cc_final: 0.7942 (tmmt) REVERT: F 23 LYS cc_start: 0.8905 (mptt) cc_final: 0.8491 (mptt) REVERT: F 337 MET cc_start: 0.8868 (mtm) cc_final: 0.8634 (mpp) REVERT: F 344 HIS cc_start: 0.8436 (t-90) cc_final: 0.8225 (t-170) REVERT: F 353 ILE cc_start: 0.9408 (OUTLIER) cc_final: 0.9088 (mp) REVERT: F 416 MET cc_start: 0.8362 (tpp) cc_final: 0.8127 (tpp) REVERT: L 82 GLU cc_start: 0.9075 (tm-30) cc_final: 0.8667 (tm-30) REVERT: M 12 ARG cc_start: 0.8164 (tpt-90) cc_final: 0.7737 (tpp80) REVERT: M 34 ARG cc_start: 0.8458 (ttp-110) cc_final: 0.8026 (ttp-110) REVERT: M 57 MET cc_start: 0.6449 (mmt) cc_final: 0.4767 (tmm) REVERT: M 164 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8525 (ptmt) REVERT: M 182 GLU cc_start: 0.7981 (tp30) cc_final: 0.7296 (tp30) REVERT: a 478 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8146 (tp) REVERT: a 527 ASN cc_start: 0.7950 (t0) cc_final: 0.7545 (t0) REVERT: a 594 TRP cc_start: 0.7823 (m-10) cc_final: 0.7498 (m-10) REVERT: a 737 TRP cc_start: 0.8958 (t60) cc_final: 0.8700 (t60) REVERT: a 778 PHE cc_start: 0.7753 (t80) cc_final: 0.7500 (t80) REVERT: a 802 TRP cc_start: 0.8743 (m-10) cc_final: 0.8366 (m-90) REVERT: a 806 MET cc_start: 0.8335 (mpp) cc_final: 0.8024 (mpp) REVERT: c 61 ASN cc_start: 0.9375 (m-40) cc_final: 0.8733 (t0) REVERT: c 124 LYS cc_start: 0.8895 (tptm) cc_final: 0.8651 (tptm) REVERT: d 69 GLN cc_start: 0.6135 (tp40) cc_final: 0.5751 (tp40) REVERT: d 191 ASP cc_start: 0.8512 (t0) cc_final: 0.8024 (t0) REVERT: d 260 GLN cc_start: 0.6930 (tm-30) cc_final: 0.6195 (tm-30) REVERT: d 312 TRP cc_start: 0.6592 (t60) cc_final: 0.6089 (t60) REVERT: d 314 LYS cc_start: 0.5598 (mmtp) cc_final: 0.4782 (tptt) REVERT: d 336 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7533 (tm-30) REVERT: e 47 MET cc_start: 0.8000 (tpp) cc_final: 0.7732 (tpp) REVERT: f 57 LEU cc_start: 0.7637 (tp) cc_final: 0.7355 (tp) REVERT: g 46 ARG cc_start: 0.8801 (tmm-80) cc_final: 0.8488 (tmm-80) REVERT: g 59 MET cc_start: 0.9173 (mmp) cc_final: 0.8620 (mtp) REVERT: h 78 LEU cc_start: 0.6791 (pp) cc_final: 0.6355 (tp) REVERT: i 68 LEU cc_start: 0.8325 (mt) cc_final: 0.8047 (mm) REVERT: i 99 LEU cc_start: 0.9149 (mt) cc_final: 0.8912 (mt) REVERT: j 88 PHE cc_start: 0.8068 (t80) cc_final: 0.7748 (t80) REVERT: l 4 LEU cc_start: 0.1908 (mt) cc_final: 0.1204 (tp) REVERT: l 46 ARG cc_start: 0.8580 (tmm-80) cc_final: 0.8070 (tmm-80) REVERT: m 34 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8561 (pttm) REVERT: m 126 PHE cc_start: 0.7082 (t80) cc_final: 0.6193 (t80) REVERT: m 133 LEU cc_start: 0.8516 (tt) cc_final: 0.8267 (tp) REVERT: n 22 ILE cc_start: 0.8383 (mm) cc_final: 0.8111 (tp) REVERT: n 59 MET cc_start: 0.8535 (tmm) cc_final: 0.8276 (tmm) REVERT: o 72 TYR cc_start: 0.8198 (m-10) cc_final: 0.7947 (m-80) REVERT: o 90 TYR cc_start: 0.4713 (t80) cc_final: 0.4276 (t80) REVERT: o 93 PHE cc_start: 0.6606 (t80) cc_final: 0.6337 (t80) REVERT: o 118 MET cc_start: 0.8790 (tpp) cc_final: 0.8526 (tpp) outliers start: 148 outliers final: 112 residues processed: 868 average time/residue: 0.5365 time to fit residues: 773.7842 Evaluate side-chains 897 residues out of total 6931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 777 time to evaluate : 4.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 24 TYR Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 341 GLU Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain E residue 543 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 112 ASN Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain I residue 172 ILE Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 45 ASP Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 164 LYS Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain M residue 209 LYS Chi-restraints excluded: chain a residue 198 THR Chi-restraints excluded: chain a residue 379 THR Chi-restraints excluded: chain a residue 478 LEU Chi-restraints excluded: chain b residue 232 LEU Chi-restraints excluded: chain c residue 35 TYR Chi-restraints excluded: chain c residue 143 TYR Chi-restraints excluded: chain c residue 185 LEU Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 240 ASP Chi-restraints excluded: chain d residue 272 VAL Chi-restraints excluded: chain d residue 306 ILE Chi-restraints excluded: chain e residue 39 LEU Chi-restraints excluded: chain e residue 51 THR Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 70 VAL Chi-restraints excluded: chain h residue 141 LEU Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 73 LEU Chi-restraints excluded: chain i residue 110 ILE Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain k residue 40 CYS Chi-restraints excluded: chain k residue 70 VAL Chi-restraints excluded: chain k residue 144 LEU Chi-restraints excluded: chain l residue 68 LEU Chi-restraints excluded: chain m residue 34 LYS Chi-restraints excluded: chain m residue 130 ILE Chi-restraints excluded: chain n residue 149 LEU Chi-restraints excluded: chain o residue 63 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 751 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 444 optimal weight: 10.0000 chunk 569 optimal weight: 9.9990 chunk 441 optimal weight: 10.0000 chunk 656 optimal weight: 5.9990 chunk 435 optimal weight: 8.9990 chunk 776 optimal weight: 5.9990 chunk 486 optimal weight: 4.9990 chunk 473 optimal weight: 50.0000 chunk 358 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 170 HIS C 323 ASN D 207 ASN F 35 ASN ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 80 GLN l 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.091 54321 Z= 0.597 Angle : 0.731 12.937 74346 Z= 0.385 Chirality : 0.048 0.377 8755 Planarity : 0.005 0.061 10052 Dihedral : 5.404 136.181 8649 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.80 % Favored : 94.15 % Rotamer: Outliers : 5.19 % Allowed : 19.63 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: 0.91 (0.10), residues: 8149 helix: 2.10 (0.07), residues: 4861 sheet: -3.11 (0.18), residues: 638 loop : -1.31 (0.12), residues: 2650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 567 HIS 0.014 0.002 HIS F 344 PHE 0.050 0.002 PHE h 88 TYR 0.061 0.002 TYR j 66 ARG 0.007 0.001 ARG g 153 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 973 residues out of total 6931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 783 time to evaluate : 4.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ARG cc_start: 0.7831 (ttt90) cc_final: 0.7599 (ttt90) REVERT: A 308 LYS cc_start: 0.8077 (tptt) cc_final: 0.7195 (tmtt) REVERT: B 51 GLU cc_start: 0.8310 (tt0) cc_final: 0.8049 (tt0) REVERT: B 311 ASP cc_start: 0.8243 (m-30) cc_final: 0.7877 (t0) REVERT: B 337 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8385 (mpp) REVERT: B 412 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7326 (p0) REVERT: B 416 MET cc_start: 0.8142 (mmm) cc_final: 0.7861 (mmm) REVERT: B 422 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7438 (tm-30) REVERT: C 83 ASP cc_start: 0.8538 (m-30) cc_final: 0.8316 (m-30) REVERT: C 279 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.9129 (mm) REVERT: C 296 GLU cc_start: 0.8228 (tp30) cc_final: 0.7759 (tp30) REVERT: C 362 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7489 (tm-30) REVERT: C 497 GLN cc_start: 0.8346 (tm-30) cc_final: 0.8037 (tm-30) REVERT: C 538 CYS cc_start: 0.8861 (t) cc_final: 0.8485 (t) REVERT: D 244 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9071 (mt) REVERT: D 260 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8674 (mm) REVERT: E 40 MET cc_start: 0.9040 (mmm) cc_final: 0.8748 (mmm) REVERT: E 377 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.8396 (m-30) REVERT: F 23 LYS cc_start: 0.8901 (mptt) cc_final: 0.8506 (mptt) REVERT: F 353 ILE cc_start: 0.9459 (OUTLIER) cc_final: 0.9145 (mp) REVERT: L 82 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8660 (tm-30) REVERT: M 12 ARG cc_start: 0.8245 (tpt-90) cc_final: 0.7840 (tpp80) REVERT: M 34 ARG cc_start: 0.8496 (ttp-110) cc_final: 0.8206 (ttp-110) REVERT: M 49 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7256 (mtm110) REVERT: M 57 MET cc_start: 0.6250 (mmt) cc_final: 0.4683 (tmm) REVERT: M 164 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8538 (ttmt) REVERT: M 182 GLU cc_start: 0.7982 (tp30) cc_final: 0.7341 (tp30) REVERT: M 203 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8869 (tt) REVERT: a 478 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8278 (tp) REVERT: a 527 ASN cc_start: 0.8051 (t0) cc_final: 0.7652 (t0) REVERT: a 578 PHE cc_start: 0.8531 (m-80) cc_final: 0.8327 (m-80) REVERT: a 594 TRP cc_start: 0.7857 (m-10) cc_final: 0.7500 (m-10) REVERT: a 737 TRP cc_start: 0.9039 (t60) cc_final: 0.8780 (t60) REVERT: a 778 PHE cc_start: 0.7850 (t80) cc_final: 0.7607 (t80) REVERT: a 802 TRP cc_start: 0.8793 (m-10) cc_final: 0.8394 (m-90) REVERT: c 61 ASN cc_start: 0.9385 (OUTLIER) cc_final: 0.8826 (t0) REVERT: c 108 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7044 (mp0) REVERT: c 124 LYS cc_start: 0.8940 (tptm) cc_final: 0.8652 (tptm) REVERT: d 69 GLN cc_start: 0.6194 (tp40) cc_final: 0.5833 (tp40) REVERT: d 191 ASP cc_start: 0.8552 (t0) cc_final: 0.7951 (t0) REVERT: d 260 GLN cc_start: 0.7022 (tm-30) cc_final: 0.6404 (tm-30) REVERT: d 314 LYS cc_start: 0.5675 (mmtp) cc_final: 0.4870 (tptt) REVERT: d 334 GLN cc_start: 0.7241 (OUTLIER) cc_final: 0.6838 (mp10) REVERT: d 336 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7508 (tm-30) REVERT: e 47 MET cc_start: 0.7961 (tpp) cc_final: 0.7618 (tpp) REVERT: f 57 LEU cc_start: 0.7651 (tp) cc_final: 0.7371 (tp) REVERT: g 46 ARG cc_start: 0.8746 (tmm-80) cc_final: 0.8265 (tmm-80) REVERT: g 59 MET cc_start: 0.9259 (mmp) cc_final: 0.8644 (mtp) REVERT: h 78 LEU cc_start: 0.6946 (pp) cc_final: 0.6367 (tp) REVERT: i 68 LEU cc_start: 0.8267 (mt) cc_final: 0.8023 (mm) REVERT: i 99 LEU cc_start: 0.9193 (mt) cc_final: 0.8960 (mt) REVERT: j 10 PRO cc_start: 0.7457 (Cg_exo) cc_final: 0.6954 (Cg_endo) REVERT: j 88 PHE cc_start: 0.8130 (t80) cc_final: 0.7793 (t80) REVERT: l 4 LEU cc_start: 0.2193 (mt) cc_final: 0.1515 (tp) REVERT: l 46 ARG cc_start: 0.8587 (tmm-80) cc_final: 0.7999 (tmm-80) REVERT: m 34 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8580 (pttm) REVERT: m 126 PHE cc_start: 0.7070 (t80) cc_final: 0.6170 (t80) REVERT: m 133 LEU cc_start: 0.8541 (tt) cc_final: 0.8289 (tp) REVERT: n 59 MET cc_start: 0.8612 (tmm) cc_final: 0.8347 (tmm) REVERT: o 72 TYR cc_start: 0.8248 (m-10) cc_final: 0.8011 (m-80) REVERT: o 90 TYR cc_start: 0.4921 (t80) cc_final: 0.4495 (t80) REVERT: o 118 MET cc_start: 0.8838 (tpp) cc_final: 0.8582 (tpp) outliers start: 190 outliers final: 144 residues processed: 893 average time/residue: 0.5462 time to fit residues: 816.4453 Evaluate side-chains 934 residues out of total 6931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 775 time to evaluate : 4.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 301 ARG Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain B residue 412 ASP Chi-restraints excluded: chain C residue 24 TYR Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 304 MET Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 529 ASN Chi-restraints excluded: chain C residue 543 THR Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 341 GLU Chi-restraints excluded: chain E residue 377 ASP Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 112 ASN Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain I residue 172 ILE Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 45 ASP Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 49 ARG Chi-restraints excluded: chain M residue 164 LYS Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain M residue 209 LYS Chi-restraints excluded: chain M residue 214 THR Chi-restraints excluded: chain a residue 188 THR Chi-restraints excluded: chain a residue 198 THR Chi-restraints excluded: chain a residue 379 THR Chi-restraints excluded: chain a residue 470 VAL Chi-restraints excluded: chain a residue 478 LEU Chi-restraints excluded: chain a residue 729 HIS Chi-restraints excluded: chain b residue 232 LEU Chi-restraints excluded: chain c residue 35 TYR Chi-restraints excluded: chain c residue 61 ASN Chi-restraints excluded: chain c residue 108 GLU Chi-restraints excluded: chain c residue 143 TYR Chi-restraints excluded: chain c residue 185 LEU Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 240 ASP Chi-restraints excluded: chain d residue 272 VAL Chi-restraints excluded: chain d residue 306 ILE Chi-restraints excluded: chain d residue 334 GLN Chi-restraints excluded: chain d residue 338 ILE Chi-restraints excluded: chain e residue 39 LEU Chi-restraints excluded: chain e residue 51 THR Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 70 VAL Chi-restraints excluded: chain g residue 88 PHE Chi-restraints excluded: chain g residue 149 LEU Chi-restraints excluded: chain h residue 88 PHE Chi-restraints excluded: chain h residue 141 LEU Chi-restraints excluded: chain h residue 144 LEU Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 73 LEU Chi-restraints excluded: chain i residue 110 ILE Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain i residue 144 LEU Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain k residue 40 CYS Chi-restraints excluded: chain k residue 70 VAL Chi-restraints excluded: chain k residue 144 LEU Chi-restraints excluded: chain l residue 59 MET Chi-restraints excluded: chain l residue 68 LEU Chi-restraints excluded: chain m residue 3 GLU Chi-restraints excluded: chain m residue 34 LYS Chi-restraints excluded: chain m residue 130 ILE Chi-restraints excluded: chain n residue 149 LEU Chi-restraints excluded: chain o residue 63 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 480 optimal weight: 6.9990 chunk 310 optimal weight: 0.6980 chunk 463 optimal weight: 5.9990 chunk 234 optimal weight: 0.9980 chunk 152 optimal weight: 0.6980 chunk 150 optimal weight: 0.7980 chunk 493 optimal weight: 5.9990 chunk 529 optimal weight: 10.0000 chunk 384 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 610 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 323 ASN C 497 GLN ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 54321 Z= 0.191 Angle : 0.586 18.057 74346 Z= 0.304 Chirality : 0.043 0.494 8755 Planarity : 0.004 0.060 10052 Dihedral : 5.014 126.225 8649 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.25 % Favored : 96.70 % Rotamer: Outliers : 3.33 % Allowed : 22.33 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: 1.30 (0.10), residues: 8149 helix: 2.37 (0.07), residues: 4871 sheet: -2.82 (0.19), residues: 622 loop : -1.10 (0.12), residues: 2656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP a 737 HIS 0.010 0.001 HIS a 729 PHE 0.057 0.002 PHE h 88 TYR 0.059 0.002 TYR j 66 ARG 0.008 0.001 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 936 residues out of total 6931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 814 time to evaluate : 4.702 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: A 62 ARG cc_start: 0.7719 (ttt90) cc_final: 0.7425 (ttt90) REVERT: A 366 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8006 (mt-10) REVERT: B 51 GLU cc_start: 0.8127 (tt0) cc_final: 0.7889 (tt0) REVERT: B 281 MET cc_start: 0.8214 (mmm) cc_final: 0.7920 (mtp) REVERT: B 337 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8060 (mpp) REVERT: B 416 MET cc_start: 0.8052 (mmm) cc_final: 0.6727 (mmm) REVERT: C 279 ILE cc_start: 0.9312 (OUTLIER) cc_final: 0.9055 (mm) REVERT: C 304 MET cc_start: 0.4091 (ppp) cc_final: 0.3424 (ppp) REVERT: C 495 LEU cc_start: 0.8688 (tp) cc_final: 0.8377 (tp) REVERT: C 497 GLN cc_start: 0.8223 (tm130) cc_final: 0.7890 (tm-30) REVERT: C 538 CYS cc_start: 0.8981 (t) cc_final: 0.8680 (t) REVERT: D 244 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8844 (mt) REVERT: D 260 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8599 (mm) REVERT: D 361 ASP cc_start: 0.7777 (t0) cc_final: 0.7340 (t0) REVERT: E 40 MET cc_start: 0.8960 (mmm) cc_final: 0.8529 (mmm) REVERT: E 105 TYR cc_start: 0.9127 (m-80) cc_final: 0.8709 (m-10) REVERT: E 377 ASP cc_start: 0.8456 (t0) cc_final: 0.8172 (m-30) REVERT: E 392 TYR cc_start: 0.9148 (m-80) cc_final: 0.8911 (m-80) REVERT: F 337 MET cc_start: 0.8638 (mtm) cc_final: 0.8303 (mpp) REVERT: F 353 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.9020 (mp) REVERT: F 355 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8133 (mm-30) REVERT: L 82 GLU cc_start: 0.9123 (tm-30) cc_final: 0.8766 (tm-30) REVERT: M 12 ARG cc_start: 0.8172 (tpt-90) cc_final: 0.7817 (tpp80) REVERT: M 34 ARG cc_start: 0.8371 (ttp-110) cc_final: 0.8009 (ttp-110) REVERT: M 49 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7098 (mtm110) REVERT: M 57 MET cc_start: 0.6158 (mmt) cc_final: 0.4587 (tmm) REVERT: M 182 GLU cc_start: 0.7743 (tp30) cc_final: 0.7249 (tp30) REVERT: M 204 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8577 (ttpt) REVERT: a 478 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8112 (tp) REVERT: a 527 ASN cc_start: 0.7844 (t0) cc_final: 0.7522 (t0) REVERT: a 536 LYS cc_start: 0.8814 (mtmm) cc_final: 0.8552 (mtmm) REVERT: a 594 TRP cc_start: 0.7712 (m-10) cc_final: 0.7409 (m-10) REVERT: a 737 TRP cc_start: 0.8965 (t60) cc_final: 0.8637 (t60) REVERT: a 802 TRP cc_start: 0.8688 (m-10) cc_final: 0.8396 (m-90) REVERT: c 61 ASN cc_start: 0.9416 (m-40) cc_final: 0.8827 (t0) REVERT: c 108 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.6921 (mp0) REVERT: c 124 LYS cc_start: 0.8913 (tptm) cc_final: 0.8597 (tptm) REVERT: d 49 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8219 (p) REVERT: d 69 GLN cc_start: 0.6244 (tp40) cc_final: 0.5888 (tp40) REVERT: d 97 TYR cc_start: 0.8314 (m-80) cc_final: 0.7814 (m-10) REVERT: d 191 ASP cc_start: 0.8498 (t0) cc_final: 0.7833 (t0) REVERT: d 260 GLN cc_start: 0.7132 (tm-30) cc_final: 0.6468 (tm-30) REVERT: d 312 TRP cc_start: 0.6429 (t60) cc_final: 0.6043 (t60) REVERT: d 314 LYS cc_start: 0.5560 (mmtp) cc_final: 0.4800 (tptt) REVERT: d 334 GLN cc_start: 0.6887 (OUTLIER) cc_final: 0.6490 (mp10) REVERT: d 336 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7519 (tm-30) REVERT: e 45 PHE cc_start: 0.8764 (t80) cc_final: 0.8388 (t80) REVERT: e 47 MET cc_start: 0.7979 (tpp) cc_final: 0.7632 (tpp) REVERT: f 57 LEU cc_start: 0.7577 (tp) cc_final: 0.7324 (tp) REVERT: g 46 ARG cc_start: 0.8758 (tmm-80) cc_final: 0.8160 (tmm-80) REVERT: g 59 MET cc_start: 0.9224 (mmp) cc_final: 0.8368 (mtp) REVERT: h 78 LEU cc_start: 0.6912 (pp) cc_final: 0.6240 (tp) REVERT: h 126 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.8110 (m-80) REVERT: i 68 LEU cc_start: 0.8255 (mt) cc_final: 0.8014 (mm) REVERT: i 99 LEU cc_start: 0.9117 (mt) cc_final: 0.8879 (mt) REVERT: j 88 PHE cc_start: 0.8202 (t80) cc_final: 0.7951 (t80) REVERT: l 4 LEU cc_start: 0.2095 (mt) cc_final: 0.1297 (tp) REVERT: l 46 ARG cc_start: 0.8602 (tmm-80) cc_final: 0.8052 (tmm-80) REVERT: m 34 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8563 (pttm) REVERT: m 126 PHE cc_start: 0.7023 (t80) cc_final: 0.6078 (t80) REVERT: m 133 LEU cc_start: 0.8482 (tt) cc_final: 0.8244 (tp) REVERT: n 59 MET cc_start: 0.8598 (tmm) cc_final: 0.8362 (tmm) REVERT: o 90 TYR cc_start: 0.4711 (t80) cc_final: 0.4290 (t80) REVERT: o 93 PHE cc_start: 0.6441 (t80) cc_final: 0.6201 (t80) REVERT: o 118 MET cc_start: 0.8770 (tpp) cc_final: 0.8515 (tpp) outliers start: 122 outliers final: 76 residues processed: 874 average time/residue: 0.5368 time to fit residues: 776.7896 Evaluate side-chains 868 residues out of total 6931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 779 time to evaluate : 4.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 500 GLN Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain I residue 172 ILE Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 41 LYS Chi-restraints excluded: chain M residue 45 ASP Chi-restraints excluded: chain M residue 49 ARG Chi-restraints excluded: chain M residue 204 LYS Chi-restraints excluded: chain M residue 214 THR Chi-restraints excluded: chain a residue 188 THR Chi-restraints excluded: chain a residue 379 THR Chi-restraints excluded: chain a residue 470 VAL Chi-restraints excluded: chain a residue 478 LEU Chi-restraints excluded: chain a residue 729 HIS Chi-restraints excluded: chain b residue 232 LEU Chi-restraints excluded: chain c residue 35 TYR Chi-restraints excluded: chain c residue 108 GLU Chi-restraints excluded: chain c residue 185 LEU Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 240 ASP Chi-restraints excluded: chain d residue 272 VAL Chi-restraints excluded: chain d residue 306 ILE Chi-restraints excluded: chain d residue 334 GLN Chi-restraints excluded: chain e residue 39 LEU Chi-restraints excluded: chain e residue 51 THR Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain g residue 88 PHE Chi-restraints excluded: chain h residue 126 PHE Chi-restraints excluded: chain h residue 141 LEU Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 106 PHE Chi-restraints excluded: chain i residue 110 ILE Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain k residue 40 CYS Chi-restraints excluded: chain k residue 70 VAL Chi-restraints excluded: chain l residue 59 MET Chi-restraints excluded: chain l residue 68 LEU Chi-restraints excluded: chain m residue 34 LYS Chi-restraints excluded: chain m residue 130 ILE Chi-restraints excluded: chain n residue 149 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 706 optimal weight: 8.9990 chunk 744 optimal weight: 3.9990 chunk 679 optimal weight: 7.9990 chunk 723 optimal weight: 10.0000 chunk 435 optimal weight: 5.9990 chunk 315 optimal weight: 0.0570 chunk 568 optimal weight: 0.0670 chunk 222 optimal weight: 0.9980 chunk 654 optimal weight: 20.0000 chunk 684 optimal weight: 20.0000 chunk 721 optimal weight: 10.0000 overall best weight: 2.2240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 54321 Z= 0.307 Angle : 0.611 14.699 74346 Z= 0.317 Chirality : 0.044 0.607 8755 Planarity : 0.004 0.061 10052 Dihedral : 4.956 129.078 8649 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.04 % Favored : 95.91 % Rotamer: Outliers : 3.03 % Allowed : 22.63 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: 1.33 (0.10), residues: 8149 helix: 2.40 (0.07), residues: 4866 sheet: -2.81 (0.19), residues: 660 loop : -1.08 (0.12), residues: 2623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 567 HIS 0.010 0.001 HIS a 729 PHE 0.048 0.002 PHE h 88 TYR 0.062 0.002 TYR n 66 ARG 0.009 0.001 ARG d 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 6931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 784 time to evaluate : 6.720 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: A 62 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7511 (ttt90) REVERT: B 51 GLU cc_start: 0.8218 (tt0) cc_final: 0.7968 (tt0) REVERT: B 311 ASP cc_start: 0.8362 (m-30) cc_final: 0.8109 (t0) REVERT: B 337 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8259 (mpp) REVERT: C 279 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.9069 (mm) REVERT: C 290 MET cc_start: 0.8363 (mmm) cc_final: 0.8053 (mmm) REVERT: C 292 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7885 (tm-30) REVERT: C 304 MET cc_start: 0.4120 (ppp) cc_final: 0.3562 (ppp) REVERT: C 362 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7129 (tm-30) REVERT: C 497 GLN cc_start: 0.8236 (tm130) cc_final: 0.7993 (tm-30) REVERT: C 538 CYS cc_start: 0.8981 (t) cc_final: 0.8598 (t) REVERT: D 244 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8996 (mt) REVERT: D 260 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8527 (mm) REVERT: E 40 MET cc_start: 0.9021 (mmm) cc_final: 0.8611 (mmm) REVERT: E 59 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7547 (mt-10) REVERT: E 101 MET cc_start: 0.8290 (tpp) cc_final: 0.8014 (tpp) REVERT: E 105 TYR cc_start: 0.9185 (m-80) cc_final: 0.8854 (m-10) REVERT: E 324 MET cc_start: 0.8944 (mmm) cc_final: 0.8712 (mtt) REVERT: F 337 MET cc_start: 0.8511 (mtm) cc_final: 0.8279 (mpp) REVERT: F 353 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.9056 (mp) REVERT: M 12 ARG cc_start: 0.8207 (tpt-90) cc_final: 0.7839 (tpp80) REVERT: M 49 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7174 (mtm110) REVERT: M 57 MET cc_start: 0.6173 (mmt) cc_final: 0.4696 (tmm) REVERT: M 182 GLU cc_start: 0.7801 (tp30) cc_final: 0.7261 (tp30) REVERT: a 478 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8187 (tp) REVERT: a 527 ASN cc_start: 0.7859 (t0) cc_final: 0.7560 (t0) REVERT: a 536 LYS cc_start: 0.8834 (mtmm) cc_final: 0.8535 (mtmm) REVERT: a 548 MET cc_start: 0.8710 (tpp) cc_final: 0.8221 (mmt) REVERT: a 594 TRP cc_start: 0.7754 (m-10) cc_final: 0.7420 (m-10) REVERT: a 737 TRP cc_start: 0.8967 (t60) cc_final: 0.8649 (t60) REVERT: a 802 TRP cc_start: 0.8667 (m-10) cc_final: 0.8370 (m-90) REVERT: c 61 ASN cc_start: 0.9395 (m-40) cc_final: 0.8794 (t0) REVERT: c 108 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: c 124 LYS cc_start: 0.8943 (tptm) cc_final: 0.8622 (tptm) REVERT: d 69 GLN cc_start: 0.6260 (tp40) cc_final: 0.5901 (tp40) REVERT: d 84 ARG cc_start: 0.7365 (ptp90) cc_final: 0.7095 (ptt90) REVERT: d 191 ASP cc_start: 0.8558 (t0) cc_final: 0.8036 (t0) REVERT: d 260 GLN cc_start: 0.7155 (tm-30) cc_final: 0.6482 (tm-30) REVERT: d 312 TRP cc_start: 0.6499 (t60) cc_final: 0.6083 (t60) REVERT: d 314 LYS cc_start: 0.5583 (mmtp) cc_final: 0.4793 (tptt) REVERT: d 335 ARG cc_start: 0.7536 (mmt90) cc_final: 0.7305 (mmt-90) REVERT: d 336 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7726 (tm-30) REVERT: e 47 MET cc_start: 0.7957 (tpp) cc_final: 0.7612 (tpp) REVERT: f 57 LEU cc_start: 0.7533 (tp) cc_final: 0.7322 (tp) REVERT: g 46 ARG cc_start: 0.8761 (tmm-80) cc_final: 0.8211 (tmm-80) REVERT: g 59 MET cc_start: 0.9257 (mmp) cc_final: 0.8468 (mtp) REVERT: g 153 ARG cc_start: 0.7660 (ttt180) cc_final: 0.7431 (ttt180) REVERT: h 78 LEU cc_start: 0.6999 (pp) cc_final: 0.6522 (tp) REVERT: h 126 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.8142 (m-80) REVERT: i 68 LEU cc_start: 0.8282 (mt) cc_final: 0.8038 (mm) REVERT: i 99 LEU cc_start: 0.9160 (mt) cc_final: 0.8916 (mt) REVERT: j 88 PHE cc_start: 0.8074 (t80) cc_final: 0.7772 (t80) REVERT: l 4 LEU cc_start: 0.2188 (mt) cc_final: 0.1371 (tp) REVERT: m 34 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8584 (pttm) REVERT: m 126 PHE cc_start: 0.6932 (t80) cc_final: 0.6032 (t80) REVERT: m 133 LEU cc_start: 0.8517 (tt) cc_final: 0.8313 (tp) REVERT: n 59 MET cc_start: 0.8620 (tmm) cc_final: 0.8382 (tmm) REVERT: o 90 TYR cc_start: 0.4784 (OUTLIER) cc_final: 0.4363 (t80) REVERT: o 93 PHE cc_start: 0.6500 (t80) cc_final: 0.6272 (t80) REVERT: o 118 MET cc_start: 0.8834 (tpp) cc_final: 0.8562 (tpp) REVERT: o 152 MET cc_start: 0.7042 (mmm) cc_final: 0.6651 (tpp) outliers start: 111 outliers final: 85 residues processed: 839 average time/residue: 0.5699 time to fit residues: 800.4365 Evaluate side-chains 863 residues out of total 6931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 766 time to evaluate : 4.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain I residue 172 ILE Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 41 LYS Chi-restraints excluded: chain M residue 45 ASP Chi-restraints excluded: chain M residue 49 ARG Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain a residue 198 THR Chi-restraints excluded: chain a residue 379 THR Chi-restraints excluded: chain a residue 478 LEU Chi-restraints excluded: chain a residue 729 HIS Chi-restraints excluded: chain b residue 232 LEU Chi-restraints excluded: chain c residue 35 TYR Chi-restraints excluded: chain c residue 108 GLU Chi-restraints excluded: chain c residue 143 TYR Chi-restraints excluded: chain c residue 185 LEU Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 240 ASP Chi-restraints excluded: chain d residue 272 VAL Chi-restraints excluded: chain d residue 306 ILE Chi-restraints excluded: chain e residue 39 LEU Chi-restraints excluded: chain e residue 51 THR Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 88 PHE Chi-restraints excluded: chain h residue 126 PHE Chi-restraints excluded: chain h residue 141 LEU Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 110 ILE Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain k residue 40 CYS Chi-restraints excluded: chain k residue 70 VAL Chi-restraints excluded: chain k residue 144 LEU Chi-restraints excluded: chain l residue 59 MET Chi-restraints excluded: chain m residue 34 LYS Chi-restraints excluded: chain m residue 68 LEU Chi-restraints excluded: chain m residue 130 ILE Chi-restraints excluded: chain n residue 149 LEU Chi-restraints excluded: chain o residue 90 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 475 optimal weight: 5.9990 chunk 765 optimal weight: 10.0000 chunk 467 optimal weight: 20.0000 chunk 363 optimal weight: 6.9990 chunk 532 optimal weight: 40.0000 chunk 802 optimal weight: 20.0000 chunk 739 optimal weight: 10.0000 chunk 639 optimal weight: 30.0000 chunk 66 optimal weight: 2.9990 chunk 493 optimal weight: 5.9990 chunk 392 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 GLN C 288 ASN C 323 ASN E 288 ASN ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.089 54321 Z= 0.585 Angle : 0.741 13.825 74346 Z= 0.390 Chirality : 0.049 0.768 8755 Planarity : 0.005 0.063 10052 Dihedral : 5.261 134.541 8649 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.28 % Favored : 94.67 % Rotamer: Outliers : 3.19 % Allowed : 23.07 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: 1.05 (0.10), residues: 8149 helix: 2.22 (0.07), residues: 4867 sheet: -3.04 (0.18), residues: 656 loop : -1.24 (0.12), residues: 2626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 567 HIS 0.014 0.002 HIS F 344 PHE 0.044 0.002 PHE A 244 TYR 0.062 0.002 TYR n 66 ARG 0.013 0.001 ARG C 359 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16298 Ramachandran restraints generated. 8149 Oldfield, 0 Emsley, 8149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 6931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 771 time to evaluate : 4.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7543 (ttt90) REVERT: A 308 LYS cc_start: 0.8114 (tptt) cc_final: 0.7160 (tmtt) REVERT: B 51 GLU cc_start: 0.8277 (tt0) cc_final: 0.8047 (tt0) REVERT: B 281 MET cc_start: 0.8458 (mmm) cc_final: 0.8161 (mtp) REVERT: B 311 ASP cc_start: 0.8428 (m-30) cc_final: 0.8156 (t0) REVERT: B 337 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8404 (mpp) REVERT: B 416 MET cc_start: 0.8144 (mmm) cc_final: 0.7000 (mmm) REVERT: C 279 ILE cc_start: 0.9394 (OUTLIER) cc_final: 0.9120 (mm) REVERT: C 362 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7462 (tm-30) REVERT: C 497 GLN cc_start: 0.8302 (tm130) cc_final: 0.7916 (tm-30) REVERT: C 538 CYS cc_start: 0.8905 (t) cc_final: 0.8518 (t) REVERT: D 244 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9085 (mt) REVERT: D 260 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8618 (mm) REVERT: E 101 MET cc_start: 0.8495 (tpp) cc_final: 0.8195 (tpp) REVERT: E 105 TYR cc_start: 0.9316 (m-80) cc_final: 0.8897 (m-10) REVERT: E 355 ASP cc_start: 0.7976 (t70) cc_final: 0.7350 (t70) REVERT: F 353 ILE cc_start: 0.9469 (OUTLIER) cc_final: 0.9089 (mp) REVERT: L 82 GLU cc_start: 0.9100 (tm-30) cc_final: 0.8850 (tm-30) REVERT: M 12 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7864 (tpp80) REVERT: M 34 ARG cc_start: 0.8479 (ttp-110) cc_final: 0.7696 (ttp-110) REVERT: M 49 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7307 (mtm110) REVERT: M 57 MET cc_start: 0.6196 (mmt) cc_final: 0.4595 (tmm) REVERT: M 182 GLU cc_start: 0.7990 (tp30) cc_final: 0.7252 (tp30) REVERT: M 203 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8921 (tt) REVERT: a 120 ARG cc_start: 0.8897 (tpp80) cc_final: 0.8663 (mpp80) REVERT: a 478 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8382 (tp) REVERT: a 527 ASN cc_start: 0.7994 (t0) cc_final: 0.7686 (t0) REVERT: a 548 MET cc_start: 0.8727 (tpp) cc_final: 0.8257 (mmt) REVERT: a 594 TRP cc_start: 0.7854 (m-10) cc_final: 0.7504 (m-10) REVERT: a 737 TRP cc_start: 0.9014 (t60) cc_final: 0.8767 (t60) REVERT: a 802 TRP cc_start: 0.8693 (m-10) cc_final: 0.8372 (m-90) REVERT: c 61 ASN cc_start: 0.9386 (m-40) cc_final: 0.8828 (t0) REVERT: c 108 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7020 (mp0) REVERT: c 124 LYS cc_start: 0.8953 (tptm) cc_final: 0.8651 (tptm) REVERT: d 69 GLN cc_start: 0.6172 (tp40) cc_final: 0.5816 (tp40) REVERT: d 191 ASP cc_start: 0.8577 (t0) cc_final: 0.8004 (t0) REVERT: d 260 GLN cc_start: 0.7117 (tm-30) cc_final: 0.6444 (tm-30) REVERT: d 312 TRP cc_start: 0.6779 (t60) cc_final: 0.6252 (t60) REVERT: d 314 LYS cc_start: 0.5697 (mmtp) cc_final: 0.4888 (tptt) REVERT: d 336 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7727 (tm-30) REVERT: e 47 MET cc_start: 0.7978 (tpp) cc_final: 0.7587 (tpp) REVERT: f 57 LEU cc_start: 0.7674 (tp) cc_final: 0.7450 (tp) REVERT: g 46 ARG cc_start: 0.8805 (tmm-80) cc_final: 0.8206 (tmm-80) REVERT: g 59 MET cc_start: 0.9229 (mmp) cc_final: 0.8628 (ttt) REVERT: g 153 ARG cc_start: 0.7753 (ttt180) cc_final: 0.7517 (ttt180) REVERT: h 78 LEU cc_start: 0.6852 (pp) cc_final: 0.6388 (tp) REVERT: h 126 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.8254 (m-80) REVERT: i 68 LEU cc_start: 0.8227 (mt) cc_final: 0.7989 (mm) REVERT: i 99 LEU cc_start: 0.9188 (mt) cc_final: 0.8960 (mt) REVERT: j 88 PHE cc_start: 0.8127 (t80) cc_final: 0.7834 (t80) REVERT: l 4 LEU cc_start: 0.2356 (mt) cc_final: 0.1613 (tp) REVERT: m 34 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8552 (pttm) REVERT: m 126 PHE cc_start: 0.7009 (t80) cc_final: 0.6107 (t80) REVERT: m 133 LEU cc_start: 0.8577 (tt) cc_final: 0.8296 (tp) REVERT: n 59 MET cc_start: 0.8677 (tmm) cc_final: 0.8425 (tmm) REVERT: o 90 TYR cc_start: 0.4943 (OUTLIER) cc_final: 0.4596 (t80) REVERT: o 118 MET cc_start: 0.8875 (tpp) cc_final: 0.8604 (tpp) REVERT: o 152 MET cc_start: 0.7163 (mmm) cc_final: 0.6735 (tpp) outliers start: 117 outliers final: 89 residues processed: 830 average time/residue: 0.5384 time to fit residues: 739.0518 Evaluate side-chains 868 residues out of total 6931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 765 time to evaluate : 4.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 62 ARG Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 283 CYS Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 304 MET Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 355 GLU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain E residue 341 GLU Chi-restraints excluded: chain E residue 477 GLU Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 383 MET Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain I residue 172 ILE Chi-restraints excluded: chain M residue 12 ARG Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 40 THR Chi-restraints excluded: chain M residue 45 ASP Chi-restraints excluded: chain M residue 49 ARG Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain M residue 209 LYS Chi-restraints excluded: chain a residue 198 THR Chi-restraints excluded: chain a residue 379 THR Chi-restraints excluded: chain a residue 478 LEU Chi-restraints excluded: chain a residue 729 HIS Chi-restraints excluded: chain b residue 232 LEU Chi-restraints excluded: chain c residue 35 TYR Chi-restraints excluded: chain c residue 108 GLU Chi-restraints excluded: chain c residue 143 TYR Chi-restraints excluded: chain c residue 185 LEU Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 240 ASP Chi-restraints excluded: chain d residue 272 VAL Chi-restraints excluded: chain d residue 306 ILE Chi-restraints excluded: chain e residue 39 LEU Chi-restraints excluded: chain e residue 51 THR Chi-restraints excluded: chain g residue 4 LEU Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain g residue 88 PHE Chi-restraints excluded: chain h residue 126 PHE Chi-restraints excluded: chain h residue 141 LEU Chi-restraints excluded: chain h residue 144 LEU Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 110 ILE Chi-restraints excluded: chain i residue 116 VAL Chi-restraints excluded: chain k residue 40 CYS Chi-restraints excluded: chain k residue 70 VAL Chi-restraints excluded: chain k residue 144 LEU Chi-restraints excluded: chain l residue 59 MET Chi-restraints excluded: chain m residue 34 LYS Chi-restraints excluded: chain m residue 130 ILE Chi-restraints excluded: chain n residue 149 LEU Chi-restraints excluded: chain o residue 63 VAL Chi-restraints excluded: chain o residue 90 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 806 random chunks: chunk 507 optimal weight: 9.9990 chunk 681 optimal weight: 9.9990 chunk 195 optimal weight: 0.3980 chunk 589 optimal weight: 20.0000 chunk 94 optimal weight: 0.6980 chunk 177 optimal weight: 0.9980 chunk 640 optimal weight: 5.9990 chunk 268 optimal weight: 1.9990 chunk 657 optimal weight: 10.0000 chunk 81 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.133426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.096232 restraints weight = 96666.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.095616 restraints weight = 59861.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.096782 restraints weight = 41932.845| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 54321 Z= 0.202 Angle : 0.594 14.847 74346 Z= 0.308 Chirality : 0.044 0.716 8755 Planarity : 0.004 0.061 10052 Dihedral : 4.861 126.398 8649 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.51 % Favored : 96.44 % Rotamer: Outliers : 2.81 % Allowed : 23.45 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.25 % 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: 1.37 (0.10), residues: 8149 helix: 2.44 (0.07), residues: 4866 sheet: -2.76 (0.19), residues: 612 loop : -1.11 (0.12), residues: 2671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP a 737 HIS 0.007 0.001 HIS a 796 PHE 0.049 0.002 PHE h 88 TYR 0.060 0.002 TYR n 66 ARG 0.011 0.001 ARG d 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11807.27 seconds wall clock time: 206 minutes 21.35 seconds (12381.35 seconds total)